Narrative ruins history?

Coming from a scientific disposition, I have a scientist's rapacious desire for The Truth.


That's the beauty of science.  We get closer to Truth all the time - and the mis-steps and side alleys are far fewer and less significant than the ascientific (as are many climate change deniers) would have us believe.  Mostly, refinements are built upon refinements, and previous truths are hardly ever gainsaid - at least not significantly.  Quantum and Einsteinian physics don't negate the reality and applicability of Newtonian physics on an everyday, human scale.

 History is unlike science in so many ways, but the one that springs to mind right now is narrative.  In that sense, history is more like shoddy journalism - even good journalism - in that it tries to tell a story.  And the failing is that the whole of the truth is sacrificed: the nuance, the periphery, and the way in which life is not quite like fiction or myth; it doesn't have unity of purpose or theme, or specific point.




True history is messier, and purposes cross, narratives interact without clarity or precision.  Out of all that, historians and journalists are alike with novelists, trying to create a single strand (or multiple strands) where the full story is so much more complex, riddled with irrationality and strewn with different actors' clutter and concealment.  And of course, it's only one person - or peoples' - truth.  And even then, much of the time the truth will simply never be available.  So, from honourable motives or not, the historian as storytellers will attempt to persuade rather than prove.




I read some narrative in science.  Stephen Jay Gould and Richard Dawkins are good tellers of short stories.  But their tales are much better corroborated and agreed upon.  And if a single essay tells only part of the much wider discipline of evolution and genetics, the rest of it is there for the taking - not the disputation, disagreement, and ultimate irresolution.

Still, for the scientifically-disposed, at least history is better than fiction: there's more truth in it.  And if we long for a cracking good story, then at least we know there's more to it than we're being told.

Rees, Dawkins and Gould: finely picking the cleft between science and religion

I first encountered Martin Rees, president of the Royal Society, in the pages of New Scientist last year: a brief interview on occasion of the 350th anniversary of the Society. He talked science, but looked nothing less than an Establishment bastion (and he’s also Astronomer Royal, Master of Trinity College, Cambridge, and in the House of Lords).


Just recently, I heard him in a brief piece on the ABC Radio Science Show. He was talking on the divide between science and religion – and he rather surprised me with some non-establishment words. His conversation drilled into some finer points of this divide. Inter alia:

“I suspect my beliefs or lack of beliefs are rather similar to Richard Dawkins's…”

Then:

“I agree with Richard Dawkins that fundamentalism… is a real danger, and I think we therefore need all the allies we can muster against it, and I would see the Church of England and the Archbishop of Canterbury, for instance, as on my side against fundamentalism. Therefore it seems to me counterproductive to rubbish people like that. I'd like to see them on my side, and as a Brit who grew up in that culture, I'm rather supportive of the Church of England.
And I think there's another reason where I think his attitude is also damaging. Suppose you were teaching a group of kids in a London school and a lot were Muslims and you told them that they couldn't have their god and have Darwin. They're going to stick with their god and be lost to science, and that, again, I think is counterproductive. So I believe wherever possible one should have peaceful coexistence with mainstream religions.”

The Templeton Prize was apparently a notable point of departure between Rees and Dawkins. The prize “honors a living person who has made an exceptional contribution to affirming life’s spiritual dimension, whether through insight, discovery, or practical works”.

Rees said Dawkins labelled him a quisling because Rees was “less hostile to the Templeton Foundation than he was.” But then: “I don't go all the way with the Templeton Foundation because they believe in constructive dialogue. I think there's limited scope for constructive dialogue, I think there can be peaceful coexistence, but I don't believe theologians can help with my physics”.

Per se, that’s not too far from the resolution attempted by another scientist, Stephen Jay Gould. He coined the term Non-Overlapping Magisteria (or NOMA): “Science tries to record and explain the factual characteristics of the natural world, whereas religion struggles with spiritual and ethical questions about the meaning and proper conduct of our lives. The facts of nature simply cannot explain correct moral behaviour or spiritual meaning”.*

Of course, that satisfied few who weren’t already satisfied.  And although the two are similar, I rather like Rees' turn of phrase.



Full text of the Rees conversation available here.


*Gould, SJ (2003): The Hedgehog, the Fox and the Magister’s Pox (p87). Jonathan Cape, London.

Cambrian explained: early multicellular animals

The trifecta of interest in early evolution is: the emergence of eukaryotes (cells with nuclei), multicellularity, and animals.

There are signs of life at 3.8 billion years ago, just 700 million years after the formation of the Earth. I've discussed in more detail the advent of eukaryotic life here. The discussion below revolves around multicellular animals, and several discoveries that push back the timeline of their emergence. This ameliorates the picture of Cambrian-period "explosive" evolution, and replaces it with a more steady narrative. As in all paleontological tales, the evolution of understanding is a matter of both further discovery, and finer interpretation of existing evidence.

The first multicellular life (algae) dates back 1 billion years; the first multicellular animals date from 575 million years ago (the sponge-like Ediacarans).

From 542 to 520 million years ago in the Cambrian period was the relatively sudden evolution of more modern animal forms, which has piqued the curiosity of many, including Stephen Jay Gould. Gould explains the difference between Ediacaran animals and modern ones in terms of body layers: the former are diploblastic while the latter are triploblastic, essentially meaning they have an outer layer (ectoderm), a gut (endoderm) and, most importantly, a mesoderm in the middle, which lends the capacity for complex internal organs.


Traditionally, as a central narrative of animal evolution, the Cambrian explosion lacked context. However, more recent discoveries place the ancestors of Cambrian animals much further back, to about 850 million years.

