Not Bad For The Last Day Of The Year

Beinn Dubchraig (left), Ben Lomond (distance) Ben Oss (centre) and Ben Lui (right) from Ben Dorain

Ben More (centre left) Stob Binnien (centre right) and Cruach Ardrain (right) from Ben Dorain

The blackmount and Ben Nevis (centre right) from Beinn Dorain

Happy New year everyone

My Genome Project

Given the fact that many creationists accept evolution within rather vaguely defined kinds of animals but deny that man is the product of evolution, I’ve decided to go through our genomes and compare it with chimps (and other species). Firstly, I’ll define the genome. This is essentially the complete genetic sequence of an organism. Prokaryotes (eg bacteria) contain one copy of this sequence, and Eukaryotes (like ourselves) generally contain two copies of this information (some organisms are polyploid and contain many copies). In sexually reproducing organisms, there are often two separate sex chromosomes, so when a genome sequence is referred to in these organisms, it means all the different somatic (non sex) chromosomes plus a copy of each of the sex chromosomes (eg X and Y in humans).

In case anyone does not know, our genome has 96% identity with that of the chimp. That sounds a small difference for two easily distinguishable species. However, our genome is 3,200,000,000 base pairs (letters) long. However, that is equivalent to 128 million differences.

My plan is to go through the chromosomes from the first (largest) to the smallest (Y) and highlight the tell tale signs of evolution – signs shared with chimps – or derived from a common ancestor. Chromosomes often contain tell tale pieces of “junk” DNA (perhaps up to 50% of the genome is non functional junk acquired during our evolutionary past) or even fusions that show the ancestry of the organism. This will take some time, but I hope to learn a lot from it myself.

Interspecific Brood Care

I’ve been thinking about a few posts on cichlid evolution at the moment, but don’t have too much time. These fish make Darwin’s finches look like absolute beginners in evolutionary terms. Lake Malawi alone has at least 500 species and many geographical variations – all thought to have evolved from a single (maybe 2) common ancestor(s) in a few million years. For anyone with some spare time, this site provides some photos of them. A small section on trophic (feeding) adaptations can be found here.

Anyway, as a short post, I would like to introduce some Central American cichlids. Parachromis dovii is a rather large and nasty predator. One problem it faces is the predation of its fry by other fish. Next up is Theraps (aka Hypsophorys, aka Copora) nicaraguense. This is a medium sized fish, but is easily bullied and can be out competed for breeding sites by the aggressive Archocentrus nigrofasciatus. A 12 cm male is a very big fish for this species and I have had 6-8cm fish attack me and draw blood when looking after their fry. There is another smaller species, Neetroplus nematopus, which by all accounts is even more aggressive. So, T. nicaraguense has a problem, these little fish get all the good breeding sites. The solution is rather unexpected. See if you can guess: P. dovii is a major predator of N. nematopus and A. nigrofasciatus………


Give up?

T. Nicaraguense helps bring up the fry of P. dovii and is therefore tolerated by them. Their own fry also benefit from the numbers of P. dovii fry in the area – a predator is more likely to grab one of them as they are more numerous. Som studies estimate that P. dovii would face extinction in some areas if it was not for this interspecific co-operation. There are some costs though, as P. dovii will also eat some juvenile T. nicaraguense too. Thre have also been some recorded incidents of T. nicaraguense “cheating” on the deal too. However, that is evolution for you – cheating can be of benefit to the cheats until their numbers rise and make it disadvantageous – if P. dovii numbers drop, so do T. nicaraguense numbers. Natural selection will then start to select against the cheats and a new equilibrium will be reached – this may then allow another cycle of cheating……

There are obviously some implications for the evolution of moral behaviour here – by helping others, you are actually being selfish and helping yourself. This is something the religious just don’t get – they think being selfish means that you kill and eat every thing – not cooperate.

Favorite Photo Of The Year

Robert Craig has put up his favourite photo of the year here. That got me thinking about mine, and here it is:

It was taken by Dave in January and shows me on Ben Ledi. Some more photos of the day can be seen here on Dave's blog.

My favorite photo that I took was of a group we passed who were being instructed in winter techniques in Coir na Tullaich on Buachaille etive mor (below)

The one that Craig chose was a close runner up.

