Wednesday, 30 June 2010

Xenomorph Mystery

This is my 100th post of this year, showing just how little I posted last year and how much I have posted during this one. Today I watched the film Aliens after watching Alien last week and something struck me as odd. Why have the Xenomorph aliens travelled without viable hosts? The aliens (binomial names are Internecivus raptus and Linguafoeda acheronsis  which mean "murderous thief" and "foul tongue from Acheron" respectively) have a multi stage life cycle. They begin as eggs laid by the queen (they are eusocial) and from these hatch a parasitic stage known as a "facehugger" which attaches itself to the host and impregnates them with embryos. These embryos gestate within the host, absorbing some of its DNA. Due to this process, the Xenomorphs vary dependent on their hosts. Within the films there are mostly human based aliens, though dog Xenomorphs are seen and there is a Predator version too.

From the embryos form what is known as a "chestburster" as it kills the host by leaving its body violently through the chest. Within hours it moults and grows into the adult form.

As they require a host for the facehugger, why did the ship seen in the first two films not contain any viable hosts? There were thousands of eggs, so did they simply lay dormant waiting for any hapless victims? It would be such an odd strategy when a few hosts taken with them would have been useful. Obviously in order to evolve they must have had viable hosts on their home planet.

This perplexed me and has me wondering about their evolution as well. It can be quite interesting trying to work out how science fiction creatures evolved, especially as they were not often designed with evolutionary plausibility in mind. Perhaps that is something I can put my mind to in future. I already have in mind to write a hypothesis about the evolution of the creatures in Tremors, which has been done already but I might do a competing hypothesis based on the same data, just for a laugh.

Whilst looking for images for this post I found some interesting pictures. Click here to see a CG image which is not safe for work and is strong evidence of the truth of "Rule 34". Below is an awesome chess set I found:

Sex Drove Evolution of Pterosaur Crests

Palaeontologists have demonstrated that sex drove the evolution of the elaborate crests of pterosaurs along with features on other tetrapods such as the sails on the back of Dimetrodon. Previous thought had been varied, with hypotheses including temperature regulation and steering in flight (for pterosaurs). The features were too exaggerated to have been used in temperature regulation. There is one thing which can cause the evolution of features which would normally be detrimental and that is sex. Elaborate displays can be used to show superiority over other males, to battle other males, or to attract the attention of the female. See the BBC News article here for more and see if you notice my tutor's name.

I may soon have some images from the pterosaur display in London, provided I steal them from a friend.

Sunday, 27 June 2010

Parvancorina - the critter of today and many other days.

This organism is rapidly becoming a favourite of mine, so perhaps it is time for Microdictyon to move over. I inadvertently stumbled across Parvancorina whilst researching purported soft-bodied Ediacaran trilobites and ended up writing a fair bit about that instead, see here. It is surprising that little is said about Parvancorina outside of specialist literature, for example the Wikipedia page says very little at all and McMenamin's book The Garden of Ediacara has it on only a couple of pages. In comparison, Spriggina is very well known and almost always mentioned when potential arthropod/trilobite ancestors are brought up, despite the difficulties with such a classification. Parvancorina  remains a better bet, despite its own difficulties, yet it is little known.

Parvancorina is from the Ediacaran period and is one of the many problematic species from that time. It is shield shaped and has ridges which can be quite large in unflattened fossils. Some impressions suggest that it had 10 pairs of legs, perhaps optimistically seen as biramous by some.

Like many other Ediacaran forms, Parvancorina has been known to dominate entire beds and is found to have faced into oncoming currents. This behaviour may have implications on the possibility of it being an ancestral trilobite, as trilobite larvae in the "protaspid" stage are planktonic as can be seen in the image below.

The support for Parvancorina being a potential ancestor to arthropods, particularly trilobites, comes from its resemblance to the protaspid stage of many trilobites. The protaspid stage is the earliest stage in development where the trilobite has a calcareous shell and is not segmented. For more on trilobite ontogeny see here. Primicaris  was originally thought to be a larval naraoid trilobite before becoming its own taxon, which is a potential link between Parvancorina and the trilobites. 

If the link to the trilobites is true, then the central ridge and lobes may be analogous to the gut system of trilobites. The picture on the right shows the protaspid stage of a trilobite (a) though it should be noted that there are a wide range of protaspid morphologies amongst the trilobites. For examples, see here and here (image compares Parvancorina on the left, Primicaris in the centre, and a protaspis on the right).

