Tasmanian Devils And The Evolution Of a New Species Of Parasitic Tumour

Creationists love to misrepresent evolution and have an inordinate fondness for strawmen. These include:

1. Evolutionary change requires in increase in “genomic information”
2. Evolution only occurs within “kinds”
3. Speciation does not occur (incompatible with 2).

Number 1 would imply that genome size correlates with complexity. It does not. The largest known genome belongs to the single celled Amoeba dubia at about 600 billion base pairs. This is 200 times larger than our own genome. Even the lungfish Protopterus aethiopicus has a genome 50 times larger than ours. See here for phyletic comparisons .

This strawman also ignores the reality that some genes such as Abd-a can inhibit the development of complex structures such as abdominal appendages in invertebrates. Furthermore, subtle changes in regulatory sequences can affect morphological development that is controlled by genes already present. An example would be the expression of Bmp2 in the developing forelimb of bats .

One final problem for creationists is that natural or experimental deletions of parts (or the whole) of Alx-4 (loss of “information”) increases digit number in mammalian limbs – ie, less “information”, greater “complexity”.

Number 2 is just absurd as the spatio-temporal distribution of any number of transitional fossils shows. The creationist concept of “kind” is also confused.

Number 3. It happens! Deal with it creationists!

Now to the point, Jerry Coyne has posted this fascinating summary of work on tumours of Tasmanian Devils. It is significant because the tumours seem to have originated in an individual Tasmanian Devil and are now transferred from individual to individual by bite. Thus, making it a new species of parasite that is derived from the host species. It has obvious implications for all three points above. It is well worth a read.

Young Earth Creationism Is a Pain

I'm suffering from the cold just now and a simple refutation of the YEC position popped into my mind. If the Christian god supposedly created us in a perfect world with no pain or suffering, where Dinosaurs supposedly ate tofu , then why do we experience pain? Without going into the details, our bodies have complex pathways to perceive pain and produce painkillers (like endorphins). So, why can we feel pain and possess mechanisms to modulate it?

Closely associated with this is tissue damage. Why do we have complex repair mechanisms and the blood clotting cascade? Interestingly, Michael Behe claims that the blood clotting cascade is irreducibly complex and could not have evolved. Creationists want it both ways it seems. This idea is of course nonsense and is refuted here.

Here's an amusing if not painful song.

Book Club Chapter 3: Immortal Genes.

In this chapter, Carroll introduces a group of organisms called the Archaea and makes a good point about how the study of these obscure dwellers of hot springs has lead to a revolution in molecular biology and biotechnology, spawning a multi billion pound industry.

Part of the chapter deals with the basics of the genetic code (see here for more) and makes the point that some genes are shared between all major groups of organisms. These genes (about 500) are called immortal genes. Within the proteins encoded by
these genes, there are some “immortal” letters. These are basically amino specific amino acid residues that don’t vary and indicates a selective pressure to maintain these amino acids. He introduced a historical belief that by today’s standards seems obviously absurd – that it was once thought that mutation would rewrite the gene sequence over time. There reason that does not happen is because the functions of proteins are dictated by the chemical and physical properties of the amino acids that make them up. Some amino acids for example are essential for accepting or donating electrons or forming covalent bonds with other molecules. Similarly, some amino acids like proline are essential for sharp turns in the protein structure. So, the fact that some amino acids must not vary is not surprising. Because there is more than one way for DNA to encode a specific amino acid (see here), there is more mutational freedom in the DNA sequence than the protein sequence, and this can give a better idea of the relatedness of organisms.

Carroll ends the chapter by presenting evidence that the conventional view of life branching from a single common ancestor may not be true. He proposes that the Eukaryota (the group we belong to) probably arose from a fusion of the geneomes of a bacterial and an Archaean ancestor. He cites other examples of genome mixing such as horizontal gene transfer (a way to introduce new genetic information into organisms) and the endosymbiotic relationship between eukaryotic cells chloroplasts and mitochondria. Whether the bacteria Archaea have independent origins is still debatable though.

Book Club: Chapter 2: The Everyday Math of Evolution

In this chapter, Carroll introduces the role of probability into evolutionary theory, although, he accidentally displays how probability is often misused. It may be true that the chance of being eaten by a shark is 1 in 300 million – if 300 million people actually exposed themselves to shark attack each year. In reality, it is only those who enter shark populated water that are actually at risk – therefore, the real risk to those putting themselves in harm’s way is actually higher. This may seem to be a minor point, but it serves as a reminder of the misuse of probabilities by creationists. They often build straw man arguments to claim that evolution is mathematically impossible – usually involving inane positions that pretend 300 amino acids randomly coming together to form a functional protein.

