Letter To the Metro: Exposing Creationist Lies

There has been a flurry of creationist nonsense in the metro recently. The depressing thing is that it’s the same thoroughly refuted nonsense that keeps coming up. This time they have claimed that no transitional fossils exist and that speciation does not occur. As a result I got this letter published.

“Let me expose some creationist lies. 1. No transitional forms exist. This is rubbish! Transitions have been found for all major vertebrate groups. For example, for the evolution of whales, we have Sionyx, Pakicetus, Indohyus, Kutchicetus, Ambulocetus, Rhodocentus, Miacetus, Protocetus, Basilosaurus, Dorudon, Squalodon and Ceitotherium to name a few. They have also been found in the right places in rocks of the right age and show a gradual progression to more whale like animals. Furthermore, DNA evidence confirms their relationship to the proposed ancestral group.

2. Speciation does not occur. This is another lie and it has actually been observed. Try the Madeira island house mouse for example.

Creationists have no evidence of their own and rely on promoting the above lies and then denying the facts. Strangely, they think their ignorance of biology is evidence of their position.”

One has to wonder how these people have bypassed all the evidence at school and seem to quote lies and ignorance from fundamentalist sites. Is it a failure of our education system? They are very easy to shoot down though, but that won’t make a difference to them. I expect replies of “it’s still a mouse” (even though it is a new species) and the fossils are not complete (something I dealt with here) or the good old where are the transitional forms for the transitional forms? chestnut.

Concurrently, there is some joker claiming that Darwinism gave Hitler his justification – groan!

Flu For Jesus

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.

Zombie Jesus

I've been pretty busy recently, but here's a little something to keep things ticking over. Let's hope that one day we discover a cure.

Metro: Follow Up Letter

I thought I would follow up yesterday's letter and challenge the ideas of "normality" and "natural". I got this letter published today:

"To those still using the fallacious normality argument, I suggest that you google "lesbian Bonobos". Homosexuals can help raise the children of siblings - something also seen in nature. I presume you think infertile couples are bad people too? What about people wearing glasses or with congenital birth defects? Surely that's not normal. They must be bad people. There is also an Asian couple in my street. Everyone else is white. Therefore, they are not normal for the street. Should I gather an angry mob and hound them out of the street?"

I wonder if it will have any effect.

EDIT: Looks like bloggers formatting has gone all screwy again!

More Letters In Metro

There have been a few religious bigots popping up in the letters page of the metro after this article appeared about trying to "cure" homosexuals. It's the usual it's unnatural or "it's Adam and Eve, not Adam and Steve" bollocks. I've commented on the "not natural argument" before. Anyway, I got this letter in today.

"Monday Man, am I to assume that the only reason you are a homophobe is because you actually believe a discredited bronze age fairy tale? One about a man and a woman who got punished for eating a fruit, even though they did not know what right and wrong was until after they ate it? As for the "arguments" about normality, that's the argument from democracy fallacy. It's a bit like saying gang rape is acceptable because 9 out of 10 participants report a positive experience of it."

Forward Planning Chimps

I came across this interesting article. It shows that chimps can plan forward and that they have the ability to foresee particular mental states. This also implies that they are self aware. This is one of the last areas that the religious have clung on to in a vain attempt to claim that humans are somehow special and outwith the rest of nature.

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.

Spiders On Drugs

The fact that drugs can affect personality and cognitive processes is good evidence against the idea that the mind is something other than physical. Anyway, here is an amusing video

I'll get the next chapter of the book club up by Sunday - the dog ate my computer.

Icy Ben Vane

A friend took a couple of short videos on Ben Vane yesterday. They are linked here and here. As winter conditions go, these are quite mild. See here for a more serious version of winter conditions.

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.

Eat This Cheese, It Is My Central Nervous System

More hilarious religion bashing fromEddie Izzard:

Windae Licking Bawbag Of The Month Award

I found myself watching the one show tonight because it featured Robert Winston talking about religion. The award goes to Adrian Chiles for his comment on the atheist bus campaign, which advertises on buses that "There's probably no god. Now stop worrying and enjoy your life". Chiles claimed that this was a carte blanche to behave in an amoral way. This says more about his mindset than anything. Atheists are no less moral than christians - in fact, atheists are often under represented in prisons. For example, these stats show that atheists form about 8-16% (and growing) of the American population, but only form 0.209% of the prison population. Does this goof ball really think that without god, we will go a rapin' and a pillagin', and a committing genocide - you know like the stuff god condones in the OT. Maybe we will enslave others - hmmm, cant do that either, that's endorsed by the bible too. Oh well, that leaves racism ...... damn! the bible endorses that too. Just what can I do that is immoral that the bible doesn't endorse?

I would argue that you can't be truly moral with god, as the need to think through the consequences of your actions are deferred to some other authority ( a human one, but the god bots think it is their chosen sub - sub species of the Abrahamic deity) .

I like Darwin's definition of a moral being: "A moral being is one who is capable of reflecting on his past actions and their motives - of approving of some and disapproving of others. "

If you can bear it, there is a thread to the episode that takes comments here.

Adrian, society will not fall apart because people don't believe in god - twat!

PS, I liked this comment (no 48) :

"Science will fly you to the moon, faith will fly you into a building!"