The link to trilobites may never be fully established. Based on morphology alone the connection to the trilobite protaspid stage is quite convincing, however, behavioural evidence (facing the current) and the way they develop must not be ignored. Either way, this is a fascinating critter which does not get enough attention. Below is an image of Parvancorina with Vendia. 

Saturday, 26 June 2010

Stop the Movement of Invaluable North Sea Cores

I've not seen much on this news, yet it is very important especially to geologists. BGS plan on moving thousands of core samples, valued at around £5billion, from Edinburgh to Nottingham. The collection has been gathered over the last 40 years and contains 175,000 boxes of core rock up to 400 million years old. The move is completely unnecessary and risks ruining fragile samples, reducing them to useless sand.

The cores have many uses, being most commonly used by the oil industry in deciding where to drill. They also help scientists work out how to store carbon dioxide. Students in petroleum exploration need access to the cores, with the best courses being offered in Edinburgh.

For a recent article on this see here. If you can, join the Facebook petition group.

Return of the Soft-Bodied Ediacaran Trilobite!

I previously wrote about a mention of a soft-bodied Ediacaran trilobite in a couple of textbooks which perplexed me, see here. Whenever I come across this organism being mentioned somewhere it is likely that I am going to mention it here and will repeat the information I found about it. In this case I was reading The Garden of Ediacara by Mark McMenamin and found "Soft-Bodied Trilobite" discussed on pages 35 and 36. This unnamed organism was found in the early '90s by Jenkins and Gehling and looks to be one of those forms which will always be controversial in interpretation. There are about 7 specimens of about 9mm in length.

It does indeed resemble a trilobite as it has an apparent cephalon (the head) which appears to have eye ridges and a glabella between them. The body is a broad thorax with 21 segments and the initial report mentioned a pygidium (the tail bit). There are also many differences. The individual segments get larger away from the midline and reportedly have faint, regularly spaced lines perpendicular to the width, a trait which is typical for Ediacaran organisms which are seen as quilted in structure. 

No legs are preserved on this soft-bodied fossil, so it resembles a discarded trilobite shell, however, it cannot simply be a shell as there is no evidence that it was shed. It is even mentioned by McMenamin that it resembles a trilobite trying to expand its surface area to increase absorption, perhaps even for light.  It may be (especially under the Vendobiont view of Seilacher) a shortened frond fossil, perhaps juvenile, however, the purported cephalon is an issue for this view. If it were a Vendobiont (also referred to as Vendozoa) then it could potentially still be a head, but with the implication that these non-animals also achieved cephalisation independently of animals. They converged upon the concentration of sense organs at the anterior end. 

"Soft trilobite" is one of those fascinating mystery fossils which gets thrown about from one kingdom to another, seemingly resembling members of each and at the same time nothing is like it. If it is an animal then it is very weird and mysterious, with potential arthropod affinities; if it is a Vendobiont, then it seems they were converging on heads and concentrated sense organs. Then again, it could be something completely different. 

Thursday, 24 June 2010

Critter of the......evening. Liebea.

This is Liebea, a Permian bivalve mollusc similar to modern mussels. They were epibyssate suspension feeders, meaning that they anchored themselves to rock or seaweed and filtered food particles out of the water. Liebea  commonly formed clumps containing only that species.

The fossil above is Liebea squamosa  and is one of the bivalves I found in the Ashfield Brick-clay Pit in Conisbrough. Like the brachiopods found there, the Liebea  fossils appear to be quite small (about half the size they should be) but not to the same extent as the brachiopods. This could be interpreted as having a high infant mortality rate (due to overcrowding or a soft substrate) or small adult size due to overcrowding.

Wednesday, 23 June 2010

Is Evolutionist a Valid Term?

Among people who discuss and debate evolution but do not study it for a living, evolutionist is often seen as a term created by creationists in order to make it sound like both views are on equal footing. It is often stated that scientists do not use the term and so it is not valid. All one needs to do to show that this view is false is to present an example of a reputable evolutionary biologist using the term, for example:

Few evolutionists would deny this hierarchy in a descriptive sense, but traditions of the modern synthesis specify that causality be sought only at the level of organisms - for natural selection operates by sorting organisms within populations. 

