How Long Does It Take To Evolve A New Trait?

Fundies often claim that there is not enough time for significant evolution to take place. This is a bit strange as some of the same fundies talk about “kinds” being taken onboard the ark to get round the problem of the number of species Noah would have to gather. This however mean that all dog or cat species etc would have to have evolved from these “kinds” in a few thousand years – something they say cannot happen.

Anyway, how long would it take for a simple new characteristic to appear? Well, that is going to depend on genome size, population size, generation time and how much of an advantage the new characteristic is.

I will use the example of the rock pocket mouse (Chaetodipus intermedius). These are found in the south western USA and Mexico. They occur in two forms; a sandy coloured form and a dark form. The difference in colour is due to mutations in the Melanocortin 1- Receptor gene (Mc1r). It known that the mutation rate in the mouse genome is in the order of 2 mutations per billion bases (a mouse genome contains about 5 billion bases). Furthermore, there are 10 different mutations of the Mc1r genes that cause the dark coat colour. Therefore the possibility of a dark coat mutation is 10 (mutations) X 2 (copies of the gene) X mutation rate (2 per billion). This means that a relevant mutation will occur in 40 times per billion mice. That is 1 in 25 million mice. The local population sizes of this species is in the order of 10 000 to 100 000 individuals. This means about half this number are female. The average number of pups a female has per year is 5, so taking the lower estimate of 10 000, this means that 25 000 pups are born each year (or 250 000 for the upper estimate). Again, using the lower estimate, if we multiply this number by the probability of a relevant mutation occurring (1 in 25 million) we get a black mouse arising every 1000 years (or every 100 years for the upper estimate of population size). This is because only one mutant copy is necessary to darken coat colour. These calculations apply to producing just about any particular mutant that involves a simple change in a codon, and it should be remembered that populations contain many mutations and evolutionary change does not happen one step at a time. Many characteristics can be selected a once, so there is no reason that coat colour and hair length or foot size can not all be subject to selection at the same time.

So, what about the selectability of the mutant? What I haven’t mentioned is that these mice occur in an area that has a sandy substrate, interspersed with areas of dark basaltic lava, so sandy mice on dark rock are at a disadvantage as they are more visible to predators. So, the greater the advantage, the faster the spread of the gene through out the population will be. This is proportional to the selection coefficient (s). The equation linking number of generations (t) to s and the breeding population (Ne) is:

T = (2/s) natural log (2Ne) generations

The estimated s value for this mutation is around 0.01. This means that once a black mutation arises, most mice in the population will be black after 1981 generations. (less than 1981 years).
The lava flows these mice live on are around 1.7 million years old. This means that a black mutation has occurred independently 1 700 times (lower population estimate) or 17 000 times (upper population estimate). Then it is left to natural selection.
One final prediction is that if this scenario is true, we should find different mutations in the population. This is indeed what we find. Creationism is clearly a dishonest intellectual black hole.

Sexually Deviant Monosexual Fish

Lee asked for some more details on that sexually deviant little fish the Amazon molly (Poecililia formosa). It not only violates leviticus 18:23 , but also laughs at god's hybridisation laws (Lev 19:19) so I’m happy to oblige.

To remind you, they are an all female species that require males of closely related species to reproduce – hence their naming after the tribe of Greek mythology. They are native to the area between the Rio Grande and Tuxpan in Northeast Mexico. It is thought they arose around 100 000 years ago (about 120 000 generations) through the hybridisation of two closely related species; a female Poecilia mexicana and a male Poecilia latipinna. This is the same genus the popular Guppy (P. reticulata) belongs to. This group are unusual in that fertilisation is internal. The male has a modified anal fin called a gonopodium, that acts as a penetrative organ (techno speak for love pump). This can be a significant proportion of the male’s body length, particularly in the genera Priapichthys and Phallichthys (below). No prizes for guessing what the names mean.

