Science haiku

Haiku is one of the quickest and most fun forms of poetry to write. It’s also perfect for Twitter (which I recently joined). At some point, I intend to do some longer palaeontological poetry but for now, I have written a few haiku (mostly in the shower). I decided to tweet them all and am going to attempt to embed the first post here (I’ve never embedded a tweet before). They are mostly about the Ediacaran biota, with a few about palaeontology in general. Also birds. One of the challenges of writing a haiku about science, especially palaeontology, is the structure which limits the number of syllables one can use; a word like palaeontologist, for example, is too long for the first or last line and takes up a lot of allocated syllables when used in the second line. I had fun with that.

 

I've written a few #ScienceHaiku about #palaeontology and mostly the Ediacaran period:

Frond-like Charnia
One thought to be a sea pen
Now, who really knows? #Haiku

— Jason The Palaeobabbler Sherburn (@palaeobabbler) June 7, 2018

This first tweet was about Charnia, the important and puzzling Ediacaran fossil. The next one was about another Ediacaran organism, Dickinsonia. They are all on Twitter as well.

Dickinsonia
Your fossils are confusing
Reveal your secrets

For the next organism, I took a more tongue-in-cheek approach to its appearance.

Oh dear, Spriggina
You look like a used condom
Ribbed for her pleasure

And how could I leave out Kimberella?

Look, Kimberella
Maker of fossil scratch marks
Is that the back end?

I took a look at Ediacarans as a whole in these three:

Ediacarans
Are those animals, maybe?
A lively debate

Ediacarans
Where do you fit on life’s tree?
Pesky Rorschach tests

Precambrian life
Always called “enigmatic”
A truthful label

And onto the Cambrian:

Things got complex in
The Cambrian Explosion
But what was the cause?

I wasn’t as keen on that one as it seems to suggest a singular cause. I had written a different final line in my head but it has sadly disappeared. The next three were about palaeontology as a whole:

Wonderful life, dead
Palaeontologists find
Minds put flesh on bone

The rocks hold within
Secrets for us to unveil
Remnants of deep time

Life of distant pasts
Myriad deep connections
Try to uncover

And, finally, I thought I would hammer one particular point home:

Birds are dinosaurs
Birds? Yes, they are dinosaurs
Living dinosaurs

If you enjoyed these, drop me a message or comment on Twitter, I’d be happy to write some more.

Intelligent Design’s problem with the Cambrian explosion

Last night I made a grave error. I made the mistake of attempting to peruse the Intelligent Design movement’s main website, Evolution News and Views, to see what they have said about recent developments on the Cambrian explosion. I personally don’t think that researchers should give them much thought, but as I am currently just a blogger I will occasionally address them. It is my intention to get my hands on Stephen Meyer’s book Darwin’s Doubt and review it though that may be a long time coming, especially considering that they have made a follow-up to address critics. Until I have read their books, I don’t plan on getting into the details of their arguments. Right now, however, I am more concerned with their approach to the supposed debate.

Firstly, they sound desperate to appear original and as though scientists researching the Cambrian explosion are slowly coming round to their way of thinking. They often state things in a way which suggests that Meyer got there first, for example, Graham Budd was apparently recently “confirming Meyer’s denial” about Precambrian organisms, when the reality is that the interpretations Meyer favours were first offered by evolution-accepting palaeontologists. Cambrian and Ediacaran experts are constantly described as admitting to something which the ID crowd believes; their loaded language is meant to give the impression that they are way ahead of the experts.

The ID presentation of the Cambrian explosion appears to be that is that it was relatively short (10 million years appears to be a figure they will accept), that bilaterian phyla appeared very suddenly in the Cambrian, that there were no precursors found amongst Ediacaran organisms, and that there is no satisfactory evolutionary explanation for it. You will find all of these views, even the last one, preceding Meyer’s publications and from experts in relative fields. The problem for them here is that they are not trying to solve any problems – they already think that they have the answer, yet it really offers no explanation.

Secondly, they consistently complain that they are being ignored. Nobody name-drops Meyer, nobody cites his book, nobody addresses his main thesis. They even do this when discussing papers which focus on specific phenomena, as though every single paper relating to the Cambrian explosion must address their pet theory (I use that term loosely). They are like the guy in a bar who seems to want everyone to fight him (perhaps better left ignored). Scientists are quite happily dissecting every aspect of the Cambrian diversification, looking at the genetic changes involved, the divergence times, the environmental changes, taphonomic changes, identifying fossils and working out how they fit in, looking at the timings of the events and so on. The debate is ongoing, there are many, many voices clamouring to be heard, trying desperately to tie together an overwhelmingly large, yet incomplete, dataset which befuddles even the most astute mind. Teasing out cause and effect in deep time is difficult and frustrating, people come at it from different angles, new evidence and new ideas can cause major shifts in thought. Meyer and his crew are desperate to be the most heard voice, they want their issue addressed and until someone addresses it they will assume that they are being ignored (which is tantamount to admitting defeat, by the looks of it).

