Thursday, 17 December 2009

Facebook statuses.

I'm not sure why yet, but this is my favourite status that I have had so far:

......
is up to his knees in viscous mud as a ferric smell permeates the air, watching you stand there with a comforting cup of tea, a pack of biscuits and an alluring smile on your face which has not yet been finished by your eyes. Who are you?

Wednesday, 16 December 2009

The ever-quotable C.S. Lewis

Another oldie:

Although I have no statistics to back this claim, C.S. Lewis is probably the most quoted Christian apologist of the 20th century. He crops up in diverse discussions and many Christians have assimilated his arguments almost word for word into their apologetics repertoire. Dare I admit that I am not a fan?

In his favour I will say that he has a knack with words, perhaps one of the main reasons he is quoted. He also made, and continues to make, many Christians think about their faith seriously. I have even quoted him once or twice myself. His apologetics, however, are poor. Inevitably I disagree on some points with him, as this is to be expected, but his key arguments are poorly thought out yet widely known or used.

I first encountered Lewis' apologetics through Francis Collins' book "The Language of God". Collins returned repeatedly to Lewis' Moral Law argument, which is, in my humble opinion, a misuse of the arguments. This is yet another point used as 'proof' when it is really only useful, as many arguments are, of providing internal consistency within a world-view - in this case as another inevitable emergent property in line with God's plan. Sadly, though I recommend Collins' book to thoughtful Christians, he often conflates internal consistency with proof.

Since then I cam across Lewis' other arguments, including the easily refuted trilemma - the 'mad, bad or God' argument (did he want to give atheists an easy one?). And found his comments on Satan to be circular. I tried reading "Mere Christianity" and found it more of the same - eloquently phrased floccinaucinihilipilification (yes, I am unashamedly being pretentious). Perhaps I need to read Bishop Harries writings on Lewis, as I did enjoy an article by N.T. Wright on Lewis.

Ranting aside, I did find a quote where I thought old C.S. was spot on, perhaps more so than he realised as he was not a scientist:


Nature never taught me that there exists a God of glory and infinite majesty. I had to learn that in other ways. But nature gave the word glory a meaning for me. I still do not know where else I could have found one.

This could almost be a motto of theistic evolutionists, who, like myself, did not find God by admiring the complexities of creation. Instead, many of us understand the workings of the world and for me personally it is evolution which I am a student of. To find that God is behind all this, ordaining and working through natural laws, is glorious. Nature does not show us God unless we already accept Him, and this quote testifies to that.

I found the quote in the Green Bible, though with no mention of its origin.

Francis Collins - Posterboy of TE?

I wrote this last year for a laugh and thought it might have a home here. Certainly not a scholarly piece by any means, but worth writing (especially as problems with Word are preventing me from posting a piece on ammonites):

Whenever a prominent scientist with devout faith is needed to show that modern science (or specifically evolution) and Christianity are not at odds, Francis Collins is trotted out. It is something even I am guilty of and his credentials as a geneticist are the main reason, followed closely by his passion. Is he really a valid representative once we strip away his title of 'Head of the Human Genome Project'? (I wrote this before he took his recent position)

His book, "The Language of God" was the first I read on the topic of science and faith, one I still often recommend. My faith was fresh and science had become interesting again after several stagnant (teenage) years. I loved it. Going back to it now though and I feel I was a tad naive. It does have strengths though, which is why I recommend it.

His arguments for evolution are solid, perhaps the strongest point of the book. He efficiently provides evidence for it whilst dismissing the claims of creationists and ID. He also, in my mind, successfully shows that science and faith are not irreconcilable, and does so in an easy to read style.

My first issue came at a point where I found Open Theism very interesting and persuasive. The concept of God outside of time was not one I was prepared to declare (I still occasionally have issues with it) which renders many of Collins' points useless, as he puts a lot of emphasis on it. That said, it is the position of most Christians, so not a big issue.

A more important issue came when I looked into C. S. Lewis. Collins incessantly quotes Lewis like an amorous teenager talking about their crush. Lewis has some excellent quotes, but his theology is rather limited and often cannon-fodder for intellectual atheists. Collins never considers counter arguments, he simply repeats Lewis parrot fashion. The 'poster boy' of TE (or Biologos in Collins' terminology) needs to be a free-thinker, if Collins really is one then he doesn't always come across as such.

Another issue is his dependence on anthropic fine tuning. I found it enthralling when I first encountered it, however, I have come to realise that is is not evidence of God. Instead it provides internal consistency for a theist. Sometimes Collins appears to acknowledge this; other times he harps on about it. This may be a personal nit-pick, but it is one point where he gets repetitive (which is sadly a trend in TE).

