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.....

The Fair-Ground Fish Theory

Have you ever noticed that the majority of goldfish won at the fair, say on the hook-a-duck, die pretty soon after being won? We then go through the old routine of flushing them down the toilet only to go back and win another the next year to repeat the whole escapade. I have come to believe that this is all an elaborate plan by fair ground owners. The fish are highly trained, taught to fake their deaths in order to be flushed down the loo. Once flushed, there are two possibilities (we must test these hypotheses in future):

1) The fish are trained to revive themselves and to swim to a rendezvous point where they can be collected again.

2) Someone from the fair waits in the sewer and collects the fish immediately after flushing, ready to be revived later.

Either way they survive. They are then bagged up again and won by more hapless victims. This charade must be exposed! People are being conned into winning the same fish over and over again! Occasionally there is an anomalous fish which enjoys life in a tank and does not fake its death, but the majority do so and are forcing us to spend hard earned cash on the same old fish repeatedly. I haven't even mentioned the mental anguish experienced by a child flushing his or her favourite fishy.

Join me in exposing this fish façade!

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.

Was Adam the First Human?

The Biblical Adam is one of the most iconic religious figures, widely known as the first man in Abrahamic religious belief. The question is, was he the first human? If you are scientifically minded then the answer is an automatic no. If you happen to be a young earth creationist then you will say yes without hesitation. However, it seems that the answer is not that cut and dry.

For those who wish to reconcile Scripture with modern science there have been many answers to this. It is an important question for Christians due to Paul's writings which would make it appear necessary for Adam to have been the first. The key solution seems to be that man sinned and needs a saviour regardless of the reality of Adam, so Adam is a prototype or an archetype (see here for more on this view). Concordists generally do not like this view too much and instead see Adam as the first to commune with God, sometimes labelling him Homo divinus and declaring that he was likely a Neolithic farmer, making the genealogies more accurate. Although I have no issue with the archetype reading, I want to explore a similar idea to the concordist view.

So was Adam the first human? Yes. And no. It depends entirely on definitions. Our modern mindset would tell us that for Adam to be the first human he must be the first Homo sapiens sapiens which is impossible to pinpoint as evolution takes place in a population; it makes no sense for this to be Adam. However, we should remember that the authors of Genesis did not have our modern mindset and so their understanding of human is very different to ours. This scientific concept of human conflicts with Adam being the first human and so this is the no part of my answer. But I also said yes.

The authors had truth in mind, but not scientific truth. Theological and spiritual truth were very important and were expressed through mythic writing. Genesis itself gives hints at how we may understand this. God used the dirt to create Adam, suggesting that he is part of nature, which in our modern framework sits comfortably with the idea of Adam being a product of evolution. But it also describes God as working on Adam personally, making him a living soul. This suggests that Adam is not a mere product of evolution, but that God was involved somehow. A dualist might suggest that God endowed Adam with a soul, but that raises many other issues. Under theistic monism (which I subscribe to) Adam becoming a living soul would require communion with God, something which requires God's participation; the breath of life was now in Adam (Christ, after all, is life).  Theologically then, Adam is the first human, if we use a theological definition such as "one who is able to commune with God" (this may raise issues concerning disabilities, but the ability to commune with God comes in part directly from God, so we cannot say that the disabled cannot commune with God in their own way).

So scientifically Adam cannot be the first human, whereas theologically he can. At some point in history God changed His mode of action and communed fully with humans, going on to set up a covenant. To claim that the scientific answer trumps the theological answer is to elevate science beyond theology, it is tantamount to heresy. It imposes a modernist mindset on an ancient text in a perverse manner and should be avoided at all costs.

The issue of Adam has more depth than this, there are more facets. This is, however, one piece of the puzzle and one we should not ignore.

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.

Tuesday, 15 June 2010

Evolution as Creatio Ex Nihilio?

There is a Portsmouth based prog metal band who have a recent album which caught my eye due to its title. The band is called Enochian Theory and the album in question is Evolution: Creatio Ex Nihilio. Below is the album promo:

From what I can hear here the music sounds OK but I can't say much more than that. As a guitarist I would love to assess the guitar playing, but that will have to wait until I have heard more. The album in question is a concept album, but song titles give nothing away so far (though the track titled Triumvirate took my attention). What baffles me is the name of the album, for two reasons. The simplest being the word nihilio which seems to contain an extra i  whereas creatio ex nihilo in theology lacks the third i.  Perhaps nihilio is a clever play on words that I am missing, or a portmanteau.