Normally, eggs and sperm contain half the number of chromosomes of normal body cells. Upon fertilisation, the normal number is made up – half from the egg and half from the sperm. P. formosa females however, produce eggs that have a full complement of chromosomes, but require sperm from a closely related species (such as the two ancestral species or P. latipunctata and more rarely P. sphenops) to start off the developmental process, but the overwhelming number of offspring receive no genetic input from the male. They are effectively clones of the female. Not much is known about the mechanism, but penetrating the egg can be enough to trigger division. It has been known for a long time that physically piercing the eggs of some species is enough to trigger the first few cellular divisions of embryo formation.

There are some interesting costs and benefits to this system of reproduction. The benefits include the fact that all members of the species can produce offspring; all off which are identical to the parent. There is also an added bonus that beneficial mutations are more likely to survive. It therefore may be possible for unisexual species to take over a habitat. However, one of the drawbacks is that this species absolutely needs males of competing species. Another is that there is no genetic exchange between clones. This would be bad should a new parasite evolve. Another problem is that deleterious mutations can’t be replaced through sex with non affected individuals. In fact, it is estimated that this species would only survive for 70 000 years before accumulated mutations made it go extinct. This principle is called Muller’s Ratchet.
These is some evidence that in very rare occasions, the males can contribute to the genome of the offspring as individuals are occasionally with three or even four sets of chromosomes (four sets could potentially allow the species to one day become sexual again as chromosomes have to have an identical partner to form normal eggs and sperm). Another rare mechanism is that small sub genomic amounts of DNA may come from the sperm. This could form minchromosomes. This allows parts of these chromosomes to replace mutated genes to be repaired by cutting them out and replacing them. There is at least one report that only the somatic (body) cells receive these minichromosomes – and only a small proportion at that. So in this case at least, the minichromosomes can not be transferred to the offspring. There still seems to be a mystery about how this species still exists. Another simpler explanation might be that the species is constantly being re-created through new hybridisations.

There is also a perceived cost to the parasitized males – they waste sperm and resources mating with the wrong species – a mating that will decrease their reproductive fitness. However, it turns out showing interest in another species actually makes hisown females more interested in him. Apparently this works with women too – show interest in the friend of the one you are interested in and that will make the one you are interested in more competitive..
Finally, some species of shark can do without males altogether – at least in the short term.

God Hates Animals!

It’s been a busy day. This is my fourth post and I’ve also had a trip to Edinburgh where I bought a Carcharodontosaurus saharicus tooth (below). It made me realise though that these things deserve to be extinct because they flout god’s laws of nature. They ate meat when they should have been vegetarian (Gen 1:29-30).

So, I’ve compiled a list of animals that are in danger of god’s judgement.

Wanted for breach Leviticus 19:9: the wearing of clothes made of more than one fabric.


Yes, not only is this hermit crab wearing a shell of aragonite, but it is also covered in anemones and sponges. It truly is an abomination to the lord as it also has no fins or scales (Leviticus 11:9-12).

Also breaching Lev 11:9-12 (These shall ye eat of all that are in the waters: whatsoever hath fins and scales in the waters, in the seas, and in the rivers, them shall ye eat. And all that have not fins and scales in the seas, and in the rivers, of all that move in the waters, and of any living thing which is in the waters, they shall be an abomination unto you: They shall be even an abomination unto you; ye shall not eat of their flesh, but ye shall have their carcases in abomination. Whatsoever hath no fins nor scales in the waters, that shall be an abomination unto you.”

That’s right, these baleen mouthed bastards eat krill wholesale. Japan is god’s judgement on them.

This evil little fish called the Amazon molly laughs at the lords interspecies sex laws of Leviticus 18:23. ("Do not have sexual relations with an animal and defile yourself with it. A woman must not present herself to an animal to have sexual relations with it; that is a perversion.")


This species is all female and reproduces only through mating with males of another species.


Wanted for being a drunkard – the pen tailed shrew.
If the good lord wanted this little sinner to drink the equivalent of 9 glasses of wine a night, hang about outside chip shops, and bullying fruitbats, he would not have given us Romans 13:13.

I particularly look forward to the day the lord punishes these:



Lesbian bonobos are an abomination! Look at them, they will do anything to anything. Lord, show your deep compassionate love and drown the planet again!


Or could it just possibly be that ” because it is against nature” is not a justification for something to be wrong?