One discovery concerns analysis of the bountiful Doushantuo Formation, a seabed fossil lode from China. Dating from 550 to 580 million years - latter times for the Ediacarans - tiny spheres have been found to be early animal embryos. Hard, spiky shells ruled them out as large bacteria, and those same shells, sans embryo, have been identified from 632 million years, early Ediacaran period.


This finding was reported in 1998 (Xaio, Zhang, and Knoll in Nature), and discussed at length by Gould in Lying Stones Of Marrakesh (notwithstanding his continued maintenance of special significance he previously accorded to the Cambrian).

Going back further, to 635-713 million years ago, a form of cholesterol has been found, 4-isopropylcholestane, now found only in some sponges.

Further: 850 million year old rocks in Canada (MacKenzie Mountains), which contain stromatolites (traces of cyanobacteria), have also been found to have a particular pattern of calcium carbonate which has been identified as characteristic of a collagen mesh, which only animals build. The discoverer (Canadian Elizabeth Turner) says the life form was even more primitive than a sponge: "a few different types of cells living together in a shared, collagenous matrix".

These discoveries fit well with molecular clock calculations: that is, comparative DNA analysis had already put back the advent of animals to about this time frame - yet evidential traces hadn't been identified until now. Others cast doubt on the interpretations of the evidence above, while still accepting animal evolution as dating back further than other evidence has shown.

I think a key aspect of the emergence of multicellular animals is the environmental backdrop. Photosynthetic bacteria started producing oxygen about 2.5 billion years ago, although this did not extend beyond a few metres of the ocean surface. This oxygen had been poisonous to most life to that point, but fostered development of oxygen-tolerating life. Atmospheric oxygen propelled a chain of circumstances resulted in the lower reaches of the ocean being not just anoxic, but also laden with hydrogen sulphide. Although some bacteria thrived in these conditions, the combinations would have been a "persistent brake on eukaryotice evolution" (according to the above Andrew Knoll).

Then came the second "snowball Earth" ice age, which was seen to "reset the chemistry of the oceans" to make life more favourable to multicellular animal forms. Yet conditions at first were more conducive to smaller, soft-bodied organisms - which, over time, changed the balance, perhaps by eating inimicable bacteria. On one interpretation, increased oxygenation was a result rather than a cause of animal evolution - although it makes more sense that they worked in tandem. The same is conjectured for the set of ice ages that occurred around that time: they could have been just as much a consequence of animal evolution (by sucking out carbon when buried) as a cause. It's easy to envisage a slowly oscillating set of equilibria that eventually settled to a higher oxygen, animal-rich, warm Earth - especially as there were no more snowball Earths once larger animals had evolved (notwithstanding subsequent ice ages of smaller scale).

A fascinating narrative, and one that is more appealing than sudden bursts of evolutionary activity. More detail in the New Scientist article below.


References
Gould, SJ (2000): Of Embryos and Ancestors in Lying Stones Of Marrakesh, Vintage, London.
Fox, D & Le Page, M (2009): Dawn of the animals in New Scientist, 2009, 11 July.

Evolution: Darwin's modification by descent

There's something of a flood of media relating to Darwin, as it is the bicentennary of his birth and 150th anniversary of his book On The Origin Of Species. Even something in it for me, as I heard on the radio part of a 1987 event featuring successive addresses by Richard Dawkins and Stephen Jay Gould. They both downplayed any beatup notion that there was any fundamental dispute between them, while emphasising their different perspecitives on their field. Still it was fascinating to listen to them both.

Although I am largely not one for hero-worship, Darwin must be given strong credit for introducing ideas that were revolutionary and prescient. On the latter, he broadly predicted the existence of a mechanism for evolutionary inheritance with modification, without knowing what shape it would take, and decades before it was widely verfied and accepted.

As part of the radio programme, I heard someone give a Darwinian characterisation of genetic variation as "copious, small and undirected". One of Darwin's revolutionary points was that evolution is paradoxically "neither random nor intentional". Not intentional, in that there is no overarching will at play that can make decisions about the process. And although the fodder for variation is random mutation, the effects are not, as species survival is directed by the totality of its environment.

Someone in that broadcast commented drily that although Darwin was inspired by Adam Smith's economic theory of numerous single players in a market vying for their own survival, Smith's theory "didn't work". Now that may be a bone of contention for some, but the purity of Smith's vision relied on equal players in a market where no monopoly develops - and we all know that in the absence of a directed force (ie a government), the natural tendency of capitalistic markets is towards monopoly. The analogy was imperfect; nevertheless it is the mark of a significant mind to be able to associatively draw from other fields to forge new understandings of one's own.

Convergent evolution

This is always such a fascinating subject. Earth's natural history is positively littered with examples of different species that develop remarkable similarities to each other in complete evolutionary isolation.

An easy example is the body shapes of sharks (fish), cetaceans (mammals: whales, dolphins, etc), and ichthyosaurs (porpoise-like reptiles): all evolved fairly similar adaptions for swimming, although a notable difference is the tailfins of cetaceans, giving rise to an up-and-down tail movement, rather than side-to-side for the others. A ready observation would be that they show similar vertebrate adaptions to the similar demands of the environment.

There are so many other examples: similar-shaped and/or similar-functioned animals around the world. Try unrelated fish in the arctic and antarctic waters each with an equivalent anti-freeze-like chemical in their blood, with genetic origins quite unconnected.

Try re-invention of the eye several times. Albeit the squid's, for example, is better engineered than ours, since our retinal nerve endings emerge between lens and retina, making for less efficient vision that the squid's whose nerve endings sensibly emerge behind the retina. Moving ahead of myself in Richard Dawkins' The Ancestor's Tale (currently at p344), Dawkins mentions on p602 an expert in comparative zoology of eyes, Professor Michael Land, who identifies nine independent principles of optical mechanics, "each of which has evolved more than once".