The above quote is taken from Stephen Jay Gould's The Structure of Evolutionary Theory, a scientific text devoted to evolution. However, Gould's use of the term is vague and I have managed to identify many different meanings of it.

1) A secular "religion". Not only is the term used by creationists to create the illusion of an equal-footing, but also to create the idea that it is a religion. This furthers the same illusion and allows further, often irrelevant criticisms being advanced.

2) The nineteenth century usage. During the 19th century the term referred to people who believed that evolution had an inherent drive towards a sort of Platonic form. This view is not held today.

3) Evolution accepters. Perhaps the most common usage, this refers to anyone who accepts evolution. When referring to scientists this usage of the term is considered to be redundant. 

4) Ultra-Darwinian. This usage is another used by creationists, but is more precise than imply meaning people who accept evolution. It applies to people who believe Darwinian natural selection can be used to explain more than just biological complexity and diversity. Most believe that evolution explains culture, but also have been known to explain cosmology in similar terms. Ultra-Darwinists also believe that evolution rules out the possibility of God. In this context, evolutionist is synonymous with a specific form of atheism. 

5) As a profession. The term is also used simply to refer to evolutionary biologists, sounding like a portmanteau of the two words. This usage is often seen as anachronistic and redundant and so finds most use in the creation-evolution debate (though Gould's usage seems to contradict this and he was not alone). 

6) Theistic evolution. Someone who accepts theistic evolution is a theistic evolutionist, though they are never referred to as simply evolutionists unless the term is being used in a broader sense. 

The sixth definition can of course be dismissed as it always has the "theistic" qualifier. The second definition is outdated. The first and fourth definitions both deal with belief and are very similar, but neither is a religion in the formal sense so they can be dismissed. This leaves the term as meaning anyone who accepts it, which seems pointless, or as a profession, which is considered redundant. 

It certainly appears to be a term which needs defining before it is used, unless the context is incredibly obvious. This renders the term rather useless for most situations.

What's in a name?

Fast forward several years and let's suppose that I have a successful career along the lines of what I am currently studying. When people ask for my job title, what should my answer be? This might sound like a stupid question as the answer might clearly be "palaeontologist" but that's no fun when so much can be done with it. Some answers might be obvious, as I could say "I'm a scientist" and there are different academic titles depending on which route I take (lecturer, reader, curator etc.).

My course title offers another option, the title of "palaeobiologist" which is one I rather like, but also I could label myself a geologist, a biologist, an Earth scientist and a life scientist. Expanding on these opens up more possibilities. As a palaeontologist the answer can be expanded to "invertebrate palaeontologist". As a biologist perhaps "evolutionary biologist" is more accurate. With some palaeontologists the name of what they study becomes a title; one who studies dinosaurs is sometimes informally referred to as a dinosaurologist, though trilobitologist appeals to me more.

One of my lecturers labels all the palaeobiologists "necromancers" as we like to play with dead things. I should someday give that as my answer, if only to see the response. A friend of mine prefers the title "dead-thing-ologist" which sums us up nicely. One I am rather fond of, due to how pretentious it sounds, is "historian of life". Bask in that one for a moment please.

I suppose I could also combine some of them, perhaps my job title could be "evolutionary invertebrate palaeobiologist". Overall though I think it makes sense to choose the title dependent on situation. Saying "I'm a geologist" would be useless when discussing evolution, when "evolutionary biologist" asserts authority. Conversely, saying "I'm a life scientist" would get you nowhere when a geologist's opinion is needed. The declaration that one is a geologist may also offer difficult situations; imagine hearing that a geologist is needed, only to find that they need an expert in vulcanology and there is not a sedimentary rock in sight!

And for the record, if I reach the level of gaining a PhD, I probably would stride forward with pride when someone shouts "we need a doctor" despite the fact that much of what I want to study preceded the pulse. Give the poor injured person a few million years to lithify and I will be useful....

Monday, 21 June 2010

How Evolution Works - Part 1 - Chance and Necessity

The main driving force behind evolution is understood to be natural selection acting upon genetic mutations. Each organism has slight genetic differences to their parents and so there is variation in a population at any one time. Often there are variations which improve fitness of an individual.