My main point of confusion is more due to curiosity. There is obviously meaning in the title, but the meaning I get from it may be very different. Evolution is not ex nihilo, it is a process with the co-option of existing parts. It can therefore be assumed (as long as it is not an error on their part) that a point is being made. Ex nihilo is normally used in the context of God creating, so the title suggests that either God created ex nihilo and utilised evolution, or evolution is being credited with ex nihilo creation. The latter point is absurd for the previously outlined reason; evolution also does not address the Big Bang. So it sounds like a prog metal theistic evolution album, which has me sceptical. It sure would be interesting to find out if that is their intention and what they think of that interpretation if it is not. Perhaps as they are a Portsmouth based band I may find out some day.

An interesting analogy

I've often had creationists object to the idea that God uses evolution with the argument that it limits God. I find this an odd view to hold, but perhaps an analogy I just stumbled across will clarify why God is not limited by evolution, at least not without it being His own choice. I often mention kenosis when discussing God's creating, the self-limiting of God is an important point to remember. Creationists clearly fear that evolution goes against the idea of God being omnipotent (it will be tempting to write at some point about what evolution can tell us about God's qualities such as omniscience and omnibenevolence etc.).

The analogy I came across states that God could have freely created a universe with only triangles, He would then be "limited" to creating three sided objects with internal angles adding up to 180 degrees. These limitations are chosen by God and are part of the creative process. This view is labelled moderate voluntarism. In our universe God's creative acts are limited by His own choice, by natural laws He spoke into being, as seen in the process of evolution. God's omnipotence remains intact, but His own self-limitation allows evolution to take place.

Monday, 14 June 2010

Insane Lyrics

A friend of mine just linked to a video by Insane Clown Posse and said that it was funny but that I would die inside a little. She was right. Here is the song:

In case you go insane yourself whilst listening but still want to read the lyrics, here they are:

If magic is all we've ever known
Then it's easy to miss what really goes on
But I've seen miracles in every way
And I see miracles everyday
Oceans spanning beyond my sight
And a million stars way above em at night
We don't have to be high to look in the sky
And know that's a miracle opened wide
Look at the mountains, trees, the seven seas
And everything chilling underwater, please
Hot lava, snow, rain and fog
Long neck giraffes, and pet cats and dogs
And I've seen eighty-five thousand people
All in one room, together as equals
Pure magic is the birth of my kids
I've seen shit that'll shock your eyelids
The sun and the moon, and even Mars
The Milky Way and fucking shooting stars
UFOs, a river flows
Plant a little seed and nature grows
Niagara falls and the pyramids
Everything you believed in as kids
Fucking rainbows after it rains
There's enough miracles here to blow your brains
I fed a fish to a pelican at Frisco bay
It tried to eat my cell phone, he ran away
And music is magic, pure and clean
You can feel it and hear it but it can't be seen

Music is all magic
(Are you a firm believer in miracles)
You can't even hold it
(Do you notice and recognize miracles)
It's just there in the air
(Are you a firm believer in miracles)
Pure motherfucking magic
This shit'll blow your fucking mind
(Do you notice and recognize miracles)

Music is a lot like love, it's all a feeling
And it fills the room, from the floor to the ceiling
I see miracles all around me
Stop and look around, it's all astounding
Water, fire, air and dirt
Fucking magnets, how do they work?
And I don't wanna talk to a scientist
Y'all motherfuckers lying, and getting me pissed
Solar eclipse, and vicious weather
Fifteen thousand Juggalos together
And I love my mom for giving me this
Time on this planet, taking nothing for granted
I seen a caterpillar turn into a butterfly
Miracles ain't nothing to lie
Shaggy's little boys look just like Shaggy
And my little boy looks just like daddy
Miracles each and every where you look
And nobody has to stay where they put
This world is yours for you to explore
There's nothing but miracles beyond your door
The Dark Carnival is your invitation
To witness them without explanation
Take a look at this fine creation
And enjoy it better with appreciation
Crows, ghosts, the midnight coast
The wonders of the world, mysteries the most
Just open your mind, and it ain't no way
To ignore the miracles of every day