Euthyphro, Logic And The Impotence Of Moral Theology

Mark left an excellent comment on the previous thread. He said:

“for morality to be absolute, it must not be able to have been different; in other words, god’s nature from which the absolute morality flows, must necessarily be the way it is. But, if god is necessarily the way he is, then there must be laws that make this the case, and these laws must therefore precede or be higher than god. Thus god becomes essentially a middleman and is not necessary. If, on the other hand, god's nature is not necessarily the way it is, then morality is relative to his non-necessary nature, and thus not absolute.”

This is essentially the Euthyphro dilemma. The problem is that either god is not necessary for morality, or nothing is good until god commands it. Therefore, morality is relative to the tastes of god and there is no reason then why evil acts could not be considered moral if god so choosed.

To try and get around the dilemma, theists often claim that it is not a dilemma and that morality is fixed by the very nature of god. This is however nonsense. If god’s nature is fixed, he is still a god of moral relatives. He just so happens to have a particular set of moral values. He could still be evil. There is no absolute law.

Another problem is that if he can not change his mind, then he is either beholding to a law greater than himself, or he is not omnipotent. The omnipotence of god is of course logically absurd. He could not make a square circle for example. This also means that god is not necessary for the laws of logic either, as he himself must abide by a higher law.

Other things god could not do include making a being greater than himself (already defined as the greatest possible being – what ever greatness means) or make a weight so heavy that he would not be able to lift it.

Theology is just one big inconsistency after another. How can something so problematical have any value? Moral law is one of the “evidences” Christians cite for god, but it is not a tenable position – even if we assume god exists to start with. Christianity needs absolute moral laws or the concept of sin is meaningless. If the concept of sin is meaningless, then the idea of god killing himself to appease himself as punishment for our sins is just absurd – but then, there are lots of reasons to think that is absurd.

Compsognathus Longipes's Last Supper

OK, one final dinosaur post for the weekend. In the poo post, the implication of carnivory for “ original sin” was touched upon. I never tire of laughing at this article written by everyone’s’ favourite bearded cleric, where he thinks tsunamis, volcanic eruptions and death are the result of eating an apple. I particularly love the paragraph that starts off saying that atheists are becoming more frustrated as our aguments are shown to be limited - he then goes off on a truley ignorant rant of biblical proportions - and he claims to accept evolution, which makes his ignorance all the more incredible. It is a common belief that I don’t think many Christians think about seriously enough. Anyway, here is another example of carnivorous behaviour before the arrival of man. It is a drawing of the rib cage of Compsognathus longipes. Inside, a small skeleton of Bavariasurus (in darker shading) can clearly be seen. It appears to be swallowed whole.

Young earth creationists have to deny this comes before man and claim it ate it’s meal after man and woman sinned. However, let’s ignore the serrated teeth that are so good for hunting for a moment and ask why Elephants or squirrels don’t bring down lions and eat them. Could it be because they are not adapted to be hunters? Theists who accept evolution are confronted with the only credible alternative: god caused large scale industrial suffering to bring his “flawed” masterpiece into being.

Finally, to both sides: a challenge – show some evidence that 1) man existed with dinosaurs and explain the consilient nature of fossil dating techniques, or 2) a role for god in directing evolution that meets the standards of a scientific theory.

T. Rex, Warrior Or Wimp?

I linked to part of this program on the feeding behaviour of Tyrannosaurus rex in the previous post, but it is worth a view in its entierty.

Incidentally, David Houston was one of my Zoology lecturers

Jumbo Dinosaur Jobbies

Having a degree in Parasitology tends to familiarise you with the value of Jobbies; as one of my tutors said, “shit is tour bread and butter as a parasitologist”. This is because many parasites produce cysts or lay eggs that pass out the body in the faeces. These infect the next host and this spreads the disease. The eggs are often characteristic to a particular species or genus. So, you can work out infection rates and parasite loads of particular species in individual hosts. One quarter of the world population is infected by just one parasite – Ascarais lumbricoides. One of my class mates became infected with this and the first she knew of it was when she saw 20 one foot long worms thrashing in the toilet bowl. If you want to feel uncomfortable (or lucky) check out this picture out of someone who has just been "wormed"
Another thing that shit can tell you about diet. I remember one gross practical class where we had to sift through someone’s fudge. It was supposedly collected in the Dominican republic, but contained saw dust- turns out, it had been supplemented with veterinary material. What I remember most though is the huge chunk of onion in it. The person obviously ate onions, but didn’t chew properly or process their food that much either (probably the prof). Apparently, the prof had just discovered that not processing food properly can contribute to severe malnutrition in areas where intestinal parasites are prevalent. He found lots of unprocessed and therefore indigestible corn in the crap.