Try the proliferation of parallels between eutherian (placental) mammals and metatherian (marsupial) equivalents. Thylacine and timber wolf skulls, for example are said to be nearly identical, despite being completely unrelated.

It sounds like a rash of grossly unlikely coincidences, ready-made for creationists to fan argumentative flames. Yet in some ways it makes perfect sense: evolution is about species expanding to fill environmental niches, and
a) Over many times and locations, there are sets of all but identical niches
b) What developed and survived was what was most successful in the environment, so the directive forces of nature operated in a similar way on what was often a relatively similar genetic material.

This is obviously quite a source of frustration for taxonomy. Whereas in the relatively recent past, classification was based largely on morphology (body shape and features), modern molecular analysis has demonstrated that many of the connections drawn in the past were examples of convergence.

Dawkins also describes three different moles. The African golden mole (Chrysochloridae) was grouped with the Eurasian mole (Talpidae) in the defunct order Insectivora on the basis of such close similarity as burrowing machines: forepaws modified as spades; atrophied eyes (superfluous underground) and no visible ears. Then there's the marsupial mole: Wikipedia says they are so similar to golden moles that they were once thought to be related despite the marsupial/placental divide. Of course, all three are now classified quite separately; molecular analysis has in fact torn down the whole disputed Insectivora order altogether.

Interesting to note convergent evolution depicted as a criticism of Stephen Jay Gould. One of Gould's consistent themes was the contingent nature of evolution: how randomness played such a role that any slight re-alignment would have resulted in totally different outcomes.


I don't see these concepts as being entirely in opposition. Gould's theme plays out on a much larger tapestry than the micro-evolutionary outcomes. Convergence doesn't necessarily mean, for example, that had the K-T meteor not wiped out non-avian dinosaurs, reptilian humans would have evolved. In the absence of that meteor, dinosaurs could have remained successful in their niches for many millions more years given no other environmental pressures.


I suspect that certain paths are available only for species at a certain level of complexity; yet evolution is not specifically directional towards complexity (merely towards variation in complexity)...


How convergence does and doesn't work, what it does do and what it doesn't, is a fascinating area of study.

Reference
Dawkins, R (2004): The Ancestor's Tale. Phoenix, London.

End of life: sooner than you think

Stephen Jay Gould was fond of emphasising the contingent nature of life - and in particular the emergence of humans.

The earth is 4.5 billion years old, and it had been estimated that we are at about the halfway point in the planet's existence.

As we saw previously, life emerged about 3.5 billion years ago, about as soon as it theoretically could. However, it was not until around 540mya that complex multicellular animal life (as we know it) appeared.

A new paper by a University of Sussex astronomer, Dr Robert Smith, actually calculates that the Earth has another 7.6 billion years to go. But now for the bad news. According to Smith's team, the slow expansion of the sun will cause temperatures to rise well before that: "the oceans will boil dry and the water vapour will escape into space. In a billion years from now the Earth will be a very hot, dry and uninhabitable ball."

So, we actually have less than a billion years left on this planet. We're here near the end of its cycle, not the middle.

Of course, a billion years is a long time for us to come up with other means of survival. If we don't kill the planet earlier.

But the point is, in the great contingent nature of our planet's history, there's effectively only a small window of time in which such complex life as ours could have developed.

Lucky our war against prokaryotes (see previous entry) has been balanced as much in our favour as this. But are we already starting to tip the balance back the wrong way?

Mass Extinctions explained: prokaryotes vs eukaryotes

An article in the New Scientist points to an important way to trace evolution through the sedimentary rock record.


In the development of life into multicellular organisms, there is some difference of opinion on the most significant step: whether it's from simple single-cellular organisms (prokaryotes) to complex ones with nuclei (eukaryotes), or the evolution of single-cellular life to multicellular. Most seem to favour the former.


Whereas stromatolites give a record of when the earliest lifeforms first emerged 3.5 billion years ago (according to Stephen Jay Gould this was just about as early as it could) there has been no way to trace back first emergence of eukaryotes - until now.
Peter Ward reports on chemical biomarkers in rock. Certain biological molecules break down under heating, cooling and pressure into highly stable organic compounds that could not be made by any known inorganic process. That last phrase is the kicker, which indicates that any such occurrence of the relevant compound would be an indicator of life. Moreover, some of the compounds are unique to particular groups of organisms. For example, C28 to c32 polyenoic fatty acids have been found to be unique biomarkers of sponges.


In the late 1990s, two Australians found steranes - biomarkers for eukaryotes - in Australian rock dating back to 2.7 billion years (but no older). This gives a good indication of the first emergence of lifeforms with cell nuclei.


By 800 mya, the biomarkers indicated multicellularity.


By 542 mya, the biomarkers indicated animal life - but we know this already as the Cambrian explosion.


In 2005, a Japanese team investigating the K-T extinction event (65 mya) they found, as expected, biomarker indicating a deluge of dead plant material. One study then found a decreased abundance of land plants for the next 7000 years.


Then to the Permian mass extinction event, the biggest of the lot. In 2005 a biomarker called isorenieratene was found at this point. These indicate green and purple sulpher bacteria, which cannot tolerate oxygen in water, in turn suggesting the oceans were [largely] devoid of oxygen and "saturated with hydrogen sulphide". A poisonous balance. A suggestion since (by Lee Kump) has been that hydrogen sulphide as the primary cause of the Permian extinction: so much in the ocean that it escaped into the atmosphere, poisoning land-based life and depleting the ozone layer.


The cause of this was in turn traced to global warming triggered by greenhouse gases from the Siberian Traps - the biggest ever volcanic eruption episode. The coinciding of the Permian extinction with the Siberian Traps has long been identified. although not all the mechanisms had been strung together: the global warming lessened the temperature differential between polar and tropic regions, in turn slowing ocean currents, causing stagnation (deoxygenation) then a buildup of anaerobic (oxygen-shunning) bacteria.