Their third issue is that their main focus isn’t actually at the heart of the Cambrian explosion, despite their best wishes. The diversification can be perceived in many ways, with current thought often favouring its interpretation as an ecological explosion. It has often been perceived as an explosion in disparate body plans, which is not exactly the wrong way to look at it, but can be seen as the result of the ecological driving forces. The ID proponents take this a step further; it isn’t simply about body plans – it’s about the new information behind those body plans. With their rapid appearance narrative of the Cambrian explosion, this perspective on the diversification seems like a major issue, a sudden, unprecedented influx of biological information. Understandably, when addressing some of the ecological forces at play we don’t necessarily need to address the genetic changes, but they can’t always accept that. The genetic changes are important, but it does seem to be the case that the genetic toolkit necessary was already largely in place well before the Cambrian explosion (sponges, for example, appear to have some functioning genes which are used in more complex organisms in the development of the nervous system). So some Precambrian organisms may have had the capacity for evolving some of the body plans we see in the Cambrian, but nothing to cause them to do so – having a football pitch, a ball and 22 people does not ensure that a football match will take place.

This pushes the issue back, which ID theorists would like to present as a retreat, as hiding from the problem. The reality is that when you are concentrating on the Cambrian explosion you look at the stage which has been set and then analyse the changes. The environment is part of the stage, the organisms which preceded the radiation are part of it too, and the genetic toolkit is part as well. This is not to say that no new genes were necessary for the Cambrian explosion, but that it is not a major issue. The evolution of regulatory networks and of new genes is a separate question, which I get the impression that they know as it allows them to paint this picture of retreating evolutionary biologists. They can keep pushing back and back because ultimately they know that the origin of information goes back to the origin of life and that is where they truly set up camp, not the Cambrian explosion.

In summation, one tactic of the ID proponents is to try to sound original, when the reality is that the majority of their views on the Cambrian explosion are taken from actual researchers who accept evolution. They also complain repeatedly that they are being ignored, often because their personal favoured views are not being addressed. Finally, their issue is not really with the Cambrian explosion, but with the origins of information at life’s beginnings. The Cambrian explosion isn’t what they think it is, but as long as they continue to present it their way they will always feel ignored and as though experts are conceding to them. They will just persist in offering only criticisms and complaints.

Ediacaran ecosystem engineers – the Savannah hypothesis and our Skynet-type origins

Image from Wikipedia.

Out on the savannah, it is easy to find certain resources as they tend to be concentrated in limited areas. Trees, termite mounds, changes in terrain, all contribute to this concentration of resources. It is this sort of environment which has been hypothesised as resulting in our own bipedality which enabled human ancestors to move efficiently between resource hotspots. In a recent review, Budd and Jensen have proposed a ‘savannah’ hypothesis as an explanation for the evolution of bilaterian animals and consequently the Cambrian explosion.

Bilaterian animals are widely thought to have driven the Cambrian explosion, particularly as they function as ecosystem engineers altering the environment around them. The burrowing activities of bilateral organisms altered ocean chemistry and the nature of the sediment, opening up more resources to be exploited and resulting in a cascade of diversification. But why did bilaterians evolve in the first place? Ecological causes for the Cambrian explosion tend to presuppose features they should be explaining, such as the ability to burrow or the presence of predation (both likely contributed enormously to the diversification, but were also caused by it). Environmental causes tend to suggest limiting factors such as a lack of oxygen, which may actually be mistaking cause for effect.

The savannah hypothesis suggests that the Ediacaran biota also functioned as ecosystem engineers, causing carbon hotspots in the sediment and water around the organisms which were exploited by bilaterian animals which went on to diversify, eventually displacing their Ediacaran providers. Dissolved organic carbon in Ediacaran seas would not likely have clumped together, instead being spread out through the water column – not an economical resource for active organisms. Burrowing is highly energetic and would require dissolved carbon to be concentrated; without the Ediacaran organisms it would have been too diluted and sequestered away by the abundant microbial mats. Just like trees on the savannah, the Ediacaran biota concentrated dissolved organic carbon, providing sufficient resources for active burrowing and the need for motility.

In their thorough review, Budd and Jensen challenge the view that Ediacaran organisms went extinct by the start of the Cambrian period having been outcompeted and devoured by bilateral organisms. Instead, they survey putative evidence that shows that bilaterians first appeared towards the end of the Ediacaran period and that Ediacaran-type organisms persisted well into the Cambrian (and perhaps longer). At first, bilaterians would have been dependent on the Ediacaran ecosystem engineering, but went on to evolve their own sessile forms, such as crown-group sponges, and predatory habits which made them a threat to the Ediacaran biota – comparable perhaps to humans in the Terminator franchise creating Skynet and setting up their own demise.

They also reviewed the phylogeny of basal animals and take the view that sponges form a single clade which is the sister group to all other animals. They coined the term “Apoikozoa” which encompasses all animals and their sister group the choanoflagellates. And they made a case for Ediacaran organisms being early animals, albeit hugely problematic, whilst being highly critical of some of the optimistic interpretations. It is a paper which has provided a lot to mull over.

References 

Budd, GE. and Jensen, S. 2015. The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution. Biological Reviews. doi: 10.1111/brv.12239

Darroch, SAF., Sperling, EA., Boag, TH., Racicot, RA., Mason, SJ., Morgan, AS., Tweedt, S., Myrow, P., Johnston, DT., Erwin, DH. and Laflamme, M. 2015. Biotic replacement and mass extinction of the Ediacara biota. Proc. R. Soc. B 2015 282 20151003; DOI: 10.1098/rspb.2015.1003

Tribrachidium – three arms and a lot of mystery

If you were to have been wading out into the Ediacaran seas, waves lapping against your legs, the slime of the microbial mats squidging under your feet, you might have noticed groups of a unique little organism called Tribrachidium. About the size of a coin, Tribrachidium had three ‘arms’ spiralling gently away from its centre, resembling a Celtic pattern. It rested on the sea floor in a variety of settings, mostly shallow with wave action, not moving, just letting the waves wash over it. It’s one of those organisms which is difficult to classify, but it has been possible to make inferences about its ecology as a recent study has done.

