The Evolution Of Lady Bumps

You know how it is, you search for something and something unrelated (remember, I said unrelated :-) ) pops up that grabs your attention.

This video gives an account of the evolution of the mammary gland from simpler secretory tissue that has an immunoprotective role.

I'll post what I was originally searching for in a day or two.

Book Club Idea

I've been thinking of trying a book club thing for a while. It would depend on people indicating that they are interested though. Since regular posters have expertise in a wide variety of subjects, I think this would be a good opportunity to get into depth about subjects that are not our area of expertise. Perhaps folk could indicate if they are interested and recommend some books. The offer is open to lurkers and Christians too - differing points of view would be good.

I would suggest either The selfish gene, The making of the fittest, Darwinism and its discontents, The problems of philosophy or Godless morality.

We could also take turns hosting one in an area we are familiar with.

Let me know what you think and we can try and arrange something.

Convergent Evolution Refutes The "Argument" For A Common Designer

The “argument” from design is basically nothing more than saying god did it. We often see strawman arguments comparing things like bicycles, that we know are designed, but don’t acquire mutations that are passed on to their offspring where they are selected with examples of organisms, which do accumulate and transmit selectable mutations. No matter what you say to a creationist, he will just say “ah well, that’s just the way god made it”. They can never predict how it would be. One piece of evidence for evolution is the existence of homologous structures in groups of organisms. These are structures built on a similar “blue print”. The classic example is the vertebrate limb, where the different bones can be identified in various structures from flippers to wings. Creationists of course claim that this is the work of a common designer and not the result of common decent. A problem in consistency then arises when you point out analogous structures (those that perform the same function, but are structurally different; the classic examples being the wings of birds and insects. Surely then the creationist should argue that this is then evidence of more than one designer – the problem of course is that they only believe in one god and pull an answer out of their assess like “god made it that way for a reason”, which really isn’t an answer at all. Using their straw man analogy further, the person (more accurately people) who designed your computer did not design the seat you are sitting on. Why then should we assume fish have the same designer as earthworms or palm trees? The creationist response of course is that their god did anyway – no evidence, just an assertion.

Although the planet “allows” life, it is not exactly life friendly. Life has many problems to solve – too hot, too cold, too wet, too dry, too much oxygen, not enough oxygen etc…. Sometimes we see different species “solve” the same problems in similar ways. Would we then not predict that a designer should engineer in the same solution?

Previously I posted on the loss of haemoglobin genes in ice fish as an example of evolution over a long period of time. These fish have another interesting adaptation; they produce antifreeze molecules. There are two unrelated group at either pole that produce nearly identical antifreeze glycoproteins (AFGPs). These are the northern Arctic cods (superorder Paracanthopterygii) and the Antarctic Nototheneiods (superorder Acanthopterygii). These proteins, which bind to and prevent the growth of ice crystals, are based on repeats of the amino acid sequence (threonine – alanine (occasionally proline)- alanine)n. The sugar galactosyl-N-acetylgalactosamine is covalently linked to each threonine in the repeat sequence. There are several forms of the molecules that vary in the number of repeats of these three amino acids, but they are all encoded by the same gene: there are sites in the protein that are later processed to produce AFGPs of different lengths. So, here we have two unrelated groups with almost exactly the same protein serving the same role – creationists must be cumming in their pants at this point.

However, if we look at the structure of the genes, there are significant differences. To recap, (eukaryotic) genes are composed of exons (that appear in mature RNA sequences) and introns (which do not encode for proteins and are chopped out of mature protein encoding RNA (which links protein encoding instructions from DNA to proteins). The gene from the Arctic species Boreogadus saida contains 3 exons (E1-E3 of Bs3-1 Figure1), whereas the gene from the Antarctic species Dissostichus mawsoni contains only 2 (Dm3L).

Another interesting feature is the sequence of an area called the signal peptide (this directs the newly synthesised proteins to particular areas in a cell). These are totally different – as can be seen from their single letter amino acid sequences.

Fig 1

One final difference is the actual gene sequences themselves. There is more than one way to code for most amino acids, and the sequence threonine – alanine – alanine can be encoded by the sequences (codons) ACA, ACT, ACC or ACG for threonine and CGA, GCT, GCC or GCG for alanine. What we find is that the codon usage is different in the two different genes. B. saida uses the codons ACA/ACT (45%/42% for Threonine)-GCA/GCG (51%/30% for the first Alanine and GCA/GCG (53%/37% for the second Alanine). D. mawsoni uses ACA (85% for Threonine)-GCG/GCT (39%/55% for the first Alanine) and GCA (95% for the second Alanine). Basically, the sequences are different suggesting a different origin. This similarity in protein sequence is an example of convergent evolution.

The original publication can be found here

One final problem for creationists is that a prediction of evolution is that genes arise from ancestral genes, so we should not be surprised to find a candidate and a putative mechanism for the evolution of these proteins. Guess what creationists, for D. mawsoni, the ancestral gene is trypsinogen. Part of this gene and the control regions seem to be duplicated. Not only that, a 9 nucleotide sequence encoding the threonine – alanine – alanine repeats appears to have been further duplicated (mechanism). This is detailed here.

Oh yeah, and all this is corroborated by paleontological and geological studies concerning the appearence of these fish and the timing of the opening up of the polar oceans.

And the creationist response? That’s right, “my goddidit!” No predictive model to test required – just a bronze age book of superstition.

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.