More On The Genetic Code

Genes encode proteins. They do this by carrying information in their sequences. Genes are made up of DNA. This is made up of various combinations of 4 different nucleotides (Adenine (A) Guanine (G) Thymidine (T) and Cytosine (C)). It takes three of these nucleotides (called a codon) to code for one amino acid (proteins are covalently linked amino acid chains). There are two complementary strands of a DNA molecule, and Adenine binds Thymidine on its complementary strand and Guanine binds Cytosine on the complementary strand. Only one strand codes for the protein, and when a sequence is written, it is the coding strand that is presented.

DNA is copied (transcribed) into an RNA message (called messenger RNA – or mRNA) Where the DNA contains a G, the mRNA contains a C; where it contains a C, the mRNA contains a G; where there is a T, the mRNA contains an A. It is basically the same pairings as in DNA – this is how the information is transmitted. The only difference is that RNA does not contain T; another nucleotide called Uracil (U) takes its place. So, where the DNA contains a A, the mRNA contains a U. So, this three letter codon ATG, which encodes the amino acid Methionine, has the complementary DNA sequence TAC on the complementary strand. The mRNA that is transcribed would read AUG (basically identical to the coding strand, but with U replacing T). Transcription is illustrated below, with the complementary DNA strands are in Blue and the RNA is in orange. The top DNA strand is the coding one here and AGC is transcribed into AGC etc . The other DNA strand organises the growing mRNA molecule and is called the template strand. To make protein (translation), this mRNA binds to a different type of RNA called transfer RNA (tRNA). There are different types of tRNA that bind to different amino acids. They are recruited in the right order by the mRNA trough the same binding rules as before. So, the mRNA sequence that encodes the amino acid Methionine (AUG) will recognise the sequence UAC on the Methionine bound tRNA. In the figure below, the leucine and Alanine specific tRNAs are shown, containing the sequences GAU and CGC respectively. These bind to CUA and CGC on the mRNA, which are encoded by the codons CTA and CGC in the DNA.

Different amino acids are encoded by different codons, as shown below. You will also notice that most amino acids have more than one possible codon; some have up to six. this means that there will be one a tRNA for each codon.
So, Lets take a closer look at this short sequence from the previous post. It is only 42 amino acids long (average proteins contain over 400 amino acids!)

MCEEEDSTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQG

Here is the amino acid breakdown and the number of possible codons that can be used in the above sequence..
So, the number of possible codon strings that could produce the above sequence is (4 x 5 A) x (2 x 3 C) x (2 x 4 D) x…….... (4 x 3 V) = 19 813 556 551 680. Yet human and chimp usage are identical ! Factor in the human and chimp genomes being 98 % identical and the number of possible codon usages genome wide becomes enormous – someone with more time than me can work out that one! Therefore, there is no reason why human and chimp sequences sould be identical if they were designed. They are however identical, suggesting evolutionary relationships.

Another possible place a designer could leave a signature is in the actual genetic code. There is no reason why ATG should have to encode methionine in every species (or indeed why any codon should encode a particular amino acid).

Importantly, it is a different part of the transfer RNA that recognised the mRNA that binds its specific amino acid. It would therefore be possible to mess about and make ATG encode Methionine in one species, but have it encode any other amino acid in another species. Yet, the genetic code is the same across species. Again, this is where evidence of design could be inserted. None is found, so it would appear that if there was a designer, he is unable to write his own name, or just does not want to be found. I'll go with there not being one.

Good News

I just became an uncle for the first time today. Meet baby Brandon. Doesn't he look just like Winston Churchill?

Gene Sequences and Evolution

DNA sequences provide very important clues to the evolutionary relationships of animals. Creationism basically states that god made it that way and makes no predictions. They just say that’s how god did it. It is nothing more than an unsupported assertion.

Let’s take an evolutionary view of some genes. I randomly chose the alpha actin gene – it actually turned out to be a very good example. I compared the sequences of the first 42 amino acids between humans, chimps (predicted sequence) and mice, and they were identical. The human/chimp and mouse sequences are shown below in Red and blue respectivley (differences are highlighted by boxes).