Key term - Fitness: In evolution fitness does not mean "faster" or "stronger", but "better suited to the current environment". In this sense the fitter individual may actually be the smaller, weaker and slower organism. Fitness is entirely dependent on context.

Natural selection acts when there is variation in a population, especially in populations where organisms produce more offspring than are able to reach maturity. Individuals in a population compete over resources, whether it is food, water, space or mates. In some species, competition, especially in males, is often direct, resulting in combat. Competition can also come from other species which require the same resources.

The fitter members of the population are most likely to breed and pass on their genes to the next generation, thus passing on their own favourable variation. Natural selection concerns the organisms which are more able to pass on their genes. Success in breeding is often more important than success in survival, though the two are connected (a short life with lots of breeding can be a more successful strategy than a long life with little breeding).

A point to remember is that natural selection has no foresight and cannot select variation which are favourable in future environments; it can only select for the current environment. A change in the environment changes the context for fitness. Sometimes a trait which is fortuitous in the current environment is useful after the environment changes, sometimes for a new purpose, this is known as abaptation or preadaptation.. 

When there is continuous phenotypic variation (the phenotype is the outward appearance of an organism) there are three ways in which natural selection can act on a population: stabilising, directional and disruptive.

In stabilising selection the existing mean of the distribution of inherited variability is favoured. In other words, variance is reduced as extreme variants are selected out. For example, in a population both the largest and smallest individuals may be selected against, maintaining a mean between the two. This is often seen with birth rates in populations.

During directional selection the mean shifts as selection favours one extreme of the inherited variability distribution. This sort of selection is most common when a change in environment occurs. The famous peppered moth experiment demonstrated this as environmental change caused a shift in the mean colour of the moths from pale to dark.

Disruptive selection splits a population in two by favouring both the extremes of the variability distribution. From one phenotype emerges two distinct phenotypes. This process may be instrumental in the evolution of many new species as a population splits and adapts to new environments.

Some key points to remember about natural selection is that it is a non-random process and that it acts on very slight changes in phenotype. The chance aspect of evolution is genetic variation as mutation is a random process; natural selection does not act randomly but is instead differential reproduction, something which can be easily predicted. Changes which are too large in an organism most often result in being selected against as they are more likely to be poorly suited to the environment. Small changes do not stray far from the already favoured phenotype and so natural selection can favour those which provide even a tiny advantage, refining the adaptation.

When discussing natural selection it sometimes helps to make a key distinction. Natural selection acts on any phenotypic trait, whether it is heritable or not. Evolution requires heritable variation to be selected. The selection of a trait can also result in the selection of other connected traits, such as when a gene has multiple functions (pleiotropy).

Natural selection acts at all stages of the life cycle, the image below is useful in distinguishing the different types of selection at work:

As natural selection works on small changes it can take a long time. Each change it favours is a successful increase in fitness which accumulate bit by bit. Natural selection is a cumulative process and is therefore very important in the construction of complex adaptations in evolution.

Part 2 will go on to discuss speciation. Natural selection is a heavily studied phenomenon for which a lot can be found. I recommend The Blind Watchmaker  by Richard Dawkins for any who want to know more, particularly with regards to natural selection being cumulative.

How Evolution Works - The Plan

I have decided to do a series of posts explaining how evolution works. I realised that it could be very useful and will allow me to talk about one of my favourite subjects, so hopefully it will be educational. I have a 13 part plan though it may change. If anyone would like to suggest things I am missing I will happily try to fit them in, I will also accept any criticisms, preferably constructive, as I can alter them here on the blog and potentially make them more useful.

I intend to start off slow, with the basics, then take it up a step at a time to some of the more complex subjects, even ones I am not so sure about myself. The plan is as follows:

1) Natural selection
2) Speciation
3) Genetic variation
4) Gene regulation and heterochrony
5) Endosymbiosis and multicellularity
6) The evolution of irreducibly complex structures
7) Other mechanisms (including genetic drift, sexual selection, epigenetics etc.)
8) Patterns in the fossil record
9) The level of selection
10) Evolvability
11) Contingency and convergence
12)  The micro and macro evolution debate
13) Extras I missed

Some may seem to be in odd places, for example drift could have been mentioned earlier. The distinction between micro and macro evolution may seem odd to be at the end, but my reason for this is that a lot of people, creationists in particular, focus on it without understanding the basics. It goes beyond the basics and so I have left it for later. I do this also because I think it is irrelevant for grasping much of evolution.

