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.