As mentioned previously, amino acids are encoded for in DNA by codons. These are sequences of 3 nucleotides that make a “genetic letter”. The interesting thing is that more than one codon can encode a particular amino acid (leucine for example has 6 different codons). This is called genetic redundancy. So, we can predict that although the amino acid sequence might be the same, the nucleotide sequence will be similar in closely related species, and less so in distantly related species that last shared a common ancestor 10s of millions of years ago.

Looking at the DNA sequences of the alpha Actin genes, there is no difference between humans and chimps, suggesting they are closely related, but as shown above, there is a 7 % difference in the mouse sequence (yet the amino acid sequences are identical). To further illustrate the point, lets take a random part of the amino acid sequence (this part DSTALV). This is encoded in humans by the codons GAC AGC ACT GCC TTG GTG, but could just as easily be be encoded for by the sequence GAT TCT ACG CGA CTG GTA.

GAC AGC ACT GCC TTG GTG (actual sequence)
GAT TCT ACG CGA CTG GTA (possible sequence)

This would give exactly the same amino acid sequence, but is 53% different to the actual sequence – that is considerably different to the mouse sequence that encodes this region (a mere 13% difference). This is not the only alternative way to write the sequence: D has 2 alternative codons; S has 6 alternative codons; T has 4, as does A; L has 6 and V has 4 alternative codons. So, if a creator wanted to leave a signature, this is where he/she/it could do so. He could make “related” organisms show very little similarity in their genes – that would mess up evolution. Instead, what we see again and again is that the closer species are phyllogenetically, the more similar their DNA sequences – evolution is the only reasonable explanation.

Not Bad For A Deaf Guy.

One of the most uplifting and best pieces ever written. Only Lemmy could make it better and then perhaps dear old Ludwig van could hear it.

Shame the last few seconds are missing. Lets not spoil it though with silly theistic arguments form beauty.

Sad News

My Gran died last night. She was born in 1916, and although she had been physically deteriorating for a few years, she was still mentally sharp until a few weeks ago when she had a stroke. We are all saddened by it. We were expecting it, and I think this gave us time to prepare (something I don't think the false hope of prayer would do). There is also relief that it was not a prolonged affair for her. Right now, I am filling myself with happy memories of her, which is not difficult as she was always kind and did not have a bad bone in her body. I usually have some rolls and bacon with brown sauce for breakfast on a Saturday. Strangely, it has always been something that reminds me of my Gran. When I was a kid and we visited my Gran and Granddad, she always gave us bacon rolls with brown sauce – cooked on my granddad’s camping stove because I liked that. I also think of her whenever I have a bowl of Heinz tomato soup – whenever I was off school with the flu or some other scabby child disease, she would often look after me when my parents were at work and give me tomato soup. I think it’s the feeling of being cared for by her that I associate with these foods.

I feel particularly sad for my mum and dad as they were very close to her. She always called my Dad the son she never had. I also feel sad that she will never get to see my sister’s first child, who is due in a few weeks. That would have meant so much to her (and my sister). I don’t really think it has sunk into any of us yet, but it has impressed upon me that life is valuable and that we should live it to the full. There is no time to waste what we have, and my Gran wouldn’t want any of us moping about. She would definately tell us off for that.

The First Cause

Theist argument:

Premise 1: All things that exist have a cause.

Premise2: God does not have a cause.

Conclusion: God is the first cause.


However, we have two contradictory premises here. Premise 1 is also on shaky ground. Where is the evidence that everything needs a cause? Then we have the Casimir effect where particles can just spontaneously come into existence.

Premise 2 is equally shaky. Just defining something does not impart it with existence of a particular set of values; for example square circles are pink. Square circles cannot exist, and therefore can not be pink. Why should defining god make him any more real?

So, lets re write that argument and keep it logically consistent.

Premise 1: All things that exist have a cause.

Premise2: God does not have a cause.

Conclusion: Therefore God does not exist.

The theist now has to abandon this argument, or concede that God does not exist (If he wants to maintain consistency).

