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.

Eye To Eye

I've just been to a talk on vision, so since I plan a future post on the evolution of colour vision, I thought I would post this video. It shows how eyes could evolve in small stages- as opposed to creationist propaganda that claims that evolutionists believe it all just happened to fall together. My future post will deal with just one of these small steps; the generation of a new photoreceptor.

To continue the ridiculing ridiculous claims, here is a genuine creationist argument for a laugh.

In case any creationists are reading, commercial bananas are the result of selective breeding - oh and they have different numbers of ridges, you have to climb trees to get them and they grow in malaria infested areas. Just don't mention coconuts!

Why do creationists not wax lyrical about other so called creations - like liver flukes, Ebola and the Black Death? Oh yeah, that's right, they kind of make the claim that their their pestilential god is somehow loving look rather stupid.

Creationists And Missing Chromosomes

I have little respect for creationism as an intellectual pursuit (although I do know some creationists that have my utmost respect as people). Often though, we see a particularly nasty kind who are homophobic and boast of their ignorance, so I thought I would mix some science with taking the piss out of creationists here.

Our DNA is neatly packaged into structures called chromosomes. These are basically protein cores around which the DNA is wound. A DNA molecule can be seen here winding around proteins to form beads (nucleosomes) which are then further coiled into higher order structures. The video ends showing a cell dividing. Other proteins can then bind to these structures. The protein components of the chromosome helps regulate gene activity (expression), DNA replication and makes sure daughter cells get the correct number of chromosomes when a cell divides; or helps halve the number of chromosomes when we make eggs or sperm. Sperm cells have the smallest nucleus of all human cells and are therefore particularly good packagers of DNA.

The basic anatomy of a chromosome is rather simple. It consists of a centromere and telomeres at either end (Figure 1). The centromere is crucial in organising cell division and the telomeres stabilise the ends of the chromosome. Telomeres are made of short (usually 6) nucleotide repeats. In humans, the sequence is TTAGGG. This can be repeated over 50 times at each end of the chromosome. Interestingly, some internal chromosome structures can also be seen by staining them. Each chromosome also has its own specific pattern of bands (Figure 2).

Figure 1: chromosome structure.

Figure 2: banding in human chromosomes (arranged in pairs)

So, now to the point. Chimps have 24 pairs of chromosomes and we only have 23 pairs. This provides a potential challenge to evolution. At this point if you are a fundie, you will probably shout “Hallelujah”, dance about naked with a communion chalice on your head and claim the magic sky daddy did it. Genesis don’t talk about no evilution, so it is the work of the Devil and that's all you need to know. You then head off to your KKK meeting and claim that black men were created different for a reason before being put in jail for tax evasion – still, you can always buy some drugs off Ted Haggard – who is completely heterosexual – allegedly (wouldn’t mind so much if he kept his vitriol to himself).

If however, you wish to look beneath the surface, we can actually test evolution. Two main possibilities occur to a non creotard. The first is that a chromosome from a common ancestor with chimps split in two, this is unlikely as all chimp chromosomes have a telomere. We shall see more evidence against this hypothesis soon.
The second possibility is that two ancestral chromosomes fused after we diverged from our common ancestor with chimps. There are several predictions that can be made and tested – any one could potentially prove evolution false.

1. We should be able to align chromosome banding patterns between two chimp chromosomes and a human one if fusion has occurred. This is the case. It is Human chromosome two that lines up with two chimp chromosomes that are now called chimp 2a and 2b (Figure 3).

Figure 3: alingnment of human and chimp banding patterns

2. We should find telomere sequences inside the chromosome if a fusion has occurred. This is also what we find (figure 1). In fact, they start to reverse suggesting the ancestral chromosomes fused head to head or tail to tail. We can even tell where the fusion took place to with in 15 nucleotides. It occurred between nucleotides 114 455 823 and114 455 838.

3. Genes should appear in the same order above and below the fusion. I took a gene at random from above the fusion (RasGRP2) and one below the fusion (HOXD8). Lets see how the gene order compares:

Human chromosome 2: CARD12, TTC27, LTB1, RasGRP3, CRIM1

Chimp chromosome 2a: CARD12, TTC27, LTB1, RasGRP3, CRIM1

Human chromosome 2: PDK1, CCA7, CHN1, HOXD8, HOXD4

Chimp chromosome 2b: PDK1, CCA7, CHN1, HOXD8, HOXD4

Looks like they are in the same order to me – what do you say Mr fundie? What’s that? God did it that way to look like evolution to test our faith? My, you must feel special that god does not ask you to think.