So, shit can tell you a lot about living animals. Now, to the main point of the post – dino poo. Fossil jobbies are called coprolites. We know for example that pines were on the menu of some dinosaurs, and they were clearly capable of grinding it down – as would be inferred from the structure of the teeth batteries of some herbivores. What is particularly interesting though is the Jumbo Jobbie shown below. It is a possible Tyrannosaurus turd, and measures about 17 inches long.

This majestic Bondi cigar even contains bone fragments belonging to a sub adult herbivore. The large quantity of bone in the meal suggests that the dinosaur was not careful about butchering its meal. We know that Tyrannosaurs were capable of biting through bone, as fossils showing pre-mortem Tyrannosaur bites have been found. These include Hadrosaurs with “healed” wounds that were excised by T. rex bites (about 4 minutes in), and even a T. rex with another T. rex’s tooth embedded in its rib- with an abscess formed around it. Those wanting a laugh (or to annoy themselves) should listen to creationist nincompoop Ken Ham’s short talk on the matter here. I don’t know which is the bigger pile of shite, but at least he knows the consequences of a meat eating dinosaur for his creationist myth that all animals ate fruit and veg before two mythical human beings ate a mythical fruit, and that supposedly caused death, volcanoes, earthquakes and the Mc Chicken Sandwich. That’s why he has to deny evolution. I touch on the absurdity of this claim here (incidentally, that is a Carcharodontosaurus skull at the top of the page).

The other thing that I want to mention is that parasite eggs have been found in fossil shit too (below from left to right Entamoeboides cyst, and two Ascarid eggs). I find this fascinating, and it tells us something about the health of these animals, as well as their ecological interactions with parasites. This is not the first time evidence has popped up for dinosaur parasite interaction, but is certainly the best – and all before man “polluted” creation – yet more evidence that the creationists need to go to farcical lengths to deny.

Finally, we know that some dung beetles even used dino poo – shit’s not that shit after all.

Cure For HIV?

This article hints at a possible cure for HIV. It is interesting to note that the patient was originally being treated for leukaemia. One way of doing this is to kill the patient’s bone marrow. Often, the cells responsible for leukaemia arise in the bone marrow, so targeting that can resolve the cancer. The aberrant cells are often sensitive to the same treatments that kill the bone marrow. The problem is that all our blood cells (red and white) ultimately arise in the bone marrow from stem cells, so, the patient will die if they are not given a transplant of healthy cells. The interesting thing about this story is that the HIV positive patient was given a transplant of bone marrow from a donor with a mutation in the chemokine receptor CCR5. HIV needs two proteins to get into and infect cells. One is CD4 which is found (but not exclusivley) on “helper” T lymphocytes - this is one of the reasons the virus causes immuno-deficiency. The other protein is CCR5. This means that the virus has a hard time infecting the donors’ lymphocytes. As a result of this, the recipient has no detectable HIV a full 20 months after treatment. Caution should be taken however, as certain cells in the brain also express CD4, and are known to act as a viral reservoir – otherwise a normal bone marrow transplant – or even “cleaning up” the patients own bone marrow would be a possible cure .

This is one reason why stem cell research is important. The possibility exists that the patients own stem cells could be modified to not express mutant CCR5 – or even no CCR5. Technologies already exist to put genes into other animals. We can even insert mutants or knock out the gene entirely. We can even choose what tissues to modify, and when to modify them. Basically, if the religious don’t like that, they can go buy a dildo. I’ll stick with trying to save people.

Belated Remembrance

I followed the link to one of the christian blogs that linked to the child abuse blog. One of the commenters there was under the delusion that atheists consider children meat machines. This is a thoroughly disgusting point of view. As part of remembrance day, I listen to "The green fields of France". The lyrics are really sad and hammer home the personal tragedy of those who suffered and died, leaving a void in the lives of others. To say that as an atheist that I see people as meat really is messed up thinking. Do these people really need faith to feel sorrow and pity at the thoughts of the hopes and lives of people being ended? To me as an atheist, I believe these people are gone for ever - a one off event that is easily and tragically snuffed out. This makes life more valuable and people more precious - not something to be tossed away- or even ended in the name of some false god.

Another powerful image is that of the final scenes of "Blackadder goes forth". That is deeply sad, as you were laughing along with the characters, then they go to the trench. There is a brief moment of hope when the guns go silent and the tragic line "hooray, we have survived the great war of 1914-1917" is proclaimed. Sweeping to the poppy field after the group goes over the top is a real tear jerker - you just know they died!