The Beginnings Of An Old Earth Model

There have been many attempts to date the age of the Earth. At one extreme Aristotle believed that it was of infinite age, whereas at the other, the modern day young earth creationists claim the earth to be only a few thousand years old. Probably the most famous estimate being that of Bishop James Ussher, who not only came up with a number of years, but also the day and time of “creation”: Sunday 23 October 4004 BCE; just after tea time. He reached this figure by adding up the genealogies of the bible. I have always wondered how he managed to reach that figure as the genealogies of Jesus (found in Matthew 1 and Luke 3) are irreconcilably contradictory, with Luke also adding an additional 15 generations.
A major problem here though, is that it assumes the bible must be true. If the bible is not true, then the foundation of that figure is swept away in a flood of biblical proportions. Proper independent means show this age to be laughably false. Current estimates are that the earth is around 4.5 billion years old. This means that the creationists are out by a mere 4 499 993 996 years. The order of magnitude of this error is equivalent to thinking the distance from New York to Los Angeles is only 28 feet.

James Hutton was one of the first to realise that it takes a long time to erode mountains and form new rocks. Perhaps one of his most significant discoveries was the angular unconformity at Siccar point on the Berwickshire coast. An unconformity is a junction between rock depositions that has a significant temporal gap between the layers. An angular unconformity is one where the underlying (older) rocks are tilted at an angle and overlaid with younger more horizontal sediments. In the case of Siccar point, the older Silurian rocks (boxed in red in figure 1a) have been turned on their side by massive tectonic movements. This formed a mountain range as the ancient Iapetus ocean closed, resulting in Scotland and England joining together.

Figure 1a

Older upturned rocks in foreground and on right. Near horizontal younger rocks in distance and on left. In both cases, erosion has exposed the beding planes.

As the Silurian mountains near Siccar eroded and formed the younger Devonian sandstones (boxed in blue above) that now lie on top of the upturned older strata (chunks of the older Silurian rocks can still be seen in the sandstone matrix (See Figure 2)). Hutton reasoned that this would take more than a few thousand years and this work began to challenge the authority of the bible and earned Hutton the title of “father of geology”.

Figure 2

Sediments on the floor of the Iapetus ocean become rocks. These are buckled and turned on their sides as the ocean close, forming fold mountains. These mountains erode and become covered in younger sediments, forming the unconformity.

A Very Bad Case For Design

Creationists have a lovely way of shooting themselves in the foot by taking the worst possible example to try and justify their case. This recent comment (found here) exemplifies this beautifully

“To know something and to assume to know something is different. Example, one lives alone and he/she goes home and just saw that dinner table is served with all kinds of fruits and food. Now I am thinking and conclude that somebody prepared all the food and served it. But Steve and Dawkins ASSUME that all the food came up there by chance and Luck. This world with their related seasons which act like a servant is a very big food stale where we eat all the food according to the our body needs. Vitamin C or D etc. Who created human beings created the soil where all food fruits and veggies can grow and who created the soil, created the sunlight and rain that all cooperate with each other to serve us.”


Here is the real problem (other than the obvious misunderstanding of evolution and the absurd analogy): Our ancestors once made vitamin C for themselves. They did not need to ingest it. We lack a functional gene for an enzyme called L-gulonolactone oxidase. This forms the last step in the production of ascorbate (vitamin C) from glucose. We do however contain a pseudogene for this enzyme, which does not function because of acquired mutations. This presents a problem for the creationist.

The problem is that design requires being made to fulfil a purpose. Creationism boils down to an organism must be designed because it fulfils a purpose and all its parts are created to fit together to perform that purpose (that and a lack of imagination). So, here we have something that has no purpose and its only reasonable explanation is that it was present in a functional form in our ancestors (it probably became inactive about 40 million years ago).

Reductionism is a common theme in biology. If we don’t need a gene, there is no selective advantage in keeping it. There may even be a slight energetic advantage in losing it. Genes are lost through random mutations, and there are many examples of this occurring. It is not just the L-gulonolactone oxidase gene that we have lost; mice and humans have about 200 “genes” for a family of olfactory (scent) genes called the V1r family. Mice have about 160 functional ones. Humans have only 5! Whales and dolphins have no functional members. The non functional ones have become fossilised in our genome; they are slowly decaying. Gene loss is seen at an extreme level in parasites, as their hosts provide much of what they need for them. The record holder is Mycobacterium leprae; it has about 1600 functional genes and approximately 1100 decaying fossil genes.