The Ediacaran period has been perceived as being ecologically quite simple, followed by the Cambrian explosion which saw a sharp rise in the number of ecological habits of animals. Bush, Bambach, and Daley (2007) developed a classification of life modes based on the area of marine ecospace inhabited relative to the seafloor, the level of movement of the organism, and feeding mechanisms. Theoretically, there are 216 distinct combinations, 92 of which are found in the Phanerozoic, 98 are possibly not viable, and 26 are possible but have not evolved. When applied to the Ediacaran  (Bush, Bambach, and Erwin 2011), there are just two modes of life in the older Avalon assemblage which is dominated by frond-like organisms, there are ten in the younger White Sea assemblage, and five in the younger Nama assemblage which sees the first skeletal forms. Contrasted with this, the first half of the Cambrian saw a rise to around 30 different modes of life (still only a third of modern life-modes).

A new study by Rahman et al. (2015) looked at the possible feeding habits of Tribrachidium and suggested that it had a mode of life previously unknown from the Ediacaran, indicating that Ediacaran ecosystems were more complex than thought (add this to the optimistic approach to the Ediacaran period). They narrowed down the possible feeding habits of Tribrachidium to just two: osmotrophy and suspension feeding. Osmotrophy involves the passive absorption of organic matter dissolved in the water, a common approach in the Ediacaran due to increased amounts of organic matter in the water, found in organisms such as Charnia and Charniodiscus which had large surface areas to absorb nutrients. Suspension feeding involves the trapping of organic matter in specific parts of the organism and requires a method of directing the water towards those traps.

With the two possible modes of feeding in mind, the researchers used computational fluid dynamics (CFD) to observe how water would have flowed over the organism, a method commonly used in engineering. Osmotrophy requires that the water flow over as much of the organism as possible, as has been observed in some of the frondose Ediacarans. By contrast, suspension feeding requires that the flow would be directed and focussed. What their tests found was that the water was directed passively by the arms, funneling it towards three depressions called ‘apical pits’ where it slowed down so that food particles would fall out of suspension. This directed movement fits neatly with a rare ‘gravity settling’ mode of suspension feeding, rather than with osmotrophy. They explained it as follows:

In summary, our CFD analyses demonstrate that the external surface morphology of Tribrachidium altered ambient water flow to produce low-velocity circulation above extremely localized areas around the organism, which is consistent with the interpretation of Tribrachidium as a suspension feeder rather than as an osmotroph. Specifically, we find that the three primary branches act to slow water flow and direct it up toward the apex of the organism, where small-scale recirculation develops directly above apical pits. This recirculation occurs at a range of simulated current velocities regardless of the organism’s orientation to the principal direction of flow. We suggest that this low-velocity zone of recirculation allowed larger particles to fall out of suspension, whereupon they were collected in the apical pits and subsequently metabolized (suspension feeding via “gravitational settling”). This hypothesis suggests that Ediacaran organisms used a larger diversity of feeding strategies than is currently appreciated and that they may have played a role as rudimentary ecosystem engineers, albeit in a fashion that became rare in the Phanerozoic with the disappearance of microbial matgrounds.

Computer simulation of water flow around Tribrachidium.

If it is indeed accurate, this study sheds light on the nature of the taxonomically tricky Tribrachidium, whilst expanding our understanding of Ediacaran ecosystems as more complex than previously thought. However, it is worth noting that fossils of Tribrachidium found so far show no signs of a mouth or other feature for ingesting filtered particles, it may simply be part of a larger organism – the holdfast of a frond-like organism, for example.

References

Click here for an interview with one of the authors.

Bush, AM., Bambach, RK., and Daley, GM. 2007. Changes in theoretical ecospace utilization in marine fossil assemblages between the mid-Palaeozoic and Late Cenozoic. Paleobiology 33:76-97.

Bush, AM., Bambach, RK., and Erwin, DH. 2011. Ecospace utilization during the Ediacaran radiation and the Cambrian eco-explosion. In Quantifying the Evolution of Early Life, edited by Laflamme, M., Schiffbauer, JD., and Dornbos, SQ, 111-33. Dordecht, Netherlands: Springer.

Rahman, IA., Darroch, SAF., Racicot, RA., and Laflamme, M. 2015. Suspension feeding in the enigmatic Ediacaran organism Tribrachidium demonstrates complexity of Neoproterozoic ecosystems. Science Advances 1, 10.

Singer, A., Plotnik, R., and Laflamme, M. 2012. Experimental fluid dynamics of an Ediacaran frond. Palaeontologica Electronica 15:1-14.

 

An optimistic approach to the Ediacaran biota?

There’s a bit of a problem with the Ediacaran fossil record – it’s not what was originally expected and the organisms we do find are problematic. Based on the complex and recognisable fossils of the Cambrian, it was anticipated that more primitive forms would be found in the Precambrian, and, in a sense, they were. When they were first recognised, Precambrian organisms appeared to fit what was predicted; amongst them, palaeontologists recognised possible sponges, jellyfish, assorted worm-like creatures, putative arthropods and echinoderms. The more they were studied, however, the more problems in classifying them arose.