Pterosaurs Attack London!

So go and see them! Over the last year the University of Portsmouth (my uni) has been constructing life-size pterosaur models to go on display on London's South Bank as part of the Royal Society's Summer Exhibition. These models are huge! I've had the privilege of seeing one of them as a work in progress and they are a sight to behold. They have been modelled using up to date knowledge of pterosaurs and some of them are not in flying poses; they are the first to be shown standing and walking, of this size at least.

I sadly cannot embed the video, so follow this link, watch, and be amazed.

The image used is by Mark Witton, one of the palaeontologists who constructed the pterosaurs. 

A Shell-shaped Mystery

What on Earth is this thing? I found one whilst searching for fossils at Ashfield Brick-clay Pit in Conisbrough and could not figure it out. It could easily be mistaken for a bivalve mollusc shell (that was my first thought) but it does not appear to be fossilised, does not match the limestones it was near and does not look like a mollusc when looked at properly.

I hadn't looked at it since Easter until today when I found another, this time in my back garden. It is organic, but what is it? For all I know it could have been produced by either plant or animal. It appears to be able to close into two parts, so a seed of sorts perhaps? If anyone has any idea, no matter how crazy, I want to hear it?

Perhaps it is the shell of a grenade used by tiny people in my garden.....

Sunday, 20 June 2010

Looking Closely at Rocks

Today I'm not feeling 100% so I thought I would put myself in a good mood by looking at some rocks. Oddly enough though I have nothing useful to say about these rocks:

What I can say is that the woman in front of the rocks, someone who would make a rubbish geologist obviously, is Ivina Slavikova, ex Miss Slovakia and star of the following advert which keeps getting my attention lately:

Happy Broadband for Picky Princes

Thursday, 17 June 2010

Does Natural Selection Drive Evolution?

Natural selection is widely accepted as the driving force of the evolution of complexity, but the question is whether or not it is the only explanation. It would be naive to suggest that it was the only force, so the question should be rephrased as to whether or not it is the most significant. Connected to this is the importance of chance in evolution. The following are a selection of proposed mechanisms:

Genetic Drift

This is accepted as an evolutionary mechanism and can be very important in population dynamics. Genetic drift occurs when there are different alleles of a gene in a population which have equal survival value. Drift can cause one to be favoured over another. This is the key mechanism debated as an alternative to natural selection as it has potential to be important during speciation events. However, drift alone cannot construct a complex adaptation. With regards to adaptations drift can facilitate natural selection on occasion by randomly favouring an allele which may have future possibilities; the adaptation is still due to natural selection, but with a slight helping hand from drift. For more see here.

Neutral Evolution

Neutral theory states that areas of the genome are free from selection and can evolve at a steady pace. It is the theory underlying the molecular clock technique in dating evolutionary events. Neutral evolution cannot drive the evolution of complexity, though it is very important at the molecular level.

Epigenetics and Neo-Lamarckism

Epigenetic factors are not currently well understood so to rule them out as insignificant would be premature. Epigenetic factors appear to be too transient to be effective in the evolution of adaptation, however, they can be manifested in the phenotype and can hide genetic effects which natural selection would normally work on. It seems so far that it cannot explain complexity, but may be able to elucidate the workings of natural selection and may complicate matters. See here and here for more.

Phenotypic Plasticity

Organisms can adapt within their own lifetime due to the flexibility to change physical appearance. The important aspect of phenotypic plasticity occurs during development as it can determine the phenotype for the whole life of the organism. These phenotypic differences are not genetic, though the range of plasticity may well be and is open to be selected for. Again, this will not construct complex adaptations, but is a source of key variation that may aid in the survival of a species. For something similar, see here.


Both biotic and abiotic systems have examples of self-organisation. Protein folding and viral self-assembly are two insightful biological examples. These have an underlying selectable genetic basis, but their phenotypic variability (one could say plasticity) may provide more variation, thus facilitating natural selection in constructing complex adaptations.