Separated At Birth?

Shame Brian doesn't dwell in the Blogosphere. I'll just have to email it to him :-)

Shrimp On A Treadmill

This video shows a shrimp on a treadmill. The study was aimed at comparing the difference between healthy and sick shrimps in travelling to get food. Not surprisingly healthy ones were faster and ran for longer than sick ones. What is surprising however, is the fact that the healthy ones can run up to 66 feet a minute and keep it up for 3 hours. Beat that Paula Radcliffe - and it doesn't have to stop to piss in public either.

The Value And Curse Of Philosophy

A couple of us got together from richarddawkins.net last week and the value of philosophy was discussed. One of the group was skeptical (as I once was). We discussed that one of its values was to think about how consistent your thinking is and how how sound the premises are that you base that thinking on. A position is more likely to be valid if both the premises can be argued for and the argument is internally consistent. This creates a real problem for those who claim supernatural phenomena explain certain aspects of the universe and human nature. How do you make claims about the untestable. At best, a theological argument can be consistent, but its premises can not be reasonably argued for. An example of a consistent argument would be only god eats pencils, therefore anything that eats pencils is god. I went to school with a girl who ate pencils. Therefore, she is god. However, how sound are the premises such an argument is based on? How do actual claims about god differ?

Here is another consistent argument. Watch it and think about the following.

How do we know it is not the truth?

What tools do we have to investigate this?

Is it reasonable to reject this possibility?

It could be true, like a deistic world view could be true, but what evidence is their to back it up

And yes, it was the blondes that drew my attention to the video - wahey, down boy! :-)

Epidexipteryx Hui; A New Transitional Fossil

It looks like another of those pesky supposedly non existent transitional fossils that Satan buried to fool people has turned up in Inner Mongolia. The new fossil, an ancestor of birds, is described in the current issue of Nature is called Epidexipteryx hui. It is around 152-168 million years old, making it possibly older than Archaeopteryx (155 -150 million years old). Like Archaeopteryx, it is a maniraptorian dinosaur, but somewhat more primitive. However, it lacks flight feathers, but has two long pairs of long tail feathers (although simpler than modern feathers). This adds further weight to the idea that feathers evolved for purposes other than flight – perhaps display and or insulation (other parts of the body are covered in barbed hair like filaments). The feathers would then become a selectable pre-adaptation that enabled the evolution of modern avian flight.

E. hui

Bloodless Icefish Makes Creationism Look (Even More) Anaemic

Time for some more creationist bashing. I am preparing a post on the evolution of antifreeze proteins in Notothenoid fish. However, there is also something else interesting about this group.

Let’s see people draw their own conclusions.

Fact 1: All vertebrates have genes for haemoglobin (see fact 3).

Fact 2: 16 species of Notothenoids do not express haemoglobin. (the only known vertebrates without haemoglobin)

Fact 3: 16 species of Notothenoids do not have any functional haemoglobin genes.

Fact 4: 15 of these species have no beta haemoglobin gene and retain a shortened form of the alpha gene.

Fact 5: The remaining species (Neopagetops isionah) has two non functional pseudogenes for beta haemoglobin. One contains only part of the 3rd exon and is very similar to the same fragment of the closely related and haemoglobin bearing Dragonfish. The other pseudogene is closely related to that of other Notothenoids.

Your conclusion ladies and gentlemen: Evolution or creation?

A more technical account can be found here.


Fundies, it may be worth bearing this in mind:

Hebrews 6:18 “God did this so that, by two unchangeable things in which it is impossible for God to lie, we who have fled to take hold of the hope offered to us may be greatly encouraged."

But, then again, maybe not….

2 Thessalonians 2:9-12 “The coming of the lawless one will be in accordance with the work of Satan displayed in all kinds of counterfeit miracles, signs and wonders, and in every sort of evil that deceives those who are perishing. They perish because they refused to love the truth and so be saved. For this reason God sends them a powerful delusion so that they will believe the lie and so that all will be condemned who have not believed the truth but have delighted in wickedness.”
Ooops!

Maybe that means that you can’t trust any of the bible. The evidence above exists despite what your book says about it.

What Is Life?

The question of what is life came up over coffee this morning. It is actually not that easy to put a finger on. Some things we have no hesitation in calling alive – like ourselves. With others it is less obvious.
In my first ever biology class at school, I was taught that there were seven characteristics of life, which if memory serves me right include the fact that life has to feed (acquire building blocks), move, grow, respire (produce energy) be organised into cells, be sensitive to the environment and be adaptable. I would also add that it has to locally reverse entropy too.