At some point along the line, near enough every Ediacaran fossil which had been linked to modern phyla have been reassessed and their connections found wanting. There is a handful which can still tenuously be linked to modern groups, but there is an apparent dearth of expected animal fossils, especially when the molecular clock data is taken into account. There appears to be an evolutionary gulf between the Ediacaran biota and the Cambrian explosion fauna.

Part of the problem is preservation – comparing the fossils of the Ediacaran and the Cambrian is difficult considering that they are mostly preserved in very different ways; the fossils of the Ediacaran are soft-bodied organisms preserved mostly as moulds, the fossils of the early Cambrian are mostly tiny bits of shell and other hard parts, and then there are the exceptionally preserved organisms from deposits such as Chengjiang.

One approach we can take to link the Ediacaran and the Cambrian is to avoid trying to fit them into recognisable taxonomic groups, and instead focus on the attributes they share with modern animals, particularly their ecology. This was the process adopted by Mary Droser and Jim Gehling in a paper earlier this year, titled The advent of animals: The view from the Ediacaran. We can look at the Ediacaran period and see things which are usually associated with animals, even if we cannot properly classify the fossils in question.

Mobility

One thing which clearly sets animals apart is movement – worms wriggle through sediment, fish swim about, and, of course, us humans find as many different ways to move as possible. Many animals don’t move about for most of their lives, not least sponges and corals, both of which we might expect in the Ediacaran in some form, but movement on or in the sediment would potentially be evidence for bilateral animals milling around. Most of what we see from the Ediacaran are stationary organisms, attached to the sediment by a holdfast or resting on the surface. The earliest animal traces are from 565 Ma and are most similar to traces by the polyps of anemones, providing evidence of muscular contraction, evidence of which also comes in the form of the body fossil Haootia quadriformis which possessed bundles of muscle fibres and is a possible cnidarian. The most common trace fossils in later Ediacaran rocks are in the form of grooves and levees, called Helminthoidichnites, and are interpreted as being caused by an animal too small to be preserved and limited in size by the chemical conditions of the sediment. They appear to have been mining the microbial mats, also showing evidence of avoidance behaviour, and are likely to have been created by bilaterian animals.

A few Ediacaran body fossils are associated with traces as well, lending to their interpretation as bilaterian in nature. Kimberella is a box-shaped body fossil which is often associated with scratch marks (Kimberichnus) that has been commonly seen as bilateral and has even been considered to be a possible mollusc. The associated traces have been interpreted as evidence of mat grazing though there are differences between the grazing habits of Kimberella and those of molluscs. The likely related Dickinsonia and Yorgia have been found associated with faint casts of their bodies, which appear to be resting or feeding traces where they sat ingesting the microbial mat before moving on to another patch. They often also have possible muscular contraction marks, though this interpretation depends somewhat on their phylogenetic affinity. The advent of mobility is therefore not confined to the Cambrian period though it does see an increase in the number of modes of mobility, as it is a behavioural trait of bilateral animals found in the Ediacaran.

Reproduction

Sexual reproduction is another trait associated with modern animals found in the Ediacaran period. The puzzling organism Funisia is a collection of tube-like structures which were previously not even recognised as body fossils. They demonstrate branching patterns which are potential evidence of asexual budding, whilst their distribution appears to be due to the production of spats, a form of reproduction mostly found in sexual organisms. Though their phylogenetic affinity is puzzling, the likely sexual reproduction of Funisia highlights another metazoan trait found in the Ediacaran period.

Skeletonisation 

The Cambrian explosion was first recognised in the fossil record due to the geologically sudden appearance of skeletal parts. The evolution of hard parts appears to have been a key stage in the evolution of Metazoa though it is not restricted to the Cambrian. Droser and Gehling discussed the example of Coronacollina, a cone-shaped organism with long, straight spicules radiating outwards, interpreted as a sponge-grade organism which is important for being the oldest known multi-element organism. Other Ediacaran shelled organisms include Cloudina and Namapoikia which are possibly cnidarian-grade organisms but had their study been released more recently they would likely have included the latest interpretation of Namacalathus as a lophophore. Even if we cannot place them phylogenetically, the appearance of skeletal parts, particularly multi-element organisms, is a key step in metazoan evolution found in the Ediacaran.

Ecosystems 

Ediacaran fossils tend to have been preserved in the places they lived, as opposed to having been transported and dumped elsewhere. This allows them to be studied as communities and permits insight into their ecological nature. The Flinders Ranges of Australia contain a succession of beds which are characterised by a range of organisms in shallow marine settings. The same organisms tend to appear on each bed but with different abundances, suggesting a level of sophistication in communities similar to that in the Phanerozoic despite there being a lack of predation, organisms living in the sediment, and widespread skeletonisation.

Conclusions

Setting aside phylogenetic affinities, traits of modern animals are found in the Ediacaran period. An optimistic approach to the Ediacarans allows us to see signs of mobility and the presence of muscles, skeletonisation, sexual reproduction, and the beginning of complex ecosystems – all possible links to the animals found in the Cambrian, suggesting that poriferans, cnidarians and bilaterians were all found in the late Precambrian.