Most of the answers, it seems, will come from studies into embryological development. The processes which translate genotype into phenotype still need some elucidation and may unlock the secrets of evolution. As is shown, my view is that none of these other processes can construct complex adaptations, natural selection does that, however, they can facilitate it through their alteration of the variation available for selection (whether by muting it as with epigenetics, or by bringing more diversity as with plasticity). To say natural selection is the only driving force is to be too simplistic, though it does seem to be the most important.

For more on natural selection  I recommend The Blind Watchmaker  by Richard Dawkins. He champions it in a lot of a detail and discusses neutral theory as well. For more on the topic of other mechanisms see here.

Wednesday, 16 June 2010

Interesting News Round-up

I am going to try not to make the news round-up a regular thing, but having been to Download festival for several days means that I missed out on some news which I found interesting. So here it is.

Molecular Data Insufficient in Systematics?

A recent study has shown that molecular methods used for studies in systematics and evolution are not sufficient. The researchers amply demonstrate that methods such as using mtDNA (mitochondrial DNA) did not give enough of the picture to be relied upon alone. See the article here for details. Any ecologists who thought they were becoming obsolete due to DNA analysis can breathe a sigh of relief. Personally the idea that genetic data should be bolstered with other lines of data when constructing phylogenies seems obvious. At least now I can't be accused of having a bias towards wanting palaeontology to have a voice.

Mathematical Models and Multicellularity

This is something I really need to do more research into. The evolution of multicellularity is largely a mystery, particularly concerning differentiation. Individual cells are expected to act selfishly, making multicellularity a difficult trait to evolve. Multicellularity has actually been observed evolving, at least in a crude form, see here for details. But whether that study applies to the multicellular evolution in our ancestors remains to be seen. Now a mathematical model has been formed which elucidates this complex process. Through the evolution of developmental plasticity comes the evolution of differentiation. I would love to say more about this, but as I am not mathematically minded I would probably make a mess of things until I do more research, it is exciting though. Here is the simpler article.

More Insight into Abiogenesis

Recent experiments have successfully synthesised guanine, one of the nucleotide bases found in DNA and RNA. This is a big step as it much of the evidence supports the concept of RNA being the precursor of DNA and so far all RNA bases had been synthesised in prebiotic conditions except for guanine (those are adenine, cytosine and uracil). The experiments were elegantly simple, using UV light to cause the reaction. Not only did it produce guanine, but also facilitated the production of the other molecules as well. This is a big yet simple step in our understanding of life's origins. For more info check the ScienceDaily article here or the journal paper here.

Warm Blooded Ichthyosaurs

After looking at the gorgeous ichthyosaur fossil in Doncaster museum today this story was particularly exciting. Using techniques I mentioned in a previous blog, a team have determined that marine reptiles such as ichtyosaurs, plesiosaurs and mosasaurs were warm blooded. Again, for the ScienceDaily article see here, for the journal paper see here.

Monday, 14 June 2010

Fossils to find...

I'm not very well travelled and sadly have not looked for fossils in Palaeozoic rocks, barring my local Permian fossils (I've also never even seen Precambrian rocks, to my knowledge at least). So it is not surprising that even though I love trilobites and know that they can easily be found in Britain. They are top of my list of fossils I want to find for my own pleasure, however, that is being challenged. I am quite fond of Microdictyon and have found out that M. sphaeroides can be found in Atdabandian age rocks in Britain. I still don't know where, but it is likely in Wales, if not in Scotland as well, so travelling is required (I've never even been to Wales). I think I have a friend who goes to uni near Welsh Cambrian rocks, hmmm.....

Monday, 7 June 2010

News Round-up

I am a bit behind with relaying news which I found exciting, the last update was also late at the time, the one about new Ordovician species. Well, I thought seeing as I have not reported anything new since the end of May and am going away from Wednesday to Monday, I would relay the stories I find most interesting. Lazily I went to and found the most interesting stories, but at least I am trying. Here are my favourite science news stories of the last few weeks:

Archaeopteryx was a poor flyer.

A study into the feathers of Archaeopteryx and Confuciusornis has found that they were poorly suited for flight. These early birds were unlikely to have used powered flight, if they even flew at all. This shows that the evolution of flight was slower than previous thought. The feathers were likely evolved in dinosaurs for insulation and display, but when elongated they provided a parachuting surface and later a gliding surface. For the ScienceDaily article see here. For the published paper in Science see here.