Via that biomarker isorenieratene, the same mechanism is seen to have happened - on a smaller scale, obviously - with the Devonian and Triassic extinctions. Ward comments that "it is beginning to look as if the K/T mass extinction was unique in having been caused by an impact [meteor]".


Ward's ultimate comment is that the planet is effectively a battleground between the early-emerging prokaryote life and the later-emergent eukaryotes (including us).


These periodic patterns seem only to serve to delay the emergence of tail-end complex life. And, as Gould would say, we just happened to get our chance due to that preceding history. Otherwise, it would have been down to the descendants of more advanced creatures than were our ancestors of the time.

some Paleontology sites

A few useful references:

Tet Zoo - Tetrapod Zoology blog. Always something of interest. Somewhat skewed to dinosaurs?

Palaeos - A very good reference for cladograms and geological times

Paleo news - A reasonable summary of recent news, generally stuff that's broken through to mainstream media.

StephenJayGould.org - an "unofficial archive"

Paleoring - for a bit of a trawl

Evolution: Size change may not be what you think

In his book Life's Grandeur, Stephen Jay Gould has a salutory point to make about evolution and size. In typical Gould fashion, he knocks on the head a "conventional wisdom" that is not really so.


Foraminifera are small, single-celled marine organisms that form shells. Their abundance is such that they have been used as fossil markers that help in dating sedimentary rock. Mostly, they are fairly small, less than a millimetre.


Gould details three episodes in their evolution: their emergence in the Mesozoic (dinosaur-dominated) era; in the following Paleogene period; then subsequently in the Neogene period to the present day.


The boundaries between those three episodes are marked by extinction events, where most foram species died. In each case, the foundation (or surviving) species were relatively small; conventional wisdom goes that they increased in size over the course of each episode.
There is a generality called "Cope's Rule" that observes that most taxons tend to increase in size over the course of evolutionary history. In this case, "most" is around two-thirds, and foram evolution would seem to follow that form.


However, Gould argues (rather successfully, I'd say) that this apparent trend is not so, as such. Evolutionary changes occur through random mutation (with environmental* selection being the winnowing process). One might expect that of mutations that affect size, if they are random then a change could equally be an increase or a decrease in size. However (and this is Gould's point), if the starting point is close to the small end of the range of viability for that organism, then over time the spread of size changes would favour increases over decreases. This would lead to the appearance of an increase in size, if one measured the mean (average) size. Also true, of course, if one measured the upper limit of size. If size was displayed in a standard bell curve distribution, the change in form of the curve over time would illustrate a "wall" at the lower end - a lower limit against which size movement would not be able to penetrate. The figures Gould used showed minor change over time in smallest size, but much more marked change in largest size.


When you think about it, it makes intuitive sense - an organism cannot simply dwindle away at the lowest end of the size range. The lesson is to avoid taking at face value any narrative that includes an increase in lineage size over time.




I do have a couple of comments to make on this. The first is that it has certainly been demonstrated that colder climates lead to larger size (on an evolutionary time scale) in animals that have over time adapted to such changes. There is some intuitive sense here, in that a larger body has a smaller surface-to-mass ratio, which is more efficient for heat retention.


The other comment is that one could also try Gould's measurements on a sort of logarithmic index, to see if size changes (from a starting point based to 1) would demonstrate some evenness of logarithmic change.




*Clearly the standard term here is "natural selection". My preference for "environment selection" is intended to make clear the encompassing of selection not just on the basis of inter- or intra-species competition, but environmental changes and also the human hand.




Reference

Gould, S J (1996): Life's Grandeur. Jonathan Cape, London

Evolution: Non-directional (The Hox Gene, part 1)

One of Gould's recurrent themes is that evolution is not necessarily a process of increasing complexity. Parasites present a useful example of this. It's all about streamlining.

Gould: parasites "often adapt to their surroundings by evolving an extremely simplified anatomy, sometimes little more than a glob of absorptive and reproductive tissue".


Protozoa are mobile, single-cellular animals. Metazoa are complex, multicellular animals.

Then there are Mesozoa - literally, "middle animals". The major group, Dicyemida, are parasites residing in squids and octopuses.

They comprise one central cell, with about 10 to 40 cells arranged in an outer layer. The debate around these animals had been where to place them in the evolutionary map. A 1999 article in Nature (Kobayashi et al) announced the discovery within them of a Hox gene. These are known only in higher order metazoa, specifically those with three cell layers (triploblasts - they include an inner body cavity).


Thus it has been concluded that these creatures evolved to the most efficient design necessary to survive in that environmental niche. Evolution is about developing the best fit to environment. At times, that constitutes an "arms race" between species; other times it involves a paring back.

Survival is what counts, not persistently marching up a metaphorical hill. The metaphor is more akin to negotiating an endless, multi-path maze. There are many directions that work, some are dead ends, and sometimes there's a park bench to rest at - there's no specific goal other than to be.


Reference
Gould, SJ (2002): I Have Landed; Jonathan Cape, London.

Evolution: Wonderful Life 2: the pattern of early diversification

Recapping on the Cambrian explosion: this was pretty much the beginning of modern multicellular animal life about 530 million years ago. In The Lying Stones Of Marrakesh, Stephen Jay Gould characterised this as constituting the greatest of all mysteries: "the causes of both the anatomical explosion itself and the 'turning off'of evolutionary fecundity for generating new phyla thereafter."

