Perception of deep time by geologists and biologists

Following the Darwin Year a colloquium lecture by zoologist Prof. Wolfgang Maier from Tübingen dedicated to "Darwin and deep time" discussed Charles Darwin’s role as a geologist who (among others) introduced the concept of deep time (a term later coined for million to several billion year long time ranges in geology) to biology.

Darwin did this by translating a hierarchy of (anatomical) similarity into a tree scheme that linked organisms from successive time slices with thousands of generations separating each two slices (see the scheme from Darwin’s "Origin of Species": [link]). The time slices can be related to certain units of the geological time scale.

Deep time correspondents in stratigraphy …

The problem of imagining time ranges far outside the scale of human experience has been approached by geologists with the method and concepts of stratigraphy: Strata of rock can be interpreted as a succession of time slices. Relative ages and age differences often manifest in an amount of rock which is loosely corresponding to certain a time span if similar rockforming processes are underlying. The relationship between the duration of a process and the amount of materal it creates can be inferred from direct observation of recent systems, allowing the assignment of absolute time (in years or millions of years) to a succession of strata. Given that long-term geological processes are rarely gradual, a more reliable absolute age is provided by radiometric dating.

If you would ask a geologist how he/ she percieves deep time I suppose he/ she would explain that it becomes clear from the slowness of present-day geological processes on the one hand and from the vast amount of products of such processes on the other hand.

… and phylogenetics

The evolution of organisms yields another approximation of deep time: The passing of time manifests in the hierarchical distinctness of living systems. Seeing how slow evolution works in a human being’s life span and how much change in anatomy/ biochemistry etc. must have occurred since last common ancestor of mouse and elephant or of mouse and lemon tree, leads to another way of percieving long time spans.

Regarding a certain distinctness and species richness of a group as a product of a certain number of character changes and speciation events (which is more or less well correlated with time) was probably enhanced by the more quantitative look at phylogenetics since the introduction of cladistics and molecular methods.

When I was attending a workshop on molecular paleobiology in 2008 specialists of that field were using the expression “(addressing) deep time problems” synonymous to phylogenetics of higher systematic groups, i.e. as the study of evolutionary changes that occurred deep down in the tree of animals and other organisms – opposed to let’s say the comparative analysis of human and neanderthal genomes or the radiation of Darwin finches.

The viewpoints of paleontologists…

But how do (present-day) paleontologists percieve deep time? You would expect them to share the view of both, phylogeneticists and stratigraphers, as most of them are taught at least a bit about both fields. However, for a paleontological fieldworker who employs the study of fossils as a means to understand and describe geological processes and paleoenvironmental contexts the flow of time is much easier grasped as a series of events preserved in a succession of rocks (and not as a phylogenetic tree scheme).

On the other hand, as a consequence of the so-called paleobiological revolution, you don’t need to be a field worker to contribute to the understanding of ancient organisms. In fact many aspects of paleobiology require mere laboratory and magazine work and you can spend a lifetime on that without ever considering rocks – naturally the perspective of such a modern paleobiologist on deep time will be strictly that of a phylogeneticist.

…can lead to conflicts?

These different perceptions on deep time and evolution are probably the background why cladistics was (and still is) met with some scepticism by “old school paleontologists” (or by “Eastern Europe school paleontologists”): Instead of considering all kinds of data for phylogenetic hypothesis-making I am supposed to use merely data from the (anatomical, molecular, etc.) comparison of organisms, as if evolution does not manifest in other ways in the geological record.

One could argue that it is possible to integrate other data, i.e. stratigraphic ages and palaeobiogeographical relations, in a cladistic analysis or at least in the discussion of its results, and so assure that hypotheses from the tree perspective on evolution are tested under consideration of independent data.

The idea to use time directly as a character in a parsimony analysis with consecutive time slices as character states may be epistemically unsound, as it is problematic to justify any kind of model assumption how time is weighted with respect to anatomical characters (and implicitly would this mean a post-hoc failure if proximity in time is regarded as indicative for degree of relationship?).