4. We should see evidence of two centromeres. Guess what, that’s right, we do. The functional one lines up with one of the chimp ones, and the other one is still identifiable but non functioning. It also is in the same corresponding position as the other chimp one.

That's mankind's missing chromosome sorted. Now we just need to find out what happend to the ones that creotards are lacking.

Transitional Fossils - The "Frogamander"

Transitional fossils are great. Darwin recognised their value when he lamented their scarcity:


“But as for this theory, innumerable transitional forms must have existed, why do we not find them embedded in countless numbers in the crust of the earth?” (Origin of species 1859).

Not surprisingly, creationists intentionally misuse this quote to claim such fossils do not exist and use Darwin as an argument from authority. Of course, only 4 years earlier, perhaps the most famous transitional fossil of all; Archaeopteryx lithographica was discovered, and the second specimen, now called the “London specimen” was discovered 3 years after the “Origin” was published. Their importance was not realised until later though, but every time a new transition is found, this prediction of Darwin’s is further confirmed. It also means creationists have to spend more and more time with their heads in the sand in denial, or spread lies about the nature of the fossil. Every now and then they concede that the fossil does display the characteristics of two related groups, but childishly claim that there are now two gaps that need to be filled – one before the transitional form and one after it. This truly is the stuff of desperation, and often these gaps are filled. Even worse for creationists though is the fact that we can predict where and in what age of rocks we will find transitional fossils of a particular lineage in – it’s called geographic distribution of lineages fundies!

Since Darwin commented on the rarity of transitional forms (150 years ago – take note fundies) hordes of transitional forms have been discovered. A small fraction of which are noted here. With every new transitional fossil, a further nail goes into the creationist coffin. Recently, a new one has been described that sorts out the evolution of frogs and salamanders. It had been suggested that frogs and salamanders evolved from a tetrapod group called the Temnospondyli. These are an ancient group that are found in early Permian rocks. This new specimen called Gerobatrachus hottoni has been dubbed a “frogamander” (pictured above) as it displays characteristics of frogs, salamanders and other Temnospondyls. Thanks to this fossil, we can also propose that frogs and salamanders diverged from each other some 240 and 275 million years ago.

More information can be found here.

Pale Blue Dot

This is always Humbling. Our galaxy alone contains an estimated 200 - 400 billion stars.

Thanks to Steven for reminding me about this.

Evolution Of Antibody Recombination

As this is my first molecular evolution post, I would appreciate any feedback on clarity. No question is too trival either.

Vertebrates have an amazing capacity to produce proteins called antibodies. These form an important part of our immune system. It has been estimated that humans can produce up to 10 billion different antibodies. In our life time, we will produce antibodies that neutralise toxins (eg tetanus toxin) and recognise components of bacteria, viruses and parasites. If we are unlucky, we can produce antibodies to our own molecules (eg systemic lupus erythyamatosis and some forms of arthritis). We may also produce antibodies to food substances or pollen and develop allergies. We can even produce antibodies to chemicals that do not occur in nature. This is even more amazing when we consider that antibodies are proteins, and proteins are encoded by genes. Why is this amazing? Well, estimates suggest that humans may contain as few as 25 000 genes. How this large antibody repertoire is possible will be explained shortly. But I better introduce these molecules first.

Antibody structure

Antibodies are generally made up of 4 protein chains that are stuck together to form a Y shaped molecule. Each antibody consists of two identical heavy and two identical light chains. This molecule shown in Figure 1 is called an immunoglobulin and has two binding sites for recognising other molecules (called antigens). It is differences these sites (also called the variable regions) that determine what molecules an antibody can bind to. Some types of immunoglobulin (called Ig for short) can also consist of 2 (Ig A) or 5 (IgM) copies of these Y shaped immunoglobulins stuck together. This can increase their ability to keep antigens bound.