So, we all do these things, but are they universal? Viruses for example don’t grow or move. They don’t even respire in the sense that they make their own ATP. They get that from their host cells. They are not cellular in nature and are only adaptable in the sense that mutations can occur – they can’t adapt in the sense that a Venus flytrap can turn on antifreeze proteins when they are chilled. So, are viruses alive? They do reverse entropy and appear sensitive to the environment in that some can use cues inside the host cell to reproduce – Herpes for example lies latent for long periods of time.

So, are viruses alive?

Many invertebrate embryos are not initially cellular either – they are syncitial (no cellular divisions between nuclei). Slime Moulds also spend much of their lives in a syncitial state too.

What about salt crystals? It can grow by reversing entropy. Split them in two and given the right conditions, they can grow into two new crystals. It is sensitive to the environment; it “knows” when to grow and when to dissolve. Its component parts have all the information needed to produce an identical crystal, and is organised into unit cells, so is it alive?

Discuss!

Picture Round

This is more one for the climbers. Following on from Dave's mountain and bothy tests, I thought I would see if anyone can identify these.

1 Where is this? (I only think I know, so confirmation will be nice).

2 Name the peak and the climber.

3 Name the peak this is taken from (I'm sure someone I know wasn't there).

4 Name the bothy.

5 Would you tell this guy he looks like Martin O'Neill?

6 What drugs is he on?

7 Name the islands and where it was taken from

8 Name the bothy and who supposedly lived in a cave on the hill on the left? (Other than Charles Edward Papist)

9 Cold is God's way of telling us to burn more Catholics, so who is up the chimney? Also, name the bothy.

10 Name the Bothy. Dave and Craig can't answer this one. The other Dave can. Everyone can name the physical feature in the background. What physical feature is the glen also famous for?

11 What hill was this taken from?

12 Name the two faults. The second is below the knob on the right. (Dave may not answer)

13 From last weekend - who couldn't make it? :-)

Wasp Stings Young Earth Creationism In The Bum

Over at the Mac Gafraidh blog, I questioned Chelsea on whether she took the following verses literally:

“And God said, Behold, I have given you every herb bearing seed, which [is] upon the face of all the earth, and every tree, in the which [is] the fruit of a tree yielding seed; to you it shall be for meat. And to every beast of the earth, and to every fowl of the air, and to every thing that creepeth upon the earth, wherein [there is] life, [I have given] every green herb for meat: and it was so.” (Genesis 1:29-30).

Like all biblical literalists, she said that she does believe this. These verses basically says that all animals were created to be vegetarian - an absurd position to hold. We need only think about carnivores and their killing adaptations like the canines of big cats that that are so good a piercing flesh – and just happen to be at the right spacing to dislocate the cervical (neck) vertebrae of their main prey species. Then there are species of fish specifically adapted to eat scales and fins (eg Perissodus sp and Exodon paradoxus). One species, the Sabre tooth blenny (Aspidontus taeniatus) even mimics that Cleaner wrasse (Labroides dimidiatus). Cleaner wrasse pick parasites, which are themselves highly specialised non vegetarians (see my article on Trypanosomes for an complex example of adaptation to living inside and off of another species). Fish approach cleaner wrasse to be serviced and the wrasse signals back. This signifies the intentions of both parties and wrasse are even allowed into the mouths of large predators, where they are unharmed. Sabre tooth blennies on the other hand do a similar display but instead of cleaning the other fish, they take a chunk out of it. This is a problem for YECs.

However, I want to use an example that Darwin used (more against the idea that god was a loving creator). He cites the Ichneumonoidea – a group of parasitoid wasps that lay their eggs in the living bodies of their insect hosts (usually caterpillars).

Darwin writes:

“I own that I cannot see as plainly as others do, and as I should wish to do, evidence of design and beneficence on all sides of us. There seems to me too much misery in the world. I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of Caterpillars, or that a cat should play with mice.”


There are several special adaptations that are needed:

A suitable host must be located.

The host must become infected – hence the long ovipositor. Some species (eg Ephialtes manifestator) can locate their host through wood and drill to them . Other species also paralyse their hosts, so the toxin is yet another adaptation. Many species also parasitize dangerous spiders so avoiding becoming dinner is another adaptation.