Not uncommon to evangelicals, he has an obsession with atheists. He often takes the Alister McGrath route of talking about his atheistic past as thought it makes him an authority. Oddly, I (who have never been an atheist) feel he doesn't know much about atheism, especially when he labels them fundamentalists. It appears 'know thine enemy' was lost on him, he thinks he knows them better than they know themselves.

Another point of issue is not academic by any means. He is cheesy. He likes to whip out his guitar and sing his own songs. I'm not into happy clappy stuff like this, it makes me cringe. I would not be surprised if non-Christians simply vomited at this.

In his favour though, he has brought awareness to this position. He has also recently provided the Biologos website which is proving to be a useful resource for theistic evolutionists. It is like an anti-AiG, addressing many tough questions comprehensively. It also contains the work of multiple authors, so is not simply a regurgitation of his book (though it does appear to give only him the title 'Dr' when mentioned).

There are others who would be better suited. Kenneth Miller is often mentioned, his books are often recommended by atheists too. His first book, "Finding Darwin's God" covers more topics in greater details than "The Language of God" and most criticisms of it have sounded shrill, often erecting straw men. Miller has shown to have a better grasp, though perhaps he is lesser known. Other good choices are scientists who have become theologians, Alister McGrath is perhaps the best known, but John Polkinghorne is a favourite of mine and Dennis Lamoreaux may be an excellent choice (if a 'poster-boy' is even needed that is).

Maybe I will have to simply live with the fact that the most famous proponent of TE is Francis Collins. His scientific credentials are strong, he has brought attention to the position and has passion and drive. Hopefully critics will look beyond his easily criticised positions and at those who have better thought out their views. Like me for example.....

Ammonites and Scientific Writing

I recently had to write a short piece for my tutor on the use of ammonites in palaeontology. It was a slight departure from my normal style of writing, as he prefers things to be succinct and straight to the point.

Had I been allowed to write in my usual self-indulgent style, my essay may have started something like this:



Ammonites: More Than Just a Paperweight.

The iconic fossil ammonite, elegantly simple in outward morphology, provides lucid prose for palaeontologists perusing what lays written in the rocks. Their Mesozoic ubiquity, with a characteristic evolutionary pace (which appears geologically hasty, almost eager) renders them excellent index fossils. The gradual evolution their lithified remains display is the bread and butter of biostratigraphy, facilitating dating for even shy, phlegmatic geologists.

As it stands, that is not what I wrote, here is my essay:


The Applied Palaeontology of Ammonites

Introduction

The iconic ammonites are a group of cephalopods of Subclass Ammonoidea which are invaluable in their application in palaeontology. ‘Ammonites’ is the vernacular term (after Order Ammonitida) for the Mesozoic forms of Ammonoidea, a Subclass which spans approximately 325 Ma from the Devonian to the Cretaceous. The major use of ammonoids lies in biostratigraphy where they are regularly used for zoning the rocks in which they are found, particularly the Mesozoic forms which have allowed for zones to be erected equivalent to less than a million years.

Ammonoid Biostratigraphy

Good index fossils need to have a wide distribution with high abundance, a high rate of evolution and be easily identified; all of which are characteristics of the ammonoids. Shortly after their first appearance in the Devonian, the ammonoids rapidly spread world-wide (House, 1981) and maintained this distribution until their demise in the K/T extinction. They are ubiquitous, particularly in Mesozoic strata, rendering them a highly effective tool for stratigraphy in the field. Although some orders, such as Order Phylloceratida, display little evolution over millions of years (Clarkson, 1998), the vast majority of ammonites show the characteristic rapid morphological change and high speciation rate preferred in index fossils. The identification of an ammonite (excluding heteromorphic ammonoids) is relatively easy, hence their iconic status, and they can easily be used to quickly identify whether the rock is Palaeozoic or Mesozoic with little inspection by an amateur.

The ammonoids display many evolutionary trends and diverse morphological characters readily identifiable in single specimens which allow for their specificity in dating rocks. Ammonoids are commonly found preserved as internal moulds which display the sutures between septa and shell. Fossils with preserved suture lines demonstrate a clear stratigraphical trend from the relatively simple Devonian and Carboniferous sutures, to the extremely complex and flamboyant Mesozoic sutures. Changes in sutures can be used to quickly differentiate between the two eras; Palaeozoic ammonoids have generally zigzagged sutures, whereas Mesozoic ammonites possessed sutures with complex lobes and saddles. Although some ammonoids do not easily fit into this trend – some Permian ammonoids have similar sutures to Mesozoic ammonites – these deviations can be identified using other morphological characters, allowing suture morphology to be utilised for high stratigraphical accuracy when studied in detail and can also be used in the study of ontogeny.