Figure 1

Generation of Antibody Diversity
As mentioned above, it is the chemistry of the variable regions that determines which antigens a particular antibody can bind. Both the heavy and light chains contribute to antigen binding, so, juggling different heavy and light chain combinations is one way of increasing the number of possible different antibodies an organism can produce. This however is not the main mechanism employed.

Antibodies are the products of different gene segments that are stuck together in different combinations at random. These segments fall into three different classes called Variable (V) Diversity (D) and Junctional/Joining (J) genes. The human heavy chain variable region has 50 functional V segments, 30 D segments, and six J segments to choose from. These segments all occur on the same chromosome. Also on the same chromosome, are the constant region genes of the heavy chain (basically the non variant part of the heavy chain). The light chains also have a constant region. They however do not use D segments. Their V and J segments also occur on the same chromosomes as their constant regions. The light gene situation however is slightly more complicated. There are two types of constant chain, termed the kappa and lambda chains - each antibody contains only one or the other. The Kappa chain can choose from 40 V and 5 J genes and the lambda chain can choose from 30 V and 4 J genes.
So, to summarise, and antibody is made up from a light chain that is stuck together from either a kappa or a lambda gene stuck to a randomly chosen J gene, which is then stuck to a randomly chosen V gene. The protein chain that this codes for is then stuck to a heavy chain that is coded for by a constant region gene (one of either a,b,g,d or e) fused to a randomly chosen V,D and J gene segment. These joining events can also be imprecise, further increasing the antibody repertoire. This can be increased yet further by an enzyme called Terminal Deoxynucleotidyl Transferase, which can incorporate up to 15 new nucleotides in to the heavy chain V and J gene segments. The cell then turns these chains into a Y shaped immunoglobulin molecule. Once the genes have been rearranged, further mutations can occur. This can help select for B cells producing higher affinity antibodies by a natural selection like process.
The intervening DNA that is not used is cut out and discarded (figure 2)


Figure 2


Michael Behe uses the above process as an example as an irreducibly complex system that he claims could not arise by natural means and must require a “designer” (euphemism for the Christian god). At the Dover county intelligent design trial, he boasted in his ignorance that “the scientific literature has no detailed testable answers on how the immune system could have arisen by natural selection and random mutation”. A problem with claims made from the argument from incredulity (I prefer the term personal ignorance) is that it is easily dismissed in an instant – not to mention that it shows a distinct lack of imagination and intellectual laziness. Behe was presented with a tiny fraction of the scientific literature that he claimed did not exist. This included a pile of peer reviewed research papers and text books on the subject.

Behe claims that to generate antibodies, you need the gene segments, recombination signals and the Recombination Activating Genes (called RAG1 and RAG2) all present at once, or the system cannot work. This also displays a lack of understanding about how evolution works – it tinkers and refines what is already there. Behe’s claim displays as big a misunderstanding of evolution as the creationists who claim the eye evolved in one step.
After the long introduction, it is the RAG1 protein that I wish to concentrate on.


Mechanism of RAG action

As mentioned previously, when antibody gene segments are chosen at random, the intervening DNA is cut out. This is achieved by the RAG proteins, and animals with function destroying mutations in these genes are severely immuno-deficient. Figure 3 shows the mechanism of action. The enzyme recognizes the Recombination Signal Sequences (yellow or orange triangles) that are located before or after the gene segments to be spliced together. Any combination of segments can occur and the process is random. The RAG proteins then cut out the intervening stretch of DNA and other DNA repair enzymes stick the two ends of the gene segments together (in this case V49 to D28).


Figure 3


Evolution of recombination

So, what would we need to evolve such a system? Firstly, an antibody like molecule. Interestingly, antibodies belong to an ancient family of proteins called the immunoglobulin superfamily. The family is defined on the basis of of a common structural feature called the immunoglobulin domain. Furthermore, this class of protein is found throughout the animal kingdom from sponges up, where their function is molecular recognition. So, we have a starting material to evolve an antibody gene. Michael Behe has claimed that since the chance that an antibody of a single specificity would be unlikely to recognise anything of importance, it would be of little advantage and could not evolve (Darwin’s black box pp. 130-131) . This is where the ignorance and intellectual laziness of the creationist is exposed. The immune system is packed with single specificity proteins, such as the Toll like receptors that recognise repeating molecular patterns. Secondly, If the ancestral antibodies recognised a more restricted set of molecules like a particular carbohydrate structure that is only found in pathogens (and there are plenty), it would be of significant advantage. Many invertebrates use a group of carbohydrate recognising proteins called lectins to recognise infectious agents.