The mystery of Nectocaris is solved

In the famous Burgess shale was a problematic organis called Nectocaris (meaning "swimming crab")which was first described by Simon Conway Morris in 1976. With only a single specimen it was difficult to classify and was sometimes seen as an arthropod due to some features, though others made it difficult to support this view. One palaeontologist actually tried to class it as a chordate. Recently, 91 new specimens were found and described, allowing Nectocaris to finally be classified. Their analyses show that it was a cephalopod and pushes the origins of cephalopods back 30 million years and has refined understanding about the origins of this group. I will be tempted to write about this critter in future, but for now here is the ScienceDaily article, and here is the paper in Science.

The brown algal genome is completed

Great news for comparative genomics as we now have a completed genome for each multicellular group (animals, plants, fungi, red algae and brown algae). This project, which took 5 years to complete, will allow the genomes to be compared and will shed light on two key evolutionary events: multicellularity and photosynthesis. Here is the ScienceDaily article for more.

I thought I had selected more to discuss than this to be honest. Ah well, what I have presented is thrilling stuff, for me at least.

Saturday, 5 June 2010

Disagreeing With Dawkins?

I wrote this a while ago but only recently typed it up. The font is probably going to go crappy on me, but ah well.The picture I have chosen contains a gorgeous ammonite fossil which is clearly from the Mesozoic. It has quite well developed sutures so came quite late during the period which is often seen as the age of the dinosaurs when it was equally the age of the ammonites, particularly in the oceans.

Professor Richard Dawkins (1941-) is a world renowned author and scientist from Oxford university who has increased public awareness of evolution over the years. Studying under the eminent Niko Tinbergen, as a scientist he is an ethologist who studied the adaptive significance of animal behavioural patterns such as "Selective Pecking in the Domestic Chick". With this as his basis he has written some of the best popular science books expounding evolution, with selection and adaptation being prominent topics. He has, in recent years, shot to fame in wider circles due to his book "The God Delusion". I have decided to take a little time to show where I agree and disagree with Dawkins.

It barely needs stating that we both agree that all life has evolved over the last 4 billion years from a common ancestor which probably resembled bacteria. Dawkins' books make it clear that evolution is a distinctly non-random process and that it occurs in a very slow, incremental fashion; we are again in agreement. We both clearly agree on the main concepts in the theory of evolution, but when looked at deeper some differences occur.

Much of Dawkins' work focuses on the power of natural selection. He rightly states that selection is the only mechanism which can construct adaptations (though some recent evidence suggests that drift can give it a little helping hand). Genetic drift and neutral theory are not ignored as 'pluralists' would claim, but are both acknowledged as occurring but with no adaptive advantage.

"The Selfish Gene" and subsequent books presented his gene selection views, which are perhaps what e is best known for in evolutionary biology. It is not always obvious that this is not a case of overzealous reductionism. Dawkins talks frequently of gene complexes and of bodies as vehicles or 'robots' of the genes; these are not to be ignored. He eloquently argues that selection must act on agents which persist over generations with a degree of conservation; only genes satisfy this replication criterion.

Gene selection overlooks some key issues. One issue with the statement that selection requires a degree of conservation is that phenotypes do fit this if it is viewed broadly. Although the individual phenotype is broken down by recombination with each generation, the differences between each generation are most often very small; enough perhaps for selection to be at work.

It also overlooks the concept that selection acts upon interactors, which is fulfilled by selection on the individual organism. Genes go through complex processes before being expressed phenotypically, the web of development can make gene selection seem implausible. Moreover, Dawkins has occasionally made it appear that gene selection is synonymous with selection on the individual. This is not to say that gene selection does not occur, for outlaw genes are proving increasingly common and there are genes with direct phenotypic expression (likely the exception to the rule and often deleterious). I also do not know Dawkins' views on epigenetics, as some experiments have shown epigenetic factors altering phenotypic traits, effectively muting the voice of the genes. I therefore reject gene selection as most prominent and appear to be more open to other levels of selection. I view it as predominately on the individual, though modular selection is also an attractive prospect. My mind is open to group selection, though I do not feel I have sufficient mathematical knowledge to judge it properly.