This has troubled biologists since before Darwin, and is less likely to be due to a simple gap in the exposed fossil record than to other phenomena, such as an extinction event covering the preceding Ediacaran fauna (sessile - non-mobile sponge-like marine animals). That's just a guess, but it parallels what happened 65 million years ago (the KT event, the end of the dinosaurs), when a meteor caused mass extinctions and specifically allowed mammals to proliferate.

The Cambrian Explosion saw the emergence of most major animal body types (phyla), bar the relatively insignificant marine bryzoa.

I'll restate a key passage of Gould's book Wonderful Life:

"The major argument of this book holds that contingency is immesurably advanced by the primary insight won from the Burgess Shale - that current patterns were not slowly evolved by continuous proliferation and advance, but set by a pronounced decimation (after a rapid initial diversification of anatomical designs), probably accomplished with a strong, perhaps controlling, component of lottery." (p301)

(Here, decimation doesn't refer to the literal reduction by one-tenth, but more the common understanding of much more dramatic paring to a relatively small fraction.)

If you can picture this as a spindle diagram, as Gould suggests, the direction of time would be bottom to top, and the spindle's width at various levels would represent diversity. And the appearance of animal body types would be like a christmas tree - the bottom would depict a small diversity of type, followed by a rapid (relatively instantaneous) expansion, followed by a gradual reduction. This is probably contrary to popular understandings of evolution of animal variety, as being either like an inverted cone - a constant increase in variety - or perhaps like a diamond, where a constant increase is followed by a constant decrease.

example of a spindle diagram

Gould depicted the Cambrian phenomenon as one of sudden explosion of so-called disparity - that is, sudden appearance of a variety of fundamental animal body types, or phyla.

This is where it gets interesting: he notes that in recent studies, he "concluded that the pattern of maximal early breadth is a characteristic of lineages at several scales and times, not only of major groups at the Cambrian explosion". In effect, the bottom-heavy christmas tree shape happens often. He "surveyed the entire history of marine invertebrate life - 708 spindle diagrams at the level of genera within families". With only one exception, he found lineages that arose early in the history of multicellular life - Cambrian or Ordovician periods - had spindles with 'centre of gravity' less than 0.5 - ie more like a christmas tree than a diamond.

This is certainly food for thought. Why such a regular pattern?

The KT experience does suggest that mass extinction permits remaining life to proliferate into the ecological vacuums, but there is no immediate suggestion that this happened in the Cambrian explosion. Yet the disappearance of the Ediacarans shortly beforehand (in geological terms) must have left a gap.

In The Lying Stones Of Marrakesh, Gould details evidence of phosphorised embryos in precambrian rock [the phosphorisation process can preserve soft tissue that would otherwise decay, but it works only on very small entities], with some suggestion that modern animal phyla had emerged before the Ediacarans disappeared. Then there is the SSF (small shelly fauna) of early Cambrian times to account for.

The story continues, and there are obviously more discoveries to come, more theorising. The mystery is too big to remain unaccounted for too much longer.



References
Gould, SJ (1989): Wonderful Life. Penguin, London
Gould, SJ (2002): The Lying Stones Of Marrakesh. Vintage, London.

Evolution: rivalry between the sciences

The advancement of evolutionary thought is most definitely a multidisciplinary affair. At its core, it requires an understanding of natural history (paleontology) and genetics - the macro and the micro, if you will.


They're all meant to be united in a detailed understanding of biology, but writings on the subject often betray the specialist's perspective on the other scientists involved in the quest for knowledge.


What I have read sometimes reveals the bias of the particular discipline. If I personally have a bias, it would be towards the sweeping overview of natural history. I find geneticists (such as John Maynard Smith and George C Williams), to paraphrase Mark Twain, all seem to talk about sex but not do anything about it. This apparently places me around the middle rung in the hierarchy.


I think it was Stephen Jay Gould who revealed that a traditional bias of paleontologists was that taxonomists (those essential scientists who analyse similarities and differences between species) are sometimes disparaged as being akin to stamp collectors.


John Maynard Smith in turn revealed that a traditional attitude to paleontologists had been to wish they would "go away and find another fossil, and stop bothering the grownups".
Smith bookended this with context. By way of introduction, he claimed that in the modern synthesis of evolutionary theory that emerged in the 1940s, paleontologists took part, but essentially only to confirm the facts uncovered by "the rest of us", and not to propose any new theory.


This at the beginning of an essay that ultimately praised paleontologists, and Gould in particular for advancing theory in recent times. Then again, Smith admitted to some surprise at the knowledge revealed in the narratives of paleontologists (ably assisted by geologists, climatologists and the like). Genetic analysis is relatively silent on major events such as mass extinctions.


Paleontology is often regarded as being insufficiently hard a science specifically because it often inclines to persuasive narratives, whereas geneticists would have you believe they own the realm of detailed analysis and logic.




Yet the geological and fossil records are thoroughly essential for an understanding of the origins, history and direction of life.





References

Maynard Smith, J (1984): Did Darwin Get It Right? Penguin, London.

Williams, G.C. 1996. Plan and Purpose in Nature. Weidenfeld & Nicolson, London.

Evolution: Wonderful Life 1 - overview

Stephen Jay Gould's book Wonderful Life is subtitled "The Burgess Shale and the Nature of History". Its twofold perspective discusses a) The Burgess Shale, an extremely fertile lode of fossils from the Cambrian period (characterised as an "explosion" of new life forms), close to the dawn of multicellular animal life; and b) the history of scientific thought on the Burgess and on Cambrian life.

It's a great read - one of my favourite books of the last year. It provides much insight for the general reader into evolution and the history of life, although I have to say that much of what it says makes much more sense after having read a fair bit of background on biology and evolution.

In this post, I will give an outline of the book; in subsequent posts I will comment on some specific issues raised.