The next thing a primitive recombination system would need would be the RAG genes. It has been hypothesised for about 25 years that the RAG genes may have evolved from pieces of selfish (or if you wish, parasitic) DNA called transposons. There are two interesting features of transposons; they insert into genomes and often encode genes that allow them to cut themselves out and paste themselves elsewhere in the genome. They often contain structures at either end called Terminal Inverted Repeats, which are essential for function. These are structurally very similar to Recombination Signal Sequences. Many transposons also make copies of themselves and these become incorporated throughout the genome – this is also a possible source of V,D and J gene segments.
To test this hypothesis, we would predict that RAG like sequences exist in transposons elsewhere and that they pre-date the evolution of jawed vertebrates. Both these predictions have recently been realised. A family of transposons (called Transib) that contain structural similarities to RAG1 and Recombination Signal like Sequences has been described from the sea slug Aplysia californica. These Transib family members have now been shown to be present in insects, nematodes, fungus and hydra, so they clearly are of ancient origin.

One further line of evidence confirms the link between RAG and transposons: RAGs have recently been shown to be able to act as transposons.

Interestingly, if RAG genes and antibody gene fragments are put into an organism that does not rearrange antibody genes – like yeast, they are perfectly able to. This points out that the rest of the machinery needed to stick the broken ends of gene segments together was already present – that’s what evolution does, it uses material already there and builds upon it.

Finally, it would appear that the ancestral RAG gene was originally of viral origin.

This illustrates the weakness of the argument of personal ignorance. Behe could not conceive how antibody rearrangement could evolve – shame he did not look at the available evidence.

More Thoughts On Perfection

Jonathan made a good point on the perfection thread and has sent me on a philosophical ramble. He pointed out that “creation” was not perfect. It made me realise (the blindingly obvious) that anything that does not conform to the qualities of god cannot be considered perfect. Genesis tells us that man did not originally know right from wrong or live forever (two qualities that god supposedly possesses). Man was therefore not created perfect! It makes the biblical narrative all the more bizarre when we consider that god created man in an imperfect state then punishes all mankind for the consequences of this. Is this fair?

This is a bit of a loaded question, if you say yes, then you are basing that solely on faith that god knows better than you – not a rational position. If you say no, you are subscribing to the view that there is some sort of standard by which to judge actions by.

However does this mean that there is an absolute moral standard that we are using here? Well, of course it doesn’t, it just means that there is a standard –and obviously one not accepted by everyone. If it is absolute, we have no means of knowing it is. A more serious problem for the theist however is that if an absolute does exist, then it must be something that is defined in a manner not dependant on god. This is because to be perfect you cannot deviate and act in an imperfect manner – something is restraining you.

Can God himself define the nature of perfection? Only if he limits his ability to act in certain ways. This would then define choice as something that is not a requirement of perfection. As any fundie will tell you, man’s original sin was a question of free will – a choice (although how you can be accountable for doing what you don’t know is wrong escapes me). If God then created man with free will, he has then given him yet another quality of “imperfection”. The free will argument then becomes internally inconsistent with the idea that choice corrupted mankind. The ability to choose would have meant that mankind was already less than perfect.
As an aside, if you have free will thrust on you, is it really free will? You can’t choose free will either, because that means that you have to have it already to make a choice. Can free will then logically exist? Does it exist at all or do other factors influence our choices?

A god who restricts his power would also not be omnipotent (presumably another feature lacking in perfection). The idea that god cannot be omnipotent is not new though. For example, can god make a weight too heavy for him to lift? If yes, then he lacks the ability to lift it, if no, then he lacks the ability to create such a weigh. I also doubt that he would be able to make square circles or make 2+2=27 while keeping the values the same.

I hate and love philosophy in equal measures. You can use it to justify or deny any concept. Personally I think it is more of a problem for the religious, as they are the ones who have the burden of proof.