An a posteriori fit to other data – e.g. looking which of the equally parsimonious morphology-only-based time-calibrated trees has shorter lineages of no record (ghost lineages) – might be a better approach, but is still hard to swallow for some people who have problems with parsimony analyses on the basis of (too) small character samples (i.e. with inherent biases due to sample size/ character poorness or ambivalence of fossils).

Lineage concept vs cladistics in continental biostratigraphy

The white hair of my chief Ph.D. supervisor is to some degree explained by his livelong efforts to get a grip on Carboniferous to Permian continental biostratigraphy - trying out different groups such as cockcroaches, conchostracans, freshwater sharks, and amphibians.

One of the underlying concepts which I suppose I will always find hard to believe is the idea of searching for and finding so-called lineages, i.e. series of species occurring subsequently in the stratigraphic record which show stepwisely distinct anatomies because each species has descended from the respective next-oldest species.

Of course every species has an ancestor and many have descendants but how can I define them from the fossil record? Is there not the typical problem of epistemic vagueness of the ancestor in any kind of phylogeny (e.g. discussed by Wolf-Ernst Reif in some of his many theoretical papers on cladistics in paleontology)?

Searching for lineages leads to a fallacy?

The idea that whithin a continental sedimentary succession a certain species occurring deeper than a related species should be regarded as the ancestor of the latter - unless disproven - always reminded of a type of logical fallacy called post hoc ergo procter hoc: "B occurred later than A, therefore A must be the reason for B." In terms of imposing the lineage concept: "Species B occurred subsequent to species A, therefore A must be the ancestor of B."

If a multiple- and irregularly branched bush is a good analogon to how evolution works I daresay the idea of a biostratigrapher to pick up the isolated fragements of branches (i.e. fossils) and glue them together in a few long continuous branches results in a bad model of the bush.

The problems occur after I have established a biostratigraphic zonation concept on the basis of what I think is a lineage: Someone working on the same material puts the species of my 'lineage' into a cladistic analysis and finds that there is almost no concordance between the appearance date of a species and its likely phylogenetic position.

If I do agree that similarities/ dissimilarities in morphology, histology, behavior, etc. should form the basis of a classification and consider the data basis of the phylogenetic analysis as sufficient I will have to admit that my scheme has been proven wrong. Or else if I suppose that the data are not sufficient and I myself cannot add more then I will have to concede that my scheme is at least no more valid than the alternative.

Proving microevolution depends on the sufficiency of "population" samples?

Im not saying that it is impossible to find arguments in favor of an ancestor-descendant relationship: Imagine I have large enough sample of specimens of the supposedly related species A, B, and C from three successive horizons. For A, B, C the empiric distributions of morphological parameters can be compared:
If the mean value & variance for A is not signficantly distinct from the mean and variance of B and
if the mean value & variance for B is not signficantly distinct from the mean and variance of C
but given a significant difference in the mean values/ variances of A and C,
I could infer that from A to C microevolution took place...
...but do we have such samples, let's say for tetrapods?

An example: Amphibian Biostratigraphy

These problems have been discussed for the amphibian biostratigraphy of the European Permocarboniferous as developed by Werneburg and Schneider and applied for various amphibian occurrences, see for example:

R. Werneburg & J.W. Schneider, 2006, Amphibian biostratigraphy of the European Permo-Carboniferous. In: S.G. Lucas, G. Cassinis and J.W. Schneider, Editors, Non-Marine Permian Biostratigraphy and Biochronology: Geological Society of London, Special Publications 265 (2006), pp. 201–215. [Link]

R. Werneburg, A. Ronchi, and J.W. Schneider, 2007, The Early Permian Branchiosaurids (Amphibia) of Sardinia (Italy): Systematic Palaeontology, Palaeoecology, Biostratigraphy and Palaeobiogeographic Problems. Palaeogeography, Palaeoclimatology, Palaeoecology, Volume 252, Issues 3-4, 3 September 2007, Pages 383-404 [Link]