The first chapter gives some background on evolutionary thought - more specifically, it goes some of the popular conceptions and misconceptions of evolution. Gould is particularly disparaging of the common depictions of evolution as a series of progressively more complex beings, culminating with humans as a pinnacle of achievement.

The next chapter places the Cambrian period in the context of Earth's history, but more specifically gives some background on the discovery of the Burgess Shale.

The following chapter, comprising the bulk of the book, traces in detail the history of scientific discovery from the Burgess Shale, and in particular the early scientific mis-steps in analysis of the life forms represented by Burgess. It brings us up to date (specifically, to 1989) on the current consensus of scientific opinion on a number of animals that were originally represented as arthropods (the phylum containing diverse animals such as crustaceans, insects, spiders and trilobites). It specifically recounts the reconstruction of a number of very odd creatures - and includes a number of very good illustrations of those creatures made especially for this book.

However, the journey - for me at least - reaches its apex with the final, fifth chapter, in which Gould synthesises a number of lessons learnt from the study - particularly via some of his own research in several earlier papers. This chapter outlines a number of significant insights, discussion points - and contentions that are or should be contentious at least. This chapter provides much food for thought, which I hope to canvas shortly.


Reference
Gould, SJ (1989): Wonderful Life: The Burgess Shale And The Nature Of History. London: Penguin.

Evolution: Arthropods

In reading Wonderful Life, Gould's book on the Cambrian explosion (some of the earliest multicellular life forms), I find Gould spending much of his time dwelling on arthropods. It's worth spending time on them, as that phylum (one step below Kingdom - Animal) constitutes most animals in the world: insects spiders and crustaceans in particular.

At first they look quite alien close up, but after a while, patterns emerge. And believe me, there are more alien-looking lifeforms around (eg the Cambrian creatures Opabinia or Hallucigenia). You can get used to arthropods...

Characteristics:

The prototypic body is constructed of a number of repeated segments. However, from that basic design, differentiation evolves. Typically, over time, the segments may become fused; further, different segments evolve different functionality - the head in particular, as well as the tail. Each segment begins with a pair of jointed appendages, one on each side of the segment. The appendages are jointed - arthropod means "jointed foot". Each appendage of the prototype is biramous - meaning each has two branches! - typically a leg for walking and a gill. However, this pattern can modify over evolutionary time, leaving at least some of the legs uniramous.

Arthropods have exoskeletons - that is, the skeleton is on the outside - although not what you'd consider bone.

The key to understanding them is how the segments fuse differently, how the appendages specialise, and how the exoskeleton can modify.

Often the segments are fused into three: for example, the head, thorax and abdomen of insects. Typically, the head is composed of several fused segments, and the attached appendages specialise, for example, as antennae or for feeding. With spiders, for example, the actual legs are on the head; in the posterior the walking legs have disappeared, and the gills have modified into oxygen-breathers.

Frequently, there are two pairs of appendages before the mouth and three after. Sometimes (eg in crabs) a carapace has formed over the body; sometimes that carapace is divided - bivalve.

The five major kinds are:

1. Trilobites: extinct marine creatures with three lobes across, and numerous segments

2. Chelicerates: spiders, mites and scorpions

3. Myriapods: centipedes and millipedes

4. Hexapods: mainly insects, typically six legs. By far the most numerous arthropods, with millions of species. Wikipedia aligns them with crustaceans, although Gould united Myriapods and Hexapods as 'Uniramia'

5. Crustaceas: mainly marine, mainly biramous; includes lobsters, crabs, barnacles, and many more.

Although this may seem an odd group, there are enough similarities to unites them; enough to posit a common ancestor.

References

Gould, Stephen Jay (1989): Wonderful Life: The Burgess Shale and the Nature of History, Penguin, London.

Wikipedia: Arthropod (extracted 12-Dec-2007)

Evolution: On Stephen Jay Gould

For over 25 years from 1974, Stephen Jay Gould produced an essay for every edition of the magazine Natural History. A number of these were subsequently re-edited and produced in book form. In his tenth and last book of collected essays, I Have Landed, Stephen Jay Gould explicitly classified (as is his wont) his particular approach to essay writing.

From the beginning, he specifically chose to write for the general (non-technical) reader while avoiding conceptual simplification. This is significant, something few academics do. It exposes an important amount of detail of his subject, evolution, in a way that is approachable for all, yet permits analytical depth.

He further characterises his own writing as intellectual puzzle-solving, although I would say that much of the time he simply elaborates on a specific issue in evolution, worrying the finer detail. He also attempts to posit his treatises within a humanistic context - which is to say he often places the particular point in a wider human context of how scientific discoveries are wrought, and how social context interacts with those discoveries.

Yet most important is his treatment of finer concepts of natural history in non-jargon terms, such that any intelligent reader can see meaning without (indepth) training in the specific science.


I came to his writing by chance, one in a pile of library books once I was already delving into the subject. And his approach supercharged my enthusiasm.

Although he writes for the lay reader, if there is to be active pursuit there is no escaping the necessity to engage in background reading. Biology is the first place to start; included is genetics, paleontology, geology, and some anthropology, amongst other subjects.

It is also helpful to read in parallel. I am currently in the middle of his book Wonderful Life, a history and exposition of scientific discovery of the Cambrian era, close to the beginning of the emergence of modern animal forms. It is certainly a book of wonder, making an engaging narrative of a particularly dry subject like the classification of arthropods ( easily the largest grouping of animals, which includes insects, spiders, crustaceans, trilobites and others). The name arthropod, by the way, refers to jointed legs; the unifying feature is multiple body sections (some fused together in later evolution) with pairs of legs for each section.

However, where Gould sets forth four general groups of arthropods, the consensus-driven Wikipedia lists five - dividing uniramia into hexapods (insects) and myriapods (millipedes and centipedes), and placing the latter group closer to crustacean arthropods.