References

Droser, M.L. and Gehling, J.G. 2015. The advent of animals: The view from the Ediacaran. Proceedings of the National Academy of Sciences 112: 16. [Link]

 

I Chuffing Love Correcting Science Headlines – Namacalathus

Science journalism has a bit of an issue. With science news sites all over the internet, many take on the clickbait approach, sometimes unintentionally. It seems that whoever decides the title has often not read the article itself, and certainly hasn’t read the research upon which it is based. This mismatch would not be as big a deal if people read past the title, but many seem not to bother. One of the repeat offenders for this is the website I Fucking Love Science. In case you were not in the know, it is effectively a site for perving on the sexier side of science, those bits that make the public say “wow” and then go about their day thinking about other things. They do, from time to time, have some genuinely interesting and informative content, but they still need to tighten things up a bit.

My example today is due to their coverage of a story I posted about myself very recently. The late Ediacaran shelly fossil, Namacalathus, has a new interpretation being offered, and this is fascinating for anyone interested in the Cambrian explosion. I took a more conservative approach, much as I have with the title of this post (I actually don’t mind swearing, I just didn’t feel the need), in part because I intend to look at many more putative Precambrian animals, but also because I like to remain sceptical with potentially big news.

From McCall (2006) http://www.sciencedirect.com/science/article/pii/S0012825205001662

The offending article can be viewed here and is actually one of their better offerings, but there are issues. Firstly, they went with the title Newly Discovered Fossil Suggests Complex Skeletons Evolved Earlier Than Thought. It isn’t a huge error, and thankfully the attractive part of the headline isn’t blatantly false, but Namacalathus was described fifteen years ago, which is hardly a new discovery. They don’t even go on to mention that Namacalathus was previously thought to be a possible cnidarian, nor do they mention that this previous interpretation was based partly on the nature of reproduction (asexual budding) which is now used to suggest that the organism within the shell was bilaterally symmetrical. They are dead on with their information about the shell formation (something I personally covered in little detail) but didn’t include this standout gem.

The part of the title which is meant to pique your interest is the fact that these complex skeletons evolved earlier than thought. Yet the quotation at the end of the article, from researcher Rachel Wood, quite clearly says that these complex animals were suspected, and perhaps it would have been worth mentioning the discrepancies between the fossil record and molecular clocks.

There are some other issues which crop up time and again with this subject. The first is that science journalists seem a bit baffled about how to present the Ediacaran biota, which is no surprise, as they are baffling, but the article puts it in a rather misleading way, saying, “Paleontologists still aren’t sure what kind of life they are, but they were likely plant forms, algae, microbial mats, fungi or very primitive life forms called protists.” Putting possible plant affinities first in the list could potentially mislead as this was stated in a sentence after mentioning the Avalon explosion, which involved the arrival of frond-like organisms such as Charnia, an organism which does resemble a plant despite it living too deep for photosynthesis to work. They also neglect to mention many of the attempts to classify Ediacaran organisms which have placed them close to the base of the Metazoa and even within it. They could simply have called them “possible primitive animals” and they would not have been mistaken.

The second issue is that they misrepresent the Cambrian explosion, describing it first as “the period of ancient time complex life appeared to suddenly and rapidly evolve in,” and later as a “sudden appearance of life.” This is especially odd, considering that they provide links along with each statement, the first of which describes most of the change happening in the second and third stages of the early Cambrian, “a period of about 13 million years,” which is hardly sudden. The second link mentions that apparent new evidence suggests that the Cambrian explosion may have involved more gradual change. It is misleading, though common, to state that the Cambrian explosion was sudden, especially without qualifying in its geological context, where “sudden” can mean several million years.

Overall, the article does not do a terrible job presenting Namacalathus in its new light, as it does manage to sound exciting to laymen and gives some good information on the shell structure (even if I did feel that it neglected the reproductive strategy), but it does commit the sins of having a misleading title, a confusing approach to the already confusing Ediacaran biota, and an exaggerated description of the Cambrian explosion. They could also have done with some dissenting or sceptical views from a leading Ediacaran palaeontologist, but that’s not always as easy.

The Cambrian Explosion – The old fossils vs animals debate

In a world without fossils, we might never have known about the event commonly known as the Cambrian explosion. This perplexing episode in evolutionary history has been known since early geologists and palaeontologists first started piecing together the history of life on our planet; what they found was that the oldest rocks contained no fossils, overlain by rocks containing complex fossils. A lack of precursors for complex fossils, such as trilobites, did not fit the evolutionary narrative gaining traction at the time. Charles Darwin’s explanation for this puzzle was that the fossil record was incomplete; these ancestral forms had existed, but had either not been preserved or not been found. Since then, more fossils have been found, including a large variety in Precambrian rocks, and the timescale has been constantly refined, allowing for a better understanding of the timing of key events. The questions raised by Darwin’s ideas have not quite gone away: is the Cambrian fossil record a true representation of the emergence of major animal groups? or is it an illusion caused by the paucity of the fossil record?