A famous example of a useful lineage of ammonites in biostratigraphy is the Jurassic Family Cardioceratidae, which spanned 20 Ma and can be traced through 28 zones and 62 subzones. They have been described in monospecific assemblages, making them easily identifiable, and they rapidly diversified, allowing for many easily observed trends and accurate dating. These include easily identified changes in the compression of the whorl, in rib shape and in the ornamentation of the keel.

During the Mesozoic, the abundance and diversity of ammonites has even allowed for accurate stratigraphy during extinctions in conjunction with other techniques (Guex et al, 2004).

Other Uses

Aside from biostratigraphy, their global distribution and rapid diversification has allowed ammonites to be used in determining the position of continents during continental drift (Kennedy et al, 1975) along with facilitating the dating of these events.

Conclusion

Ammonites form a group with a basic common shell plan along with a propensity for fossilisation, exceptional diversity, rapid evolutionary change and wide distribution, making them easily recognisable and one of the most useful fossil groups for application in biostratigraphy to a high degree of resolution; they are an invaluable tool for any palaeontologist studying the Palaeozoic and Mesozoic.

References

Clarkson, E.N.K. (1998). Invertebrate Palaeontology and Evolution (4th ed.). Oxford: Blackwell Science.

Guex, J., Bartolini, A., Atudorei, V., & Taylor, D. (2004). High-resolution ammonite and carbon isotope stratigraphy across the Triassic-Jurassic boundary at New York Canyon (Nevada) [Electronic version]. Earth and Planetary Science Letters, 225(1-2), 29-41.

House, M.R. (1981). Early Ammonoids in Space and Time. In M.R. House, & J.R. Senior (Eds.), The Ammonoidea. The Evolution, Classification, Mode of Life, and Geological Usefulness of a Major Fossil Group (pp. 359-367). London: Systematics Association Special Volume No. 18, Academic Press.

Kennedy, W.J., & Cooper, M. (1975). Cretaceous ammonite distributions and the opening of the South Atlantic [Electronic version]. Journal of the Geological Society, 131(3), 283-288.

Punctuated Equilibria Explained (or PEE if you like...)



Note: there is something bizarre going on in the references which I can't seem to alter.


In 1972 a landmark paper was published in ‘Models in Paleobiology’ titled, “Punctuated Equilibria: an alternative to phyletic gradualism.” The paper, by Stephen Jay Gould and Niles Eldredge, was in many ways nothing new, yet at the same time purported to challenge many long cherished ideas in evolutionary biology. Over the years it has simultaneously been embraced and reviled by scientists, and consistently distorted by creationists.


In many ways Eldredge and Gould had simply connected the dots between different lines of evidence and come to conclusions. They took common knowledge from biostratigraphy and combined it with known models of speciation used by neontologists (those that study living organisms). Here they saw that species appeared in a geologically abrupt time and persisted unchanged for most of their duration. At the time biology and palaeontology were only beginning to overlap, so Eldredge and Gould were the first to realise that the pattern they perceived in the fossil record was exactly what should be expected if Ernst Mayr’s peripatric speciation model were applied to the fossil record.


During peripatric speciation a small group becomes peripherally isolated from the main population. Gene flow between the two populations stops, allowing the two to accumulate separate mutations. Smaller populations can evolve more rapidly, and as they are small they are unlikely to yield fossils. When the isolated group is reintroduced to he larger population, if sufficient time has passed they will no longer be able to interbreed – they have become a new species. Over geologic time this appears sudden.


So why the fuss if these were well established views? Creationist distortions aside, Gould and Eldredge were interested in some of the implications of the theory. They changed ideas of tempo and mode in evolution; they challenged the way we think of natural selection; they raised the possibility of unknown mechanisms; and often claimed to separate micro- and macro-evolution. These were strong boasts which led to years of feuding and bickering among scientists.


The punctuational aspect of ‘punk eek’ (or evolution by jerks as some used to call it) has received the most attention from detractors. It was also one of the main focuses (at first) of Gould and Eldredge, as they loudly proclaimed that Darwinian orthodoxy had been challenged. The first to protest often misunderstood. Many biologists interpreted rapid to mean saltation, where a new species is born instantly from an old one. Creationists also made this mistake and believed they had new evidence of instantaneous creation. Both were mistaken; rapid on a geological timescale means at least tens of thousands of years.


