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?