Many palaeontologists would like to read the fossil record literally and support the idea that the Cambrian explosion was a real event, however, there is a story in the genes which is somewhat different. Geneticists can estimate the divergence times between lineages using molecular clocks, a technique which uses mutation rates to count back to the time when two species or higher groups split. When applied to the origins of major animal groups, these estimates have varied widely and have been constantly refined. One consistent theme is that these dates are always substantially before the Cambrian, including the origins of phylum-level groups. It is always to be expected that a group or species would have evolved earlier than they appear in the fossil record, but not to the degree shown by molecular clocks for the Cambrian. If the story of the genes is read literally, then there is a lot of cryptic evolution in the fossil record, making the Cambrian explosion either an illusion caused by an absence of fossils, or by an increase in preservation potential due to the origin of hard parts and/or increased size across multiple groups. The conclusions of a recent molecular clock study appear to support the idea that the Cambrian explosion is a preservation event, not the rapid appearance of major animal groups.

In a paper titled Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales, dos Reis et al. present some robust new data and provide an excellent overview of the limits of molecular clock studies. Their estimates vary widely depending on certain assumptions, which are addressed in detail, but all of them do support an early divergence of major animal clades. They conclude:

This is the long-standing conundrum of the Cambrian—whether the first animal fossils faithfully reflect an explosion in animal biodiversity or merely an explosion of fossils. The results of our study—which integrates fossil and molecular evidence to establish an evolutionary timescale—suggest that the Cambrian explosion is a phenomenon of fossilization, while biological diversity was established in the Neoproterozoic. Integrating all of the sources of uncertainty that we explore (Figure 6, Table 1) allows us to conclude that crown Metazoa originated 833–650 Ma, fully within the Cryogenian, while the component clades of crown Eumetazoa (746–626 Ma), crown Bilateria (688–596) Ma, crown Deuterostomia (662–587 Ma), and crown Protostomia (653–578 Ma) all diverged within a Cryogenian to early- or mid-Ediacaran interval.

The results of our analyses leads us to reject the hypothesis that metazoans, eumetazoans, bilaterians, protostomes, deuterostomes, ecdysozoans, lophotrochozoans, or, for that matter, any of the component phylum-level total groups, originated in the Cambrian.

Figure 6 from dos Reis et. al (2015)

The conclusion that the fossil record is not accurate for the Cambrian may seem dismissive, just as many palaeontologists dismiss molecular clocks as inaccurate when they ostensibly contradict fossil data. This incongruence between the two datasets might itself be an illusion. Might there be reasons to think that both are accurate, but that we are mistakenly expecting them to answer the same questions?

It is relatively easy to picture a number of scenarios which could create the illusion of a surprising increase in complexity when really we just do not have the fossils. The Cambrian fossil record clearly does show that there was a dramatic increase in fossilisable hard parts, as we see a handful of shells at the end of the Ediacaran, through the increasing diversity and complexity in the Small Shelly Fossils (SSFs); soft tissues do not preserve well, so it might be a case that hard parts evolved in animals which had been milling around for millions of years prior. Or could it be the case that they simply were not big enough to be preserved? An impression of a soft-bodied animal in sand cannot be smaller than the individual sand grains. The meiofauna live in those sorts of surroundings, in between the grains of loose sediment, where oxygen levels are often low; animals too small to see without a microscope, complex yet only found fossilised in exceptional circumstances. And maybe it is the case that we have fossils of them but are looking with the wrong expectations? In these scenarios, the genes are right and it is the fossils which do not give enough of the true picture.

The Ediacaran period is famous for its menageries of soft-bodied organisms, preserved as impressions in sand, or by volcanic ash smothering their soft forms; any organism large enough would surely have been preserved. Within this period of time, we also find the Doushantuo fossils, visible only through the use of high-powered microscopes. Preserved in phosphate, they are largely an assortment of little ball-shaped clusters, thought by some to be embryos, yet by others to be single-celled organisms in the process of division. During the Cambrian and later, phosphate deposits such as these contain the elusive meiofauna, yet they are absent from the Ediacaran. Instead, we see a finer degree of fossilisation. Preservation in the Precambrian is arguably better than the Cambrian and later – preservation has evolved, but not towards higher fidelity.

Geneticists can also shed light on this question of preservation potential. Animals have a number of microRNAs, which are regulatory RNA genes that can be used to track the evolution of complexity, put simply because more complex animals have more microRNAs than simpler organisms. When some of the simpler animals are analysed, such as acoel flatworms and rotifers, it is found that they have lost microRNAs and become less complex, so they cannot be used to work out what a simple bilaterian ancestor might have looked like. Instead, they seem to indicate that the common ancestor of bilaterians was relatively large and complex, and at the very least a persistent puzzle.

It is possible that we already have fossils of bilaterians from the Precambrian, but that we are not identifying them correctly. The Ediacaran form Kimberella is often considered to be a possible mollusc, whilst its contemporaries Spriggina and Parvancorina are sometimes linked to arthropods, yet all of these are questionable. Recently, the shelly Ediacaran organism Namacalathus has been identified as a lophophorate, placing it with animals like brachiopods and bryozoans, but this is undeniably controversial.

Bilaterians don’t often sit still. They wriggle around on the sea floor, they churn up the sediment in search of food and shelter, they swim around looking for food. Burrows and trails are abundant in the fossil record, often found alongside body fossils, but also in sediments where body fossils could not be preserved. They give us insight into the nature of the sediment, the life habits of animals, and the evolution of complexity. Trace fossils tell a similar story to the body fossils. The sediments in the Precambrian were quite hard and largely devoid of oxygen – not conducive to the existence of meiofauna –  and lack any clear evidence of bilaterian activity, then animals began to wriggle about in the sediment in the Cambrian, allowing oxygen to reach greater depths. The first stage of the Cambrian shows a large increase in the ways animals interacted with the sediment, but it was not until the second stage of the Cambrian when they started to burrow up to a metre deep and ecosystems took on a new level of complexity. The trace fossil record suggests that the Cambrian explosion was a very real event, but that body-plan diversification happened before changes in ecological structure.