Carroll does however convincingly demonstrate using models and real studies that evolution can produce new traits in a population in a relatively short time. He cites the change in the peppered moth population from light coloured to dark coloured in response to environmental pollution darkening the trees. This has probably happened on at least 4 separate occasions, as there are 4 known different mutations that cause the dark phenotype. He also gives a more recent example of pigeon populations developing a white rump. This gives them an advantage when it comes to avoiding attack by falcons; perhaps by momentarily confusing the falcon as the pigeon rolls to avoid the attack.

The rate of change in the population is proportional to the selection coefficient, and his example of mouse populations becoming all black in less than 2000 years is discussed here. He makes the point that not all individuals survive and that this is determined by the advantage/disadvantage a particular gene confers on its owner. There is also some discussion about whether natural selection acts on small or large differences between organisms. He comes down on the side of small changes. However, I would argue that it acts on both, as small changes in genes can actually cause a big difference in a characteristic. An example would be the genes controlling the sizes of tomato plants.

He introduces the idea of plasticity in species at the start of the chapter (and its role in Darwin forming his ideas of evolution) and ends with listing some of the possible types of mutation that occur – insertions, deletions, inversions, duplications, cut and paste, single nucleotide substitutions etc and will discuss some of these later in relation to evolving new functions. He also attacks the notion that all mutations are harmful. Some are actually beneficial (see above and here) and some a neutral and have no effect on function. This latter type of mutation can be used to study the effect of selective pressures on the rates of gene changes – by providing a reference point to the effect of random cumulative mutation.

Book Club - Chapter 1

In the preface and the first chapter, Carroll spells out his intentions for the book. He makes the point that DNA evidence is used in courts to convict criminals. This technology works because of subtle differences in the sequences of DNA amongst different individuals. These same differences when read as sequences can reveal relatedness amongst individuals too. The further back in time we go, the less we share with parents, grand parents and great grandparents. This time line goes all the way back to the hypothetical Last Universal Common Ancestor (LUCA) of all species. The result is that the more related that we are to a species, the more similarity we have in our DNA sequences.

Carroll points out the main points of Darwinian evolution; that are descent with modification and the selection of the best adapted for the environment. This occurs through random mutations and selection of these mutations over large periods of time. Organisms are shaped by their environments – both physical and biological. They can therefore be seen as solutions to problems. To illustrate this principle of physiological ecology, the author uses the examples of ice fish. Their ancestors had to deal with the problem of a cooling ocean. To adapt to this, they evolved some antifreeze proteins (discussed in more detail in this post). These came about through the random mutation of part of the trypsinogen gene. This provides evidence for the capacity of organisms to create new genes from old ones (discussed here and here). That is descent with modification and is an essential feature of evolution that religious fundies often misrepresent. They claim that complex structures like eyes are supposed to have evolved in a generation or two. This however is not how evolution works. It works through many small cumulative (undirected) steps that use genes that are already there. A proper model for eye evolution can be found here. Around the same time, their genes for tubulin became modified in such a way that allowed them to tolerate lower temperatures. This allows their cells to retain their normal architecture and function at lower temperatures than would otherwise be tolerable.
One problem, which is not fully discussed is that the presence of antifreeze proteins increases the viscosity of the blood. This would strain the cardiovascular system. However, cold water carries more dissolved oxygen than warm water. This meant that the fish could get large quantities of oxygen from solution. This allowed the fish to decrease the number of circulating red blood cells (which carry oxygen) allowing them to decrease the viscosity of their blood. A reduced demand for red blood cells meant that there was no need for haemoglobin – the oxygen carrying component of red cells. This lead to the loss of these genes (see here). Other adaptations include a loss of scales and an increase in capillary number in the skin – this allowed the skin to take up oxygen as well as the gills. Finally, some species also lost their genes for the oxygen storing myoglobin. This is an other principle of evolution – you lose what you don’t need through random mutation (see here). The non-functional remnants of these genes can still be found in these fish. This tells a nice story of how genomes can change in response to environmental conditions

Carroll then goes on to outline his plans for the book, and finishes with a ca bit on why evolution matters. He concentrates on food production, but I felt he could have spent a bit of time on the evolution of antibiotic resistance, the role of animal models in medicine and the fact that it is important in its own right regarding the origins of species.

Happy Darwin day.