The larvae must evade the hosts’ immune system.

The larvae must keep the host alive and fresh for as long as possible to ensure fresh meat.

In the example below, involving the Blue butterfly as a host, we see several adaptations. These include locating the host and distinguishing it from ant larvae (bear in mind that the ants can’t even do that) and avoiding being attacked by the ants. This latter applies to both infected pupae and adult wasps.

So, the fundamentalist is left with a problem. How did these specific adaptations arise if animals were intended to be vegetarian? They either have to claim god made them that way (lacking any evidence) or claim that some evolution occurred – although that would have to be incredibly fast for a vegetarian wasp to become a wood drilling, ant avoiding spider paralysing, immune system evading parasite.

Of course, the problems for YECs don’t stop there. They believe in the flood. There were only of two of every non clean kind on the ark. That means no ant colony to feed the blue butterfly larvae for the Ichneumon to eradicate. Mind you, the ants would have been killed by lancet flukes (Dicrocoelium lanceolatum). That’s if Anty the ant eater didn’t get them first.

Pretty Picture

This shows the ventral nerve cord(green) and muscles (red) of a freshwater leech. The blue "circles" around the chord are the nuclei of nerve cells associated with the chord (one node per body segment). Branches of the chord can be seen going into the body segments. More nice photos can be seen here.

Vasopressin Receptors And Hand Baggings

This paper on the genetics of human pair bonding came out last week. The idea that genes affect behaviour is not a new one, but the extent of their influence is argued over. Usually it is evangelicals, whose world view is dependant on the absurd notion of free will and its implications for “sin”, that make loud denial noises at the thought that our choice making may not be absolutely free. Another problem they have is that if our genes affect our behaviour and personality, then the mind becomes all the more physical and ideas of a supernatural consciousness become even less likely. From studies on flies, sexual orientation can be absolutely altered by disrupting the fruitless gene, so the precedence is there.

This recent study, which is quite timely after a hand bagging incident at work because of someone having an affair, shed some light the genetics of human pair bonding. It has been known for some time that the brain “hormone” arginine vasopressin (AVP) has an association with pair bonding in Voles. There are 3 species of closely related voles; montane voles (Microtus montanus), meadow voles (Microtus pennsylvanicus), and prairie voles (Microtus ochrogaster). The first 2 are non monogamous, whereas the prairie voles are monogamous. It was found that one of the proteins that recognizes the AVP; the vasopressin 1a receptor (V1aR) was responsible for the difference. Not surprisingly, drugs that affect the activity of this gene inhibited pair bonding in prairie voles. Furthermore, it was found that it was the promoter (control region) of the gene that determined the type of social bonding behaviour that developed, and a rather elegant study that swapped the promoter between species found that non monogamous voles could be made more like the monogamous species. The difference in promoters is an extra 428 base pairs. It is thought that this might alter the amount of V1aR in the relevant brain areas (ventral forebrain). Indeed, increasing the amount of V1aR in the ventral forebrains of non monogamous meadow voles turned them monogamous.

So, what about humans? Well, it turns out that the V1aR promoters comes in several different forms. One of these forms called the 334 allele has shown a strong correlation with marital harmony in studies of twins. There was no effect with women, but in partnerships where the man carried two copies of the 334 allele, 34% of marriages experienced a serious crisis/ threat of divorce in the last year. This figure fell to 15% in men with no copies of this allele. Interestingly, men with two copies were twice as likely to cohabit rather than marry when compared to men with no copies of the allele.
Other studies have also corroborated this by showing that 334 affects RNA (and by extension protein) levels in the hippocampus of post mortem subjects. Studies in healthy volunteers have also demonstrated an association between 334 and activation of the amygdala, a part of the brain already known to be involved in pair bonding.

It would be unlikely that only one gene affects this behaviour, and not surprisingly the dopamine system has also been implicated, so our pair bonding behaviour is probably the result of the interaction of several genes.

Anyone interested in the nature nurture debate may be interested in Matt Ridley’s talk here.

Black Hole Forms Stars At Galactic Centre

This Video (taken using the Hubble Space Telescope) shows the orbits of stars around the super massive black hole at the centre of our galaxy. It is thought that the black hole itself may be responsible for the formation of these stars.

The original article appears here.

Large Hadron Collider

Bit unusual for me to branch into physics, but it has come to my attention that the turning on of the large hadron collider may be delayed due to a Law suit. It has been filed because of fears that it may cause a black hole that could destroy the earth. So, while we are waiting on the edge of our seats for it to start producing data, here is a little song to keep us amused.