It is not just genes that are lost, but structural features too. Examples include the toes of horses that can be seen gradually disappearing in successive rock layers, our appendix and the limbs of proto-snakes (Figure 1).

An interesting recently described example of this is the eyes of blind cave fish. It was found that functional eyes could be restored by interbreeding populations isolated in different caves. This is important. The fact that they have been isolated from each other means that the blindness evolved independently in the different populations. The fact that cross breeding some populations restored sight in the offspring means that different genes are responsible for the blindness in different populations of the same species – surely design would mean this should not be possible – as the perfect designer would chose the one way to make these fish blind – unless of course he wanted to make it look like evolution – just like chromosome 2.

One final point on vitamin C: inerrant biblical literalists believe that all animals were intended to eat plants and fruit (genesis 1:29-30). However, these foods contain vitamin C, so our ancestors would not need genes to synthesise it.

As one can see below, the teeth of Carcharocles megalodon are beautifully designed to peel grapes (sarcasm in case creationists are reading).

Father Ted

Thanks to Topov the Monkey (you big bollocks) for reminding me of this. It contains the classic line "That's nearly as mad as that thing you told me about the loaves and fishes! "

Enjoy!

Here I Go Again, Pouring Some Sugar On Me

I went to see Whitesnake and Def Leppard the other night. One thing that struck me was the number of folk waving their hands in the air and jumping about. It superficially reminded me of the crazies in the previous video. Two songs in particular (below) caused an outburst of this behaviour. I was then struck by the obvious: this behaviour does not need a deity. All you need is something that touches an individual emotionally in the right way. All the breakdancing fundies are displaying is behaviour that can be triggered in many people. There is no holy spirit influencing them.

Interestingly, I have been to a few services where the minister has had a go at the congregation for not showing enough joy. I guess rock music is a better inducer of emotional outpouring than the holy delusion.

So, which do you prefer, These?

or the miserable sound of psalms sung in Gaelic as done in Wee Free Churches (instruments are a sin).

At the end of Whitesnake's session, David Coverdale said "Be safe, Be happy and don't ever let anybody make you afraid". Words more inspirational and relevant to good living than those in the bible.

By the way, I asked the baby Jesus to show me if he was real by making Rick Allen (the one armed drummer of Def Leppard) grow a new arm.

I guess he is not real.

Genes From Space?

It’s like buses, no posts for a week and then three come along at once. I found this article interesting. We have known for some time that molecules essential for life are found in space. This report demonstrates that they can be delivered to earth by meteorites. By analysing the isotopes of Carbon found in organic compounds “contaminating” a meteorite found in the Murchison meteorite, it has been shown that Xanthine and Uracil of extra terrestrial origin can survive delivery to earth.

These molecules are examples of purines and pyrimidines: molecules essential for our genetic codes. In fact, Uracil is found in RNA – which some viruses use as their genetic material. One theory of abiogenesis proposes that RNA was the original genetic material and that DNA took over at a later date.


Uracil itself can be transformed into Cytosine by a simple methylation reaction (figure 1) and Xanthine can be converted to Guanine by a simple amido substitution.

Interestingly purines all contain a pyrimidine ring (Figure 2) so purines are possible pyrimidine derivatives.

This one piece of evidence alone is more than all creationism has for the magic sky fairy.

Parasite Adaptation 1: The Trypanosome

Parasites justifiably get a bad rap. At best, they are gross things that burst out of the bodies of other organisms alien style. At worst, they can cause severe human disesase. One species (Ascaris lumbricoides) infects a quarter of people on the planet. This however is a relatively benign parasite compared to those of the malaria parasites – which infect up to 200 million new people a year, and may kill up to 3 million people a year. It is therefore understandable that we should feel uncomfortable about them. However, if we can think dispassionately about them, and consider them as organisms, they are really quite remarkable and have evolved some amazing solutions to survive in a hostile environment. In fact, parasitism may be the most popular lifestyle there is as most species have several parasites, and even parasites have parasites of their own.