The data from trace fossils hints at how the record of body fossils and the information in the genes could both be telling the same story. It is possible that molecular clocks are right about major animal groups diversifying much earlier than the Cambrian, but the conclusion that the Cambrian explosion is an illusion caused by a poor fossil record is misguided. The fossil record does indeed appear to record an actual evolutionary event, but it might not be the origins of these major animal groups – it may instead be their ecological expansion, not least the widespread evolution of hard parts. Under this scenario, we are still lacking in key fossils, but that lack is not the explanation for the incredible diversification through the start of the Cambrian period. The Cambrian explosion would therefore not be a case of “animals or fossils” but an ecological restructuring which could not have been known without the fossil record.

References

dos Reis, M., Thawornwattana, Y., Angelis, K., Telford, M.J., Donoghue, P.C.J, and Yang, Z. 2015. Uncertainty in the timing of origin of animals and the limits of precision in molecular timescales. Current Biology. [Link]

Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D., Peterson, K. 2011. The Cambrian conundrum: Early divergence and later ecological success in the early history of animals. Science 334: 1091-97. [Link]

Mangano M.G., Buatois L.A. 2014. Decoupling of body-plan diversification and ecological structuring during the Ediacaran – Cambrian transition: evolutionary and geobiological feedbacks. Proc. R. Soc. B 281: 2014003. [Link]

The Cambrian Explosion – Historical Hurdles

A lot can happen in over 500 million years. Fossils rest in rocks moving around as parts of the continents or spreading out over the ocean floor. These rocks run the gauntlet of time, facing numerous obstacles to preservation. Buried deep, they can be subjected to heat and pressure, distorting their precious contents beyond recognition. Out on the surface, they encounter erosion caused by all manner of environmental effects. Many fossils, if not most, are destroyed by nature before any hopeful fossil hunter can get their hands on them. This means that studying the past can get trickier the further back we look and the Cambrian explosion is no exception.

Study of the diversification event at the start of the Cambrian Period has advanced significantly in recent decades. In 1989, Harvard palaeontologist Stephen Jay Gould brought the bizarre beasts of the Burgess Shale – an assortment of beautifully preserved fossils from the middle Cambrian – into the public eye, presenting an image of the Cambrian explosion which has persisted to the present in many popular depictions. The fossils from just before the Cambrian, the Ediacaran biota, were presented as a failed evolutionary experiment, not as precursors to life in the Cambrian. The fossils of the Burgess Shale were understood to represent many more body plans than we see in the world today, many of which became extinct. This is an increase in disparity, rather than diversity, and it happened rapidly in evolutionary terms. How rapidly it was thought to have occurred varied dramatically, as the data just was not available.

Gould and other scientists, whose work he helped publicise, had three key hurdles which palaeontologists have since leapt over, changing the way we see the Cambrian explosion significantly: dating the rocks in question was hugely problematic; how we classify fossil organisms has changed; and how these fossils were preserved was poorly understood. Since then, genetic data has also been used, along with other techniques, to try to understand the Cambrian.

Problems with Dating 

To get a good idea of what was going on in the late Precambrian and early Cambrian rocks have to be correlated and dated accurately. During the 1980s, the base of the Cambrian was thought to be around 570 Ma and the timings of individual events were difficult to discern. Deciding which rock sections represented the base of the Cambrian was mired by nationalistic clashes, large sections of missing periods of time (unconformities) were common, fossils were difficult to use for correlating rocks as they were restricted geographically, and there was a considerable lack of volcanic rocks which could be used for radiometric dating.

In 1994, an international commission agreed that the base of the Cambrian would be marked by a trace fossil, a burrow called Treptichnus pedum, which is one of the earliest types of burrows displaying vertical penetration into the sediment – a strong indicator that behaviour had become more complex. Radiometric dating has been increasingly used, along with data from fossils and stable isotopes, to give a much-refined timescale for the events of the Cambrian and the Ediacaran periods; the boundary between the two, for example, is now dated at 541 Ma.

Image source: http://www.stratigraphy.org/index.php/ics-chart-timescale

With an increase in understanding of the timings of events in the Cambrian, we now know that over twenty million years had elapsed between the start of the period and the first exceptionally preserved faunas (Chengjiang is dated at 515 Ma and the Burgess Shale at 508 Ma).

A Systematic Issue

How we classify organisms can determine how we interpret the events of the Cambrian. In school, we tend to learn the Linnaean approach to systematics, resulting in a hierarchy often taught through a mnemonic device such as “Kings Play Chess On Fancy Gold Squares” relating to the classifications “Kingdom Phylum Class Order Family Genus Species”. Fitting living organisms into this hierarchy can be tricky, so when you factor in extinct organisms it only exacerbates the problem. The animals we see in the Cambrian are a prime example, with many given the designation of ‘phylum’ based on a single fossil – they just could not be placed in any existing phyla, yet were clearly animals and could be placed within ‘super-phyla’ which encompassed a number of closely related phyla. This is the mess which palaeontologists were trying to clear up during the 1980s and which Gould was describing in his book. The number of animal phyla appeared to far exceed our modern assembly of approximately 35, perhaps even three times as many. This rapid increase in disparity made the Cambrian diversification appear even more explosive, as this huge number of high-level taxa implied an even greater lack of antecedents and perhaps even novel evolutionary mechanisms.