Maiacetus Inuus: A New Transitional fossil Of The Whale Lineage

Whale evolution is something that I have blogged on before. This paper describes the discovery of yet another transitional fossil between artiodactyls and whales. The new species is called Maiacetus inuus, which means mother whale of inuus ( Inuus being the Roman god of fertility). It is so called, because one specimen was pregnant (the foetus is the blue shaded object below). What is interesting is that it is in a head down position; modern whales give birth tail first. This suggests that birth still took place on land. Not surprisingly, it is found in the right part of the world to be an intermediate form (Pakistan) and its morphology dates to the correct era too; 47.5 million years old. This makes it older than the more whale like Basilosaurids, and younger than the more primitive Ambulocetus, Indohyus and Pakicetids.

The Evolution Of The Bacterial Flagellum

Creationists often wheel out the bacterial flagellum (a molecular "outboard motor" ) as an example of a structure that could not have evolved. The reasoning being that it is irreducibly complex - take out a component and it is totally useless. Therefore it must have been designed – by their god of course. This of course is an argument from ignorance and limited imagination. Irreducible complexity does not imply a supernatural designer either; sea arches for example are irreducibly complex and produced by entirely natural forces.

This video provides an excellent account of the evolution of the bacterial flagellum and how the intermediate stages are useful in their own right.

Intelligent design has nothing to offer – despite their constant bleating to “teach the controversy”. There is no controversy as this short article highlights.

"Nothing in biology makes sense except in the light of evolution"

(Theodosius Dobzhansky )

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.

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.

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.

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.

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.

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.

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.

A Very Bad Case For Design

Creationists have a lovely way of shooting themselves in the foot by taking the worst possible example to try and justify their case. This recent comment (found here) exemplifies this beautifully

“To know something and to assume to know something is different. Example, one lives alone and he/she goes home and just saw that dinner table is served with all kinds of fruits and food. Now I am thinking and conclude that somebody prepared all the food and served it. But Steve and Dawkins ASSUME that all the food came up there by chance and Luck. This world with their related seasons which act like a servant is a very big food stale where we eat all the food according to the our body needs. Vitamin C or D etc. Who created human beings created the soil where all food fruits and veggies can grow and who created the soil, created the sunlight and rain that all cooperate with each other to serve us.”


Here is the real problem (other than the obvious misunderstanding of evolution and the absurd analogy): Our ancestors once made vitamin C for themselves. They did not need to ingest it. We lack a functional gene for an enzyme called L-gulonolactone oxidase. This forms the last step in the production of ascorbate (vitamin C) from glucose. We do however contain a pseudogene for this enzyme, which does not function because of acquired mutations. This presents a problem for the creationist.

The problem is that design requires being made to fulfil a purpose. Creationism boils down to an organism must be designed because it fulfils a purpose and all its parts are created to fit together to perform that purpose (that and a lack of imagination). So, here we have something that has no purpose and its only reasonable explanation is that it was present in a functional form in our ancestors (it probably became inactive about 40 million years ago).

Reductionism is a common theme in biology. If we don’t need a gene, there is no selective advantage in keeping it. There may even be a slight energetic advantage in losing it. Genes are lost through random mutations, and there are many examples of this occurring. It is not just the L-gulonolactone oxidase gene that we have lost; mice and humans have about 200 “genes” for a family of olfactory (scent) genes called the V1r family. Mice have about 160 functional ones. Humans have only 5! Whales and dolphins have no functional members. The non functional ones have become fossilised in our genome; they are slowly decaying. Gene loss is seen at an extreme level in parasites, as their hosts provide much of what they need for them. The record holder is Mycobacterium leprae; it has about 1600 functional genes and approximately 1100 decaying fossil genes.

It is not just genes that are lost, but structural features too. Examples include the toes of horses that can be seen gradually disappearing in successive rock layers, our appendix and the limbs of proto-snakes (Figure 1).

An interesting recently described example of this is the eyes of blind cave fish. It was found that functional eyes could be restored by interbreeding populations isolated in different caves. This is important. The fact that they have been isolated from each other means that the blindness evolved independently in the different populations. The fact that cross breeding some populations restored sight in the offspring means that different genes are responsible for the blindness in different populations of the same species – surely design would mean this should not be possible – as the perfect designer would chose the one way to make these fish blind – unless of course he wanted to make it look like evolution – just like chromosome 2.

One final point on vitamin C: inerrant biblical literalists believe that all animals were intended to eat plants and fruit (genesis 1:29-30). However, these foods contain vitamin C, so our ancestors would not need genes to synthesise it.

As one can see below, the teeth of Carcharocles megalodon are beautifully designed to peel grapes (sarcasm in case creationists are reading).