All organisms live in an environment that presents challenges that have to be overcome – be it a lack of water, light, oxygen or predators. Parasites though live in an environment that is actively trying to kill them. Animals (and plants) have evolved elaborate immune systems that try and kill invading organisms, and in return, parasites have evolved counter measures. Some species, such as Leishmania sp. effectivly live in baths of digestive enzymes, bleach and toxic radicals called phagolysosomes. Others can also immunosuppress their hosts. An example of this would be the hook worms (Ankylostoma sp). As an aside, these are actually being tested to treat allergies. Some species (Leishmania again) can make the host produce an entirely inappropriate immune response that actually antaganises the type of response that would kill the parasite. Some species (Schistosoma sp) even cover themselves in host molecules to disguise themselves.

One group called the Trypanosoma brucei complex have a rather interesting way of evading the immune system. These are transmitted by tsetse flies and cause a wasting disease called ngana in cattle. In humans, two subspecies (T. brucei rhodesiense and T. brucei gambiensie) cause sleeping sickness. Normally, an infected individual will show peaks and troughs in the number of parasites in their blood. See Figure 1.

Figure1

This is due to the immune system clearing the parasites from the blood and new variant parasites arising that have different properties. The surface of trypanosomes is almost completely covered by a molecule called the Variant Surface Glycoprotein (Figure 2). This coat also forms a barrier that prevents the immune system seeing or reaching important membrane proteins. This is important, because if the immune system could see and reach an essential parasite surface molecule, that does not vary, that could be the end of the infection.

Up to 10% of the Trypanosome genome may be devoted to different VSG genes. The proteins they encode invoke a strong antibody response and as this response develops, it kills the trypanosomes that express that particular VSG type. Some individual trypanosomes will suddenly change the VSG molecule they express at the surface. The result is that the immune system can no longer recognise them and has to generate antibodies to the new VSG. This process repeats itself and keeps the parasite about a week ahead of the immune system. This will continue until the host dies or receives chemotherapy. The energy costs involved in producing large amounts of antibody also affects the host and results in a reduced capacity to produce more antibodies. This means that the infection ultimately gets worse.

Now the god bit. Fundies who believe in a literal garden of Eden and talking snake claim there was no death and suffering before the fall, therefore no trypanosomes (and Tyrannosaurs ate plants!) One particular one that some readers will be familiar with wrote this sick piece on the boxing day tsunami in which he wrote “He [Darwin] makes one big mistake – he assumes that the world as it is now is the world as God created it. But that is not the case. When you read Genesis One notice the repeated refrain, ‘And God say that it was good’. God did not create the world to have natural disasters, cancer and death. Something came into the world which has upset the natural order of things and polluted the whole environment. That is why, as Paul tells us in Romans 8, the whole creation ‘groans as in the pangs of childbirth’. We are faced with two choices – either the world is as it is because that is the way things are, or things are the way things are because sin came in and corrupted a good and perfect creation.”

Apparently we are to blame, and Robertson later writes “What is the explanation and solution for all this? How can we explain and more importantly cope with this bent universe and our perverse human natures?”"

This is just total bollocks (no apologies for terminology, a spade is a spade) and contradicted by fossil tumours, fossil deformities, fossils with bites, fossils with their last meal of a conspecific inside them, evidence of volcanism and earth quakes and mass extinctions all considerably pre-dating the existence of man to name but a few. It really is pathetic that people hold this view.

Despite the total absurdity of the claim, there are also internal inconsistencies in the fundie argument – although it is also applicable to the loving god argument in general. The point is that supposedly only god creates and he does so with a purpose. Now, if there was no suffering or disease, then why invent an immune system? If he is loving, then why create a trypanosome that has “built in” methods of specifically overcoming an immune system? This leaves you with the problem of loving God designing something that could have no purpose because there was no disease, then creating something to overcome this non purpose and cause suffering. It’s too mental for words.