Many ‘phyletic gradualists’ rightly pointed out that a straw man of gradualism had been erected and defeated. No gradualist believes that evolution occurs at a strict pace (Dawkins 1986). Even Darwin had made comments that sound a lot like punctuated equilibria; discussing his tree diagram he said, “But I must here remark that I did not suppose that the process ever goes on so regularly as is represented in the diagram, though in itself made somewhat irregular, nor that it goes on continuously; it is far more probable that each form remains for long periods unaltered, and then again undergoes modification.”


Many biologists tried to ignore punctuated equilibria, focussing on the tempo aspects and dismissing them. An analogy using gears is apt, as evolution can change gears, even becoming so slow as to allow stasis (evolutionary biologists have words like bradytely, horotely and tachytely to describe pace). Is this dismissal valid? Not completely, but to dismiss only the attacks on gradualism evidence is needed. Gould himself (1993) acknowledged that it is a ‘complement to phyletic gradualism’ as gradualism has been documented in groups from microfossils (Macleod 1991) to mammals (Gingerich 1976, Chaline & Laurin 1986).


One of the best examples of punctuations as gradualistic was found by Stephen Jay Gould (1996). He was fortunate to find numerous shells of the Bahamian land snail Cerion, in a single mudflat, the equivalent to a single bedding plane in strata. Using geochemical methods he was able to date the shells; when put in order they showed a gradual, microevolutionary trend spanning 20,000 years.


The other main aspect of punk eek is stasis, the equilibrium aspect of the model. The authors had developed a little motto, “stasis is data” to remind themselves of the importance of this observation. One of Gould’s harshest critics, Jeffrey S. Levinton, agreed with this observation, stating, “This is…the issue of stasis, which I believe to be the legitimate problem spawned by the punctuated equilibrium model.” (1988).


Stasis had previously been dismissed as a lack of data, a situation which has changed a lot since 1972. Stasis is not a lack of evolution; it is a ‘wobble’ or fluctuation around means, with no substantial change (no broader than the range of geographic variation in modern species) and no directional evolution.


There are some issues with empirical verification of stasis, though it is widely acknowledged as occurring. Fossil species are morphospecies, that is they are identified by morphology and only that which fossilises. Substantial phenotypic change can occur without being detectable in the fossil record. Similarly, neontologists often discover new species through genetic testing; practically impossible with fossils. Conversely, intraspecific variation, functional polymorphisms and ontogenic variation may all be wrongly identified as separate species. Despite these possibilities, comparisons suggest that it is not too big an issue for interpreting stasis (Jackson and Cheetham 1994) as the bias is against punk eek.


Some biologists tried to explain stasis away using stabilising selection in unchanging environments. Stabilising selection removes the extremes of a population, keeping it centred around the mean. However, this could not explain stasis through climatic change (Cronin 1985, Prothero and Heaton 1996, Prothero 1999). Many possible explanations for stasis including a homeostatic mechanism resisting selection (a controversial view of Gould’s which fit with some of his other views), habitat tracking (Eldredge), constraints (Lieberman), normalising clade selection (G. L. Williams) and turnover pulses (Vrba) have all been suggested.


Gould and Eldredge originally tried claiming that all change was focussed around speciation events, a position they later changed. Douglas Futuyma (1987) gave strong insight into what may be occurring, “In the absence of isolation, differentiation is broken down by recombination. Given reproductive isolation, however, a species can retain its distinctive complex of characters as its spatial distribution changes along with that of its habitat or niche… Although speciation does not accelerate evolution within populations, it provides morphological changes with enough permanence to be registered in the fossil record. Thus, it is plausible to expect many evolutionary changes in the fossil record to be associated with speciation.”


Palaeontologists in recent years acknowledge punctuated equilibrium as a valid model of long term occurrences, one among many including phyletic gradualism and punctuated anagenesis (Jackson and Cheetham 1999). The main ‘controversial aspects focussed on are the potential decoupling of macro and microevolution; changes in understanding of levels of selection; and the prevalence of selection.


From Futuyma’s insight it is hard to see how punctuated equilibrium could potentially split micro and macro evolution, though this was a genuine early problem. It all depends on whether speciation is caused by more than simple isolation. Punctuated equilbirum presents the possibility of species selection and species sorting, and as most change is ‘tied up’ during speciation, this form of selection gains more prominence, therefore meaning that micro changes cannot be easily extrapolated as such selection would be ignored. Modern focus on speciation is on whether natural selection or genetic drift is more dominant (recent research though is favouring natural selection) therefore raising the possibility that natural selection is not responsible for all diversity (a less common view favoured by Gould).


Gould’s statement in 1993 is still a worthy interpretation, saying, “[Punctuated equilibria’s] most important implications remain the recognition of stasis as a meaningful and predominant pattern within the history of species, and in the recasting of macroevolution as the differential success of certain species (and their descendants) within clades.”