The zonation scheme and proposed lineages have been criticized by Steyer (2004) as being a stratophenetic rather than a true phylogenetic approach considering the criteria how the authors relate different species:

J. S. Steyer, 2004, Phylogenetic or stratophenetic systematics? - Comment of R. Werneburg: The branchiosaurid amphibians from the Lower Permian of Buxières-les-Mines, Bourbon l’Archambault Basin (Allier, France) and their biostratigraphic significance. Bull. Soc. géol. France, 2004, 175 (4), 423-425
[Link]

Another particular problem is that amphibians are known to be abundantly subject to heterochronous evolution - evolutionary shifts in the ontogenesis, in particular, neoteny, is a common phenomen and can obscure characteristic features.

A recent analysis by Schoch & Milner (2008) on branchiosaurids, a group of neotenic small dissorophoid temnospondylians which is often considered for biostratigraphy, features a cladistic approach and proposes a scenario, related to which nodes of the tree neoteny/ life style changes occurred:

R.R. Schoch & A.R. Milner, 2008, The intrarelationships and evolutionary history of the temnospondyl family Branchiosauridae. Journal of Systematic Palaeontology (2008), 6 : 409-431 [link]

While the relationship of Branchiosaurus forming the outgroup of major clades (Melanerpeton-clade, Apateon-clade) is correspondent to the order of occurrences in the stratigraphic record, certain long ghost lineages occur - in particular the interpretation of Apateon gracilis/Melanerpeton gracile shows a mismatch between the cladistic approach of Schoch & Milner and the scheme of Werneburg & Schneider. This divergence is also the consequence of conflicting interpretations of the gracil(e/is) material, however, it demonstrates the potential for stratigraphic misinterpretation:

If I believe that a species forms the end member of a lineage because it is the youngest in certain sedimentary sequences I may underestimate the species' stratigraphic range - unlike the cladistic analysis which (if well-founded) would imply a deep divergence suggesting that some of the earlier record of the species is missing.

Decoupling (continental) biostratigraphic zonation from the lineage concept

Assuming that evolution works rather bush-like than lineage-like, I dont' see why we can't keep a biostratigraphic zonation even in the case of sparse continental records. I still can associate a series of morphologically defined taxa with a certain stratigraphic range and spatial distribution - until the concept has been shown not to be adequate (or not outside a more narrowly defined spatiotemporal window).

Whether it is a lineage-like relationship of species or another factor (related to geography, climate, ecology or else) that makes biostratigraphy work is a question which might be solved only in some cases.

Constructivist geoscience (II)

As a natural scientist you are disposed to believe that there is something on the outside of your consciousness, and also, that you as a human being have suitable means to investigate those things.

And there is the theory of critical rationalism and the praxis of how geoscience (and palaeobiology) is really done.

So what about the chronic underdeterminedness of geoscientific (and paleobiological?) models: Is the remaining uncertainty large enough to consider much of the geoscientific knowledge as mere constructs which are (forseeably) bad descriptions of real things?

The following list of sources of uncertainty and of other problematic points is without order, representing a collection of thoughts I had during one of those late night train journeys:

(1) Uncertainty from the misunderstanding of recently active complex processes (e.g. sediment transport by a river) used as model systems for ancient processes.

(2) Uncertainty from a lack of knowledge about the longterm consequences of currently active processes.

(3) Anactualistic processes (e.g. on Hadean earth; recovery after a meteorite impact).

(4) Selectivity of geological records and the variety of factors by which it can be governed.

(5) Equivocality of deeper earth investigation methods (geophysics, "1D" outcrops from drillings).

(6) Problems arguably associated with the "descriptive tradition of geoscience", which passes along varying ideas about the necessary exactness. There can be a certain disregard for matters of decision making, the question of how to choose a favourite hypothesis, the distinction between noise and information relevant for a problem.