Stephen Hawking's voice in this reminds me of the time a couple of us tried to compose a message from him (with a ZX spectrum) to leave on a friends answer phone - crazy days :-)

Crazy question for lee: could a black hole be transported in a rocket?

Archaeopteryx: The Most Beautiful Fossil Ever!

One of the most beautiful of fossils has to be the “Berlin specimen” of Archaeopteryx lithographica (below). This was discovered in the Solnhofen limestones in 1877, and dates to about 155 -150 million years ago (or 155 -150 million years BA* ). The first specimen was discovered in 1855 but its importance was not realised until 1970. When I first saw a picture of the Berlin specimen (probably about age 11) I became convinced about the truth of evolution. It is a wonderful example of a transitional form (or at least a close relative of one). This specimen clearly shows the presence of feathers on a very reptilian skeleton. There are reports that the specimen had a plume of feathers on its head, but these were lost during its preparation. Some specimens without the feathers preserved were once thought to be coelurosaurs. Given its importance, it is not surprising that creationists have to deny it is a transitional form. They have absurdly claimed that it is a fake (Even AIG has to admit nowadays that it is not). They desperately try to claim that it was a perching bird (with reptilian tail and teeth?). Hovever, a recently discovered specimen clearly shows that it was unable to perch (It did not have a reversed toe). Creationist even try and quote mine Alan Fedducia who claims birds are evolved from a non dinosaurian lineage. What they don’t mention is that Fedducia still believes they are transitional forms butt share a common ancestor with dinosaurs, rather than being descended from them. This theory has been pretty mush refuted nowadays. Creationists have also tried to push the idea that Protoavis was a primitive bird that lived about 70 million years before Archaeopteryx. Therefore it cant be the ancestor of birds.

There are a couple of problems with creationists using this line of argument. The first is that they deny conventional dating techniques are accurate – they cannot then claim anything about which specimen is oldest. Then, they say that Protoavis is more birdlike than Archaeopteryx. More bird like? That is like an admission of grades of “birdiness” – you know, the way that evolution works. Internal consistency is not something creotards are known for – they pick and choose as long as they can pretend that it agrees with the mutually exclusive accounts of genesis 1 and 2. Anyway, let’s go with the scientific ages. Is there a problem? I would say there are two good reasons why there is no problem. The first being that Archaeopteryx could be one of those long lived “transitional” forms we see today – like the lungfishes or coelacanths (note I am not saying these are transitional forms, but transitional like forms). The second and most probable case is that Protoavis is not a bird at all. The fossils that we have are very poorly preserved (many diagnostic bones are missing and the skulls are badly crushed (you know, all the usual complaints that creationists use when they need to deny something is a transitional form (see the Ambulocetus post). It is generally thought in the peer reviewed literature (enter creationist conspiracy theories) that Protoavis is actually not of the bird lineage.

So, what makes Archaeopteryx a transitional form? Features found in Dinosaurs (particularly the group called the Dromaeosaurs that includes Velociraptor) are tagged with a D and those found in birds are tagged with a B.

Skull

Contains teeth (like those of small theropods) (D)
Long external nostrils (B)
Nasal opening located at anterior of the snout and separated by large pre- orbital fenestra (hole) (D)
Nasal bones long and depressed (D)
The quadrate and quadratojugal (two upper jaw bones) are not sutured together (B)
Brain case intermediate in structure between birds and dinosaurs (B,D)
Palatine bone dinosaur shaped (D)
No bill (D)

Vertebrae

Neck vertebrae have concave articulations (D)
Neck S shaped (B,D)
Neck attaches to rear of skull (D)
Sacrum contains 6 vertebrae (D)
23 caudal (tail) vertebrae (D) However, this is a reduction in the total number comaired to other theropods (can number over 50). Birds have several that fuse to form the pygostyle (they are more reptilian during development).

Limbs and associated bones

Strap like scapula (shoulder bone) (B,D)
Fused V- shaped wishbone (essential for bird flight (B,D)
Rudimentary sternum (breast bone) This is essential for flight muscle attachment and is more dinosaur like (B,D)
C- shaped (semilunate) carpal (wrist bone). This is essential for bird flight (B,D).
Clawed manus (hand) (D). Interestingly, one modern bird (the Hoatzin) retains a rudimentary claw in the juvenile.
Pelvis dinosaur shaped (D)
Femur head is orthogonally turned (D)
Astralagus (ankle bone) has a process extending upwards into the tibia (a diagnostic characteristic of theropods) (D)
The feet are dinosaurian. Contrary to creationist claims, there is no reversed hallux (big toe) that allows perching (D)
The second toe is hyper flexible as in dromaeosaurs (D)

Other features

Numerous hollow bones (B,D)
The presence of feathers (B, D).