(Are you a firm believer in miracles)
Magic everywhere in this bitch
(Do you notice and recognize miracles)
It's all around you, you don't even know it
(Are you a firm believer in miracles)
Magic everywhere in this bitch
Shit's crazy
(Do you notice and recognize miracles,
So many miracles, the magic miracles)

Are you a firm believer in miracles
Do you have time for the miracles
Do you notice and recognize miracles
So many miracles, the magic miracles
Are you a firm believer in miracles
Do you have time for the miracles
Do you notice and recognize miracles
So many miracles, the magic miracles
Are you a firm believer in miracles
Do you have time for the miracles
Do you notice and recognize miracles
So many miracles, the magic miracles
Are you a firm believer in miracles
Do you have time for the miracles
Do you notice and recognize miracles
So many miracles, the magic miracles 

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

Conversation With a Robot Stripper

Basically I was on MSN when somebody new added me and I accepted. This is what happened: says:
 Hey? Did you msg me??

Jason optimus est says:
 Nope says:
 oooh sorry but u r francesca's friend right?

Jason optimus est says:
 Who? says:
 what?? she gave me your chat name LOL, i'm sorry, anways im bored,what r u up to?

Jason optimus est says:
 Trying to learn how you can type 18 words in less than a second says:
 oh yea? im just doing a cam chat right now, u wanna come chat with me on there?

Jason optimus est says:
 Will you reveal your secrets about typing? Does it require extra fingers? says:
 mhhm finger it lolz

Jason optimus est says:
 The keyboard? Well, whatever floats your boat... says:
 cool, yea its pretty fun, it can get pretty hot in there sometimes! so many wild people. lemme get the info k?

Jason optimus est says:
 The suitcase is hidden under the bench next to the wheely bins. Approach from the east side with caution. says:
 Do you think i should wear my pink or black thong?

Jason optimus est says:
 It is completely up to you, you may be a bit conspicuous if that is all you wear. says:
 got em on my yahoo profile

Jason optimus est says:
 That is no use out in the field, unless you have wi-fi and good wireless says:
 kk, lemme see, okay go here look at the top of the page, make sure you click the "JOIN FREE" orange box, do you see it?

Jason optimus est says:
 I already told you, the suitcase is under the bench next to the wheely bins says:
 yup, you gotta put in your info so the system can verify your age, got it?

Jason optimus est says:
 But you are the field agent, not I, I'm just your average desk worker. says:

Jason optimus est says:
 Is that a code? says:
 yea cc is just to verify your age, don't worry it won't charge you are on the free cam, NO CHARGE
BABY!! <3. you in?

Jason optimus est says:
 Is the cam pointed at the bench next to the wheely bins? I can't cover you, but I can watch out for enemy operatives. says:
 love to show off on cam

Jason optimus est says:
 You good with your weapons then? says:
 nice, k don't keep me waiting, im burning up in here!! might have to take off more clothing

Jason optimus est says:
 But then you will definitely get spotted! You'll blow our cover! says:
 i'll blow it good!!

Jason optimus est says:
 Double Agent! says:

Jason optimus est says:
 There's that code again! says:
 k let me know when you get in so We can invite you directly to my cam sesssion.

Jason optimus est says:
 You want me to get involved? Against the country I serve? says:
 k, you in yet babe??

Jason optimus est says:
 I don't know, this is a life changing decision, not to mention, I would risk my life. Can you assure my safety? says:
 slap that ass   lolz

Jason optimus est says:
 As much as I enjoy that, I want safety, not eroticism. says:
 sweet k

Jason optimus est says:
 Your promises are empty! says:
 when u login click LIVEWEBCAMS k?

Jason optimus est says:
 Will that assure my safety? Will I even get a gun? And proper training? says:
 slap that ass   lolz

Jason optimus est says:
 With a gun? says:

Jason optimus est says:
 Ouch! What will that achieve? Is that a form of interrogation? says:

Jason optimus est says:
 I thought I was just meant to be watching, not interrogating says:

Jason optimus est says:
 Oh, I'm fine with that then,.