(7) Plurality of fieldwork procedures [and other aspects of methodology], i.e. documentation methods in the field and the decision makings/ usuals paths of inference involved. Enhanced by national/ language boundaries - there can be different schools, sometimes failing to communicate.

(8) Choice of model systems: Due to the complexity of the matter we are choosing well understood model systems, but the comparability is overestimated in the specific case.

(9) Overuse of a canon of "inherited" procedures, which lead to systematic misunderstandings or put constraints on thinking (e.g. the drawing of sedimentary logs).

(10) Metamodels and metatheories (e.g. global palaeoclimate models, supertrees) may be particular problematic in geology/palaeontology as historical sciences. There may be so various data and multiple steps of inferences that circularities are hard to avoid and/or the question is, of how much value the insight from the model is.

(11) Bad integration of data in multidisciplinary approaches, if the model assumptions on which the integration is based are not well considered.

(12) Overinterpretation as a notorious phenomenon in geoscience, coming from the chronic paucity of data, the community's failure of encouraging modest/ honest claims.

(13) Unsystematic or right-out defective handling of temporarily or principially not-available data. (Hypothesis hinges to a considerable degree on the missing data - though you as the inventor are saying the solution of the problem is only a matter of effort.)

(14) As in other sciences: the dealing with falsifying data. As your object is so complex, you as geoscientist may always find an exception demonstrating that you are not (so) wrong.

(15) Underuse of quantitative approaches, another relic from earlier times of geosciencemaking.

(16) Changing accessibility of important outcrop areas (but also archives) limits falsifiability of hypotheses.

(17) Misinterpretations from reducing/ enlarging the dimensionality of a problem in an inference step (e.g. reconstructing a time series of 3D models from a number of 1D sedimentary logs). Not always considered: There is not necessarily a proportionality between the time span of a process and the volume of "waste" it creates or deletes.

(18) Downscaling, if done without reflection/ definition of the way of doing, can reduce the reproducability/ comparability.

(19) Thinking in cyclicities and the tendency to infer cyclic processes although their support is poor.

(20) Misconception about what the data are and where the interpretation begins. One might think this is only a beginner's mistake in geoscience - however, it may happen as well on a higher level if you have multiple stages of inference.

(21) Thinking in categories as though they represent something natural which is not defined by the observer (e.g. genus, family in biological systematics; stage, era in chronstratigraphy).

So, look critically at your own models in geoscience (and paleobiology). Are they well constructed?

Constructivist geoscience and what we can learn from the financial crisis

The analyses are done. Because you are supposed to do an 'integrated approach' you are working on 'integrating' your data and doing an interpretation that fits in with everything.

After a short or long search for patterns (as a geologist you are at least talented in pattern-spotting), you will find that no easy existing model fits with all data (or worse: every existing model fits with all data) which gives you the chance to chose the model you like best and alter it a bit. You are using an auxilliary hypothesis which explaines why this model, which is adequate in general, is not working properly for the data you are involving.

The best ist to raise a whole set of model assumptions which are not easy to be proven or disproven. Imagine it as a daughter company, to which you can export your credit risks in order to keep the bilance of your adapted existing model clean.

If there are some new data that appear to falsify your model you are employing your daughter company of auxilliary theses to explain why they are not at all problematic.

Given your business concept is good you even manage to invert contradicting data - under the light of your additional theses they actually support your model.

As you can handle it flexibly, you can of course add to or remove from the stock of your daughter company at free will. A good idea is to pay attention to fashions (if 'Milankovich cycles' or 'metamorphic core complexes' or 'climate change' are en vogue you may think about including them).

Successful model constructors manage to give their constructs the appearance of inner coherence (e.g. by means of categories, definitions and a quantitative bluff package) and sell them to others who 'succesfully' convert them to new areas and problems.

And then everything collapses - some new conflicting data pushes your model to the point of absurdity. Usually the new data fit in with a much more parsimonious alternative model. And no one will understand how you could have been so stupid to overlook that possibility in the first place...