There are many more features that show the link between birds and dinosaurs. Cladistic analysis actually reveals Archaeopteryx to be more dinosaur than bird. This is only a small fraction from a single species. A list of other intermediates (some more bird like, others less so) can be found here.

*BA (years Before Apples) for those who believe that eating a fruit somehow caused death to enter the world (you know who I mean).

The Platypus: Piss Poor Creationist Scholarship Or Wilfull Mendacity?

Platypuses (Ornithorhynchus anatinus) are excellent examples of primitive mammals that retain some reptilian features – such as egg laying. But, for some reason creationists seem to claim the platypus is a problem foe evolution. I often get this link thrown at me as if it proves that platypuses are a mosaic that contain parts from reptiles, mammals and birds, and therefore could not have evolved.

Let’s look at some of the creationist claims and expose more lies and misrepresentation.

1. It has a bird’s bill.

No it doesn’t! A bird’s bill is mainly made of the protein keratin. A platypus’s is leathery, flexible and contains numerous sensory pits

2. It lays eggs like a bird.

It may lay eggs, but they have leathery shells like reptile eggs. They are not surrounded by a shell like those of birds. This is what you would expect with the evolution of mammals: egg laying “reptiles” becoming egg laying mammals, which become live birth giving mammals. So, where is the problem?

3. It has a spur on its hind limb that produces a toxin similar to that found in reptiles.

Again, so what? That is what you would expect if they evolved from reptiles. In the link above, the author is also misleading. The platypus toxin actually evolved independently of the reptile venom. Both evolved from beta-defensin genes, but different classes of them , so although they are similar, there is no claim that one is descended from the other – that is creationists being naughty trying to play up the mosaic idea. The plan is to say Ha! Look they are almost identical to reptiles, but wait, they have genes found in birds too. Therefore evolution is wrong.

4. They contain genes for the egg protein vitellogenin. As the article claims, these genes are also found in fish and birds.

Again, we have some more naughtiness by omission. As the article is read, there is no mention of amphibians and reptiles. So, if it is not present in these groups, that would be a problem. Being a scientist, I’m not scared to make a testable prediction. I predict these groups contain vitellogenin genes (why don’t creationists make testable predictions? Answers on a post card). So, lets search the best database for finding peer reviewed scientific research publications (try it yourself). Let’s search for vitellogenin and amphibians. Well, no surprise there, 398 articles containing those key words, and plenty of papers on African clawed frogs (Xenopus laevis). What about searching for vitellogenin and reptile? This time, we get 62 publications describing its occurrence in snakes, crocodilians, iguanas and turtles. So, the evolutionary scenario of fish to amphibians to reptiles; which split into birds and mammals (via egg laying mammals) stays intact.

5. They contain ZPAX genes that are found in birds, amphibians and fish.

Note, there is no mention of reptiles here. That’s because they have not been looked for in reptiles – you won’t find it in pubmed. Here is another prediction for creationists, reptiles possess these genes – wait and see. The organisms that it has been studied in show a definite evolutionary relationship between groups, based on gene similarity see here.

6. Some of the sex chromosomes are like those of birds.

Platypuses have an unusual arrangement of sex chromosomes - there are 10 of them. They do follow the basic mammalian X Y sex determination pattern, with all X causing females and Xs and Ys together causing males. If they have evolved from reptiles, we would expect some similarities to reptilian sex chromosomes. Reptiles form 2 main groups when it comes to sex determination. Those were environmental factors determine sex and those where sex is determined by sex chromosomes (Z and W for female and two Zs for male). This is the system that birds have inherited. In the platypus, the Y chromosome seems to have evolved independently, with the X chromosome alone showing some similarity to both the reptilian and avian Z chromosome – from which it evolved.

7. They contain some avian like micro RNAs.

Guess what; at least one of the X chromosomes encodes some micro RNAs (see above).

Creationism has no evidence of its own and relies on dishonest misrepresentations and straw men concerning evolution.

I’m off to put some brights cards under the wipers of cars that have “you make Jesus cry” (puke-arama) stickers on them – again!

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.