I have hopefully presented a brief and accessible explanation of punctuated equilibria, whilst clearing up any misconceptions. ‘Punk eek’ (or ‘eck’ to some) has changed a lot in the past 3 decades, yet still manages to provoke interesting debate (which is sadly misunderstood by the lay public). Gould believed it to be a “useful extension of evolutionary theory” which can clearly be seen once understood.


References


Benton, M.J. & Pearson, P.N. (2001). Speciation in the fossil record. Trends in Ecology & Evolution. 16, 405-411.

Chaline, J. & Laurin, B. (1986) Phyletic gradualism in a European Plio-Pleistocene Mimomys lineade (Arvicolidae, Rodentia). Paleobiology. 12(2), 203-216.

Chaline, J., Laurin, B., Brunet-Lecomte, P. & Viriot, L. (1993) Morphological trends and rates of evolution in arvicolids (arvicolidae, rodentia): Towards a punctuated equilibria/disequilibria model. Quaternary International. 19, 27-39.

Cheetham, A.H. (2001) Evolutionary stasis vs. change. In: Briggs D.E.G. & Crowther, P.R. (eds) Palaeobiology II. pp. 137-142. Blackwell Publishing, Oxford.

Cronin, T.M. (1985) Speciation and stasis in marine ostracoda: climatic modulation of evolution. Science. 227, 60-63.


Darwin, C. R. (1872) The origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. (6th ed.) John Murray, London.


Dawkins, R. (1986) The blind watchmaker. Norton, New York.


Futuyma, D.J. (1987). On the role of species in anagenesis. The American Naturalist. 130, 465-473.

Gingerich, P.D. (1976) Paleontology and phylogeny; patterns of evolution at the species level in early Tertiary mammals. American Journal of Science. 276, 1-28.

Goodfriend, G.A. & Gould, S.J. (1996). Paleontology and chronology of two evolutionary transitions by hybridization in the Bahamian land snail Cerion. Science. 274, 1894-1897.

Gould, S.J. and Eldredge, N. (1972) Punctuated equilibria: an alternative to phyletic gradualism. In: T.J.M. Schopf, ed. Models in paleobiology. pp. 82-115. Freeman, Cooper and Co., San Francisco.

Gould, S.J. and Eldredge, N. (1993) Punctuated equilibrium comes of age. Nature 366, 223-227.

Jackson, J.B.C. & Cheetham, A.H. (1999) Tempo and mode of speciation in the sea. Trends in Ecology and Evolution. 14, 72-77.

Kellog, D.E. & Hays, J.D. (1975). Microevolutionary patterns in late Cenozoic radiolaria. Paleobiology. 1, 150-160.

Lazarus, D. (1983). Speciation in pelagic protista and its study in the planktonic microfossil record: a review. Paleobiology. 9(4), 327-340.

Lazarus, D.B. (2001) Speciation and morphological change. In: Briggs D.E.G. & Crowther, P.R. (eds) Palaeobiology II. pp. 133-137. Blackwell Publishing, Oxford.

Levinton, J. (1988). Genetics, paleontology, and macroevolution. Cambridge University Press, Cambridge.

Macleod, N. (1991) Punctuated anagenesis and the importance of stratigraphy to paleobiology. Paleobiology. 17(2), 167-188.

Malmgren, B.A. & Kennett, J.P. (1981) Phyletic gradualism in a late Cenozoic planktonic foraminiferal lineage; DSDP Site 284, southwest Pacific. Paleobiology. 7, 230-240.

Mayr, E. (1963). Animal species and evolution. Harvard Univ. Press, Cambridge, MA.


Prothero, D.R. & Heaton, T.H. (1996). Faunal stability during the Early Oligocene climatic crash. Palaeogeography, Paleoclimatology, Palaeoecology. 127, 257-283.


Prothero, D.R. (1999). Does climatic change drive mammalian evolution? GSA Today. 9, 1-7.

Sheldon, P.R. (1987). Parallel gradualistic evolution of Ordovician trilobites. Nature. 330, 561-563.

Wei, K. & Kennett, J.P. (1988). Phyletic gradualism and punctuated equilibrium in the late Neogene planktonic foraminiferal clade Globoconella. Paleobiology. 14, 345-363.

Update

Whilst at uni I don't have the time to post anything, though now I am home for Christmas there may be an influx of posts. I have some stuff planned, mostly science, so the religious stuff will take a back seat. I may also post some stuff I wrote last year as filler. It may take time though, as it is all hand written and typing is tedious.

Enjoy.