Part of the problem here is often that evolutionary biology is, well, an evolving subject, as much today as it ever has been, especially with the advent of genetic analysis.

Wonderful Life was written in 1989. A few scant years later, revision had already overtaken the work. A good example is the species Hallucigenia. In one of his essay subsequent to that book, Gould noted that that species had always been portrayed upside down - even as recently as his encompassing book on the matter.

So read a variety of works and authors on the subject - particularly the very recent. Yet having said that, I would be happy to own the full set of his collected works. The concepts are an intellectual challenge and a learning experience, and the books make a very enjoyable read.

Two different meanings for "evolution"

The popular understanding of the term 'evolution' may be correct, but it is not the same as the biological term.

Stephen Jay Gould would have it that we hold in our minds two different sets of concepts when we use the term evolution.

The original use, and the prevailing one in general use, is as a synonym for predictable progress to an inevitable end. Gould illustrates this with quotes from the Encyclopaedia Britannica, discussing star formation. In describing the process, the term evolution is used as if the process, once it kicks into gear, is entirely deterministic - that is, given one set of input factors, the outcome is pretty much pre-ordained. And this is correct; and such determinism underpinned my years of physics training - notwithstanding different rules applying at the extremes, such as quantum levels.

According to Gould, Darwin largely shied away from use of the term, because of this determinism. There are two problems here: biological evolution lacks specific direction and predictability. Yes, it is non-deterministic.

Direction: fit to environment is the key. We can be misled into thinking that we are the pinnacle of evolution, and so all evolution is towards increasing complexity. Gould discusses a type of parasite called dicyemids, that live in the renal organs of squids and octopi. There had been much debate over whether these creatures had always been primitive, or whether they had shed functionality to adapt to their environment, simplifying in the process to little more than feeding and reproduction functions. In 1999, Kobayashi, Furuya amd Holland presented genetic evidence in Nature magazine to demonstrate dicyemids had in fact descended from more complex creatures, in the process becoming incredibly simplified. Evolution is not necessarily about increasing complexity. Progress can be in any direction appropriate to the needs of the environment.

Predictability: Darwin's "descent with modification" occurred, as Gregor Mendel demonstrated in the 19th century, via random genetic mutation. In a static environment, a species' genetic outliers are disfavoured; in a changing environment, those random outliers can be better equipped to handle the changes. Gould's example here is an elephant in Siberia: when the climate turns cold, those elephants in successive generations that are hairier are more favoured to survive.

However, this randomness is such that, were history to be replayed, there is no guarantee that the changes wouldn't play out in a different way. There is no promise of predictability, since results are entirely dependent on what mutations eventuate - and whether the bearers of the altered genes survive whatever mishaps and chance comes their way.


All this is not to deny that increasing complexity has at times been a definite trend in the planet's history. Increased complexity be a survival advantage. Further, evolution has to a significant extent been an "arms race" between predator and prey, between competitors for resources. Arsenal improvements, including lung capacity, musculature, size (in both directions) and functionality have always aided genetic longevity.


It's barely worth trying to eliminate concepts of determinism and direction from popular understanding of the word 'evolution'. But it suffices to understand the different uses in the different contexts.


Summarised from:
Gould, Stephen Jay (2002): What Does The Dreaded "E" Word Mean Anyway? in I Have Landed, Jonathan Cape, London.

Evolution: misconceiving change

Your average Harry Potter book is full of mystery, myriad unusual details, and engaging narrative. And it gets better with each book. There's the recent finale, then the series ends.
And while there's a steady flow of ideas, there are few strong insights – except towards the end, and even those are already out there, in the “published literature”, so to speak.

Stephen Jay Gould's volumes of essays are similarly laden with mystery, a welter of odd details, and reader-friendly narratives. But in contrast to Rowling, each essay yields new insights that can, sooner or later, be applied in a much wider context. And although death brought closure to Gould as to all, the extant series provides years of thought-provoking enjoyment, and doesn't close off the story of evolution, science and knowledge.

“Punctuated equilibrium writes nature's primary signature” - SJG

The following example is yet another illustration of a popular misconception of evolution.
I started his essay 'Cordelia's dilemma' in Dinosaur In A Haystack (1996, Jonathan Cape). It was a tale of nothing, as was Cordelia's response to Lear... but there are lessons in nothing.

Gould begins with the publication bias of scientific research: that journals tend to publish papers with positive results, i.e. those with a story to tell. Studies yielding negative results (eg “we've found no correlation between these factors”) far more often suffer from a) languishing unpublished; b) languishing unsubmitted for publication.

After a few illustrations, Could moves to the concept that originally made his name: Punctuated Equilibrium, that is, most species exhibit little change over the course of their existence, and actual change is relatively rapid in geological time scales.

Most of the time: no change. This narrative had been largely overlooked by paleontologists as either not carrying any narrrative, or not exactly fitting in with evolutionary thought. Gould's own thesis supervisor spent a good deal of effort on statistical analysis of brachiopod evolution to no apparent avail, before switching disciplines.

The wider misconception is, again, anthropocentric. On a human scale, we see constant change throughout history – change is the constant, the mantra runs. When it's not revolutionary, it's said to be “evolutionary” - that is, gradual. But that's the mistake: evolution is not, on the wider scale, gradual and steady. It's rather closer to our concept of “revolution”. That is not to say instantaneous and all-encompassing at all – at least in our measure. Thousands of generations is not instantaneous to us, and yet again it is, to Earth's time scale. Apart from those flashes, the narrative flatlines for much, much longer.

In capitalist economics, fluctuation is the norm, and equilbrium a mere blink. In evolutionary history, it's the other way around.