What Does Science Offer Christianity and Vice Versa?

In the modern intellectual climate there is often a gap between science and Christianity, and Christians themselves take more than one approach to science. Communication can be difficult with a chasm between the two, yet it should be necessary. One obstacle to communication is the rise of young earth creationism which creates the view that secular science and Christianity are incompatible; a view that some outspoken atheists are also keen to espouse. Another obstacle can be the compartmentalising of the two, giving them separate domains such as in the NOMA (non-overlapping magisteria) view of Gould, also known as the independence model of science and faith. Neither of these views provides for proper dialogue between the two.

The Gifts of Science to Christianity

The most obvious benefit of a Christian worldview which acknowledges and embraces the sciences is that it can give a litmus test for some religious claims. When there are competing interpretations in Scripture for a verse which mentions the material world a good grasp of science can swing the pendulum in favour of one over another. This most obviously applies to any claims about creation, though also to questions such as the soul.

The scientific view of the world is one of grandeur, of great depth and intricacy, along with an air of mystery. Scripture teaches of this grandeur, yet can it truly be appreciated without taking a peek at the findings of science? One can learn all about a beatiful location such as the Grand Canyon, but this surely cannot match the awe felt when visiting it. Christians should feel at least a little interested into the incredible insights science has to offer. 

Science does bring with it some questions, which we should of course embrace. One such question is whether or not the natural world can give us insight into the Creator. Although this might be the province of theologians, it is nothing but intellectual flailing about unless there is a solid understanding of science to back it up. Science can expand theology. 

Many Christians look to science for evidence of God. If they want a gift from science then evidence to back their position would be most welcome. This is another debate where a scientifically informed position would be more robust. My own position is that this is a misguided view; something I believe has both theological and scientific backing (another topic entirely). 

Science itself utilises a rigorous methodology and never stops asking questions when practised properly. Although theology cannot be subjected to the same sort of experimental methodology, the development of a scientific theory is a model which can be utilised in theology. Both disciplines are interested in discovering truth, almost necessitating an overlap in methodology.

Christians have certain "duties" on Earth and efficiency in achieving these would not go amiss. Advances in medicine, agriculture and conservation all help achieve the common Christian goals. Science can be a tool for achieving God's goals, but it must be embraced in order to be most effective. 

Christianity's Gifts to Science

In contrast to what science offers Christianity, what Christianity offers to science is of a different magnitude. Science offers gifts which can be universally accepted and are not confined to Christians. Christianity offers more to the individual and for the most part the benefits are nil for the non-Christian. This is not a blow to Christian belief, but merely the acknowledgement that science has a universality which goes beyond Christianity.

Science is, in simple terms, the collection and interpretation of data; it does not comprise a whole world view, though it can form a substantial portion. Christianity offers a philosophical world view within which science can find its home. Of course, each individual has their own world view and Christianity is one among many, but for the Christian it provides the broader picture within which science is but one facet. 

Christian voices, often sadly uninformed, are very often heard on issues of bioethics. Christianity, as with many major religions, offers a moral framework for the believer and so it becomes almost mandatory that Christians address ethical issues. Science does not answer ethical issues despite raising many. Christianity's moral framework provides key information for ethical decisions, whether in everyday life or in huge scientific issues. Many Christian concerns are relevant even outside of Christian circles.

One question which crops up is whether or not Christianity stifles science. It is capable of it, and has certainly done so in the past. This is why it is crucial for Christians to better understand it. A lack of understanding can be a source for fear or apathy, both of which risk putting a stop to science. Christians often also need to drop the mindset of having all the answers. 

If the animosity towards science is removed then this paves the way for Christianity actually motivating scientists. Many scientist Christians are driven by their Christian views, but sadly there often seems to be a gap between this view and the more stifling views which see science as dangerous ground. 

Embracing Christianity is often seen as a stop to the search for truth. It certainly offers answers to some questions which may otherwise have remained unknown, but at the same time it opens up more questions just as good science does. As both are a search for truth they can both be likened to a journey, one which may never end. This, to me, is an exciting prospect.