Species selection is an interesting concept which remains difficult to test. Dawkins does not often talk about species selection, though his views appear to be that it is plausible in determining which lineages diversify or go extinct, but with little to no effect on adaptation. Species have emergent properties not found in individuals such as geographical range and diversity, though such traits are arguably not passed on. My views are similar to this, though it is a difficult one as we run the risk of zooming in too close and not seeing the species as a whole, or conversely zooming out too far and seeing only species as individuals; balance is required.

Evolutionary arms races are one of Dawkins' insightful contributions which aid understanding in evolution and have evidence to back (though it must be noted that there are circumstances where it can be drowned out by other occurrences). It is a solid explanation for many evolutionary trends and adaptations. He also famously promotes the idea of extended phenotypes, a useful model for understanding the interaction of organisms with environments, particularly parasites.

"Extrapolationism" is a term which was often used by Stephen Jay Gould when referring to scientists like Dawkins who view large scale evolution as simply local events scaled up over longer time. I do not disagree with such  a view, but find it deficient as it cannot easily take mass extinction into account and tends to ignore fossil trends which need explaining. Simple speciation mechanisms coupled with genetic change in local populations cannot account for the variety of patterns found in the fossil record. For example, phyletic gradualism and punctuated equilibrium both occur on large scales; these are not plausibly extrapolated from microevolutionary trends in local populations, the bigger picture is a necessity.

Dawkins once dared to write about evolvability, almost taboo at the time, though since his effort many others have taken up the torch on this subject. I find Dawkins' case for the evolution of evolvabilityevolvability involved watershed events, Dawkins describes segmentation, which raised the upper bound of complexity and enabled lineages to become more able to diversify and adapt. Other examples include multicellularity and sexual reproduction. Interestingly this may open the door for selection of an entire clade (though then the issue would be whether the crown or stem groups are selected).

I enter shaky ground when I attempt to discuss contingency and convergence. Dawkins speaks more positively of convergence and my own position is not yet firm. I sit somewhere in the middle, finding some aspects seem inevitable whereas others seem almost to be pot luck. I don't feel that there is sufficient data to judge what would happen with a replaying of the tape.

Dawkins appears to believe that selection has a large range of variation to act upon and that the plausible variations which we do not see were selected against. This ignores the possibility that certain variation did not occur and thereby naively removes the need for an explanation of how much variation can occur. Constraints are found not only from the physical laws of nature but also from changes frozen into our lineage which cannot be reversed. Historical changes effect developmental possibilities, narrowing the variation available for selection.

Richard Dawkins had a very prominent and vocal rival in the late Stephen Jay Gould. Gould's main contribution to the theory of evolution was punctuated equilibrium. Dawkins dismissed 'punk eek' as a minor yet interesting empirical observation demonstrating different "gears" (presumably stasis, bradytely, horotely and tachytely). His dismissal was perhaps too rash, though in retrospect it was not completely out of order. Punctuated equilibrium was almost unnecessarily hyped as it carried a lot of potential which had not stood the test of time. Dawkins was clearly correct that it is still a form of gradualism, but ignored the overall pattern which had the potential to uncouple micro and macro evolution as well as bringing prominence to species selection. It necessitated a wider view of evolution, not just gene changes in a population. In recent years it is seen as one palaeontological pattern among many and appears to be a lot more than simple "gear" changes in response to environmental pressures.

An area I rarely discuss is psychology and cultural evolution, unlike Dawkins who confidently states his opinion. Evolutionary psychology clearly has value, but perhaps too much is given to it. A behavioural trait should not simply be given adaptationist explanation, for the brain is an organ which is full of possibilities for non-adapted traits to occur. Scrutiny and caution are of the utmost importance.

Dawkins kick started the field of memetics, used to explain cultural evolution. It strays close to pseudoscience, embracing 'just-so' stories and ignoring other possibilities in favour of an ideology. The only plausible place for memes to exist is the internet, or so it seems to me.

In conclusion, I agree with Dawkins on many issues within the theory of evolution. Some differences occur, though many are subtle and some are simply due to a different degree of scepticism. Unlike Dawkins I have not had a long, fruitful career allowing m to think about and test these ideas, so I am open to the possibility that our disagreements may slowly vanish as I delve deeper and deeper into the wondrous theory. On the other hand, palaeobiology may lead me closer to the views of Gould as opposed to Dawkins' ethology of the gene! Who knows?