Stephen Jay Gould, and random mutation

"Conceptual locks are far more powerful than factual lacks as barriers to scientific understanding" - S.J.G.

Stephen Jay Gould was a prominent evolutionary biologist, whose significant achievements included the concept of punctuated equilibrium (previously discussed here), and a welter of lucid writing that seeped into popular consciousness more than any other writer in his discipline since Darwin.

He died in 2002, but not before publishing a series of books based on over 25 years worth of essays for the magazine Natural History.

I'm currently journeying through his collection Eight Little Piggies (Jonathan Cape, 1993). His writing style is clear but erudite. The essays are interesting and easy to follow. But there is a trap that I believe is common to most discourse on evolution, both at a lay and a professional level: it is so very easy to misconstrue concepts. They are often subtle, writ on different scales to our own (in terms of both time and species). On the one hand, there are many fallacies built around the key phrases that sum up the popular conceptualisation of evolution, such as "survival of the fittest" and "natural selection". On the other hand, there are so many disputes between the professionals that consensus-building seems to take substantially longer than in harder physics disciplines such as cosmology or subatomic theory. This is because theory is necessarily built on small populations of fossils that each new discovery has potential to cause paradigm shift.

And interlaced throughout is the burden of anthropocentricism, the framework that lures people into thinking too much in the context of the here and now species.

And so Gould's essays are sometimes straightforward in their ramifications, but often require a re-read to catch the "correct" nuance and avoid the hidden missteps and solipsisms.

So I go carefully. And start with some clear concepts picked up from this book.

The first essay, Unenchanted Evening, follows the course of a species of snail (Gould's original academic focus) on the French Polynesian island Moorea. He traced the meticulous work of Henry Crampton last century, who made incredibly detailed studies of the Partula.

Gould illustrated how the body of measurement, description, and sampling was valuable not just as a comprehensive snapshot, but an excellent baseline for future study of changes in that species.
Unfortunately, it was driven to extinction. First, another species of snail was accidentally introduced that drove Partula to the brink, then a third species was intentionally introduced to control the second - but which instead clinched the fate of the Partula.

Biological control is fraught, absolutely. As any Queenslander ever plagued by cane toads will tell you. Introduced to control a sugar cane pest (which they never did), they are toxic and gradually spreading their way across the whole of Australia.


Yet there was a meaningful conceptual outcome of Compton's work. The island of Moorea is based on a volcano, and its topography is such that there are ridges and valleys all around the island. The Partula snail was partial to the valleys but not the ridges, so the population consisted of a series of sub-populations that were to a great extent isolated from each other. And each of those populations was physically different in form and colour. The question was whether those differences were due to unidentified differences in those niche environments, or random differences.

Crampton interpreted the differences as being due to three major causes: isolation, mutation, and natural selection. Isolation simply created the conditions for independent populations. Crampton saw natural selection as mainly negative, simply in terms of unhelpful mutations not surviving. And so the differences were due to random mutation.

"the role of the environment is to set the limits to the habitable areas or to bring about the elimination of individuals whose qualities are otherwise determined, that is, by congenital factors".

This has parallels with Darwin's Galapagos finches, with the difference here that there is no firm necessity for the sub-population differentiations.

Gould rated Crampton's labours and conclusions very highly.

World: Evolution is not steady

Many people think of evolution as a steady upward process. The phrase “survival of the fittest” is rooted in our collective consciousness, and we imagine a constant winnowing on that basis. Everything that has gone before and extinguished must, ipso facto, be inferior on the evolutionary scale.

Two – linked – concepts mitigate against this: cataclysm, and punctuated equilibrium.


Mark Maddison explained to me punctuated equilibrium, whereupon I promptly suggested punctuated evolution would be more accurate. Little did I know about the equilibrium part of the equation.

Developed by Niles Eldredge and Stephen Jay Gould, Punctuated Equilibrium postulates that evolution happens largely in discrete bursts, separated by long periods of relatively little change. This accords in general with geological records – which Darwin noted, but ascribed to the incompleteness of research.

It’s rather at odds with the popular understanding of evolution as a battle for superiority that constantly forces change. It suggests ecosystems (local or global) on the whole tend more towards stability than antagonistic competition. [however, I would note that it describes evolution as happening rapidly at points of punctuation, but is less vocal on the rate of change at equilibrium - for example, to distinguish between stasis and slow change.]

Punctuated equilibrium still strikes me as somewhat counterintuitive. But it's easy to appreciate the role of cataclysm in the course of evolution. It’s generally accepted – and fairly widely understood – that the era of the dinosaurs came to an end when a meteor hit Yucatan (Mexico). It was more or less 10 kms wide, and caused mass extinction of many species.

This is an example of survival – and evolution – being due to a very specific event that is not intrinsic to the terrestrial environment. In effect, there could well have been species on a superior evolutionary path, but which simply couldn’t survive a given cataclysm. Note that ‘superior evolutionary path’ does not equate to ‘more evolved’. All we can say is we are, of course, the most evolved of species to date: the simple proof is that only significant human artifacts remain in the geological record. But who’s to say those extinguished species wouldn’t otherwise have evolved further or faster than us in the absence of cataclysm?

Thus singular events have wiped out a number of evolutionary paths, and one could say that we’re here by circumstance – last one standing – rather than being the undisputed peak of all prior evolutionary paths.

Still, we can take comfort that no species has evolved on earth further than us.

These thoughts are encouraging: the earth has weathered catastrophe in the past (and despite what I envisioned when younger, we don’t even have the ability to blow the planet apart). So whatever we do, life on this planet is likely to continue until the sun is dying. Puts it all into perspective.

I expect that many people - not just the strongly religious - would find this hard to accept because it’s insufficiently anthropocentric.