It is now expected that extinct organisms will not fit into a grouping based on extant organisms. Using cladistics, we can place living organisms together in what is known as a crown group, where they share traits which they all inherited from their common ancestor, whilst extinct close relatives can be placed as stem groups as they possess many of those traits of crown group organisms but lack some which would result in their inclusion in the crown group.

Pink indicates the crown group, yellow the stem group, and blue the total group. Image from https://en.wikipedia.org/wiki/Cambrian_explosion

When this approach is applied to the Cambrian, we find that it is populated mostly by stem group taxa and that many of those supposed new phyla are actually stem groups closely related to modern crown groups, such as arthropods. This has reduced the number of phyla in the Cambrian down to around 14 crown groups and has helped to elucidate some of the evolutionary steps taken during this critical period in the history of animal life.

Preservation Problems

Going from dead organisms to fossil assemblages is a messy business. The environment of deposition dictates which organisms are preserved. Sometimes there is a size bias, where only larger organisms or only smaller organisms are preserved. Commonly, the bias is towards organisms with hard parts, resulting in a lack of understanding of soft-bodied organisms. The Burgess Shale of Canada is one of those exceptional sites of fossil preservation (Lagerstatten), displaying the anatomy of soft-bodied organisms in abundance. Since its discovery, it has been joined by other exceptional Cambrian deposits, most notably Chengjiang in China and Sirius Passet in Greenland. The Ediacaran biota are soft-bodied and have been preserved in very different ways to Cambrian Lagerstatten, and between those are the SSFs (Small Shelly Fossils) which are exclusively little bits of hard shell.

It is often difficult to compare fossils which are preserved through different processes, with different biases, and a lot of work has gone on in the last few decades to work out how they were preserved and how they can be compared. Take these assemblages out of their temporal context and it is difficult to make sense of what was happening in terms of their evolution. A better understanding of how they were preserved, more assemblages to compare, and a more refined timescale, have all contributed to painting a more up to date picture of the Cambrian explosion.

Conclusion

Through our increased understanding of the ways in which Cambrian and Ediacaran fossils are preserved, a more refined timescale, and a better understanding of how to classify these organisms, we have a different picture to that of Gould and the palaeontological community of the 1980s. It is no longer a diversification resulting in an unprecedented number of phyla, but one in which stem groups abound. We now have a better understanding of the timings of key events over tens of millions of years, and of those beautiful sites of exceptional preservation. I will continue to flesh out our modern understanding of the Cambrian explosion in future blog posts.

 

 

The Cambrian Explosion – An Enigma of Deep Time

Over half a billion years ago the biological world was a more peaceful place, or so the story goes. Simple multicellular organisms abounded, doing little more than filtering out food particles from the ocean waters. Then, in a geological blink of an eye, animals began to diversify, irreversibly changing the prevailing ecosystems, paving the way for modern life. They began eating each other, causing some to burrow into the sediment deeper and deeper, disturbing the slimy microbial matgrounds which had been key in the fading Ediacaran environs. Some developed armour, sporting hard parts which protected their soft flesh, leaving behind more distinct traces in the fossil record. Yet others became more mobile, learning to swim around to evade predators, or to seek out their own prey.

This event is often referred to as the Cambrian Explosion and has earned the nickname “biology’s Big Bang”. It is one of the most important events in the history of life on Earth and, due to its singular nature, is one of the most misunderstood. Misinformation proliferates on the internet, not least due to anti-evolution websites considering it to be a weapon in their arsenal, but also because it is a very mysterious time, where datasets often support multiple interpretations and cause and effect are difficult to untangle.

Image credit: Brest van Kempen

When Charles Darwin first pondered the Cambrian mystery, he was facing a fossil record where no Precambrian fossils were known – the lowest rocks contained the surprisingly complicated trilobites, not at all what he had hoped to see. Darwin invoked the incompleteness and imperfection of the fossil record as his explanation, in the hope that someday new fossils would elucidate this remarkable absence. It wasn’t until 1958 when Precambrian fossils were first recognised, but even they did little to diminish the seeming leap in complexity in the Cambrian. The Burgess Shale fossils, found by Charles Walcott in 1909, revealed a menagerie of bizarre creatures, many of which clearly had modern body plans, but many others seemed to have unique body plans, as though this Cambrian diversification was even bigger than expected.

The Burgess Shale was properly studied from the 1970s onwards and by the 1990s the diversification had been established as one of the key mysteries of palaeontology. By this point, a picture of the Cambrian Explosion had emerged which provided quite the conundrum. Those Precambrian fossils had originally been interpreted as belonging to modern animal groups but had since been questioned and even proposed as belonging to their own kingdom. Then, in perhaps as little as four million years, every modern phylum arrived on the scene, along with potentially three times as many more. It was an unprecedented diversification, expounded beautifully by Stephen Jay Gould in his book Wonderful Life. This is a picture which crops up repeatedly, despite twenty years of advances which show it to be wrong. In future posts, I will explain what has changed in our understanding of the Cambrian Explosion, which questions have been answered, and the mysteries that lie ahead.