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!