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.

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.

Pesky Pistol Shrimps

I have a pistol shrimp in my reef aquarium. They are supposed to be safe with other inhabitants, but I found one of the cleaner shrimp dead and a couple of sexy shrimp have gone missing (I presume they are so called because they "dance" while they walk). I did a bit of research and apparently not all species are safe and found the video below of one stunning a cleaner shrimp. This is quite fascinating - when the little bastards are not eating their tank mates.

They have a specialised claw that sends out a violent jet of water and a sound wave that whacks its prey. This video goes into the mechanics of the sound production.

This hunting/defense adaptation is also a problem for deluded Young Earth Creationists who believe god made all animals vegetarian. How did they get this adaptation without evolution? No doubt they will pull some bollocks out their collective chuffs like god intended them to eat coconuts and the snap breaks the shell.

A final interesting thing about these shrimp is that they often enter a symbiotic relationship with certain species of goby. The goby provides the lookout and bits of food and the shrimp provides a protective burrow and firepower. This an example of being co-operative yet selfish. It is such a creationist lie that natural selection means kill everything.

Anyway, I wonder who would win in a square go between a pistol shrimp and a mantis shrimp (which can deliver a blow equivalent to being hit by a .22 bullet). Following Bruce Lee's advice of using your longest weapon, I would bet on the pistol shrimp. All we need now is Harry hill to proclaim Fiiiiight!

Book Club

It seems a close run thing, but I will go with "The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution" by Sean B Carroll. I will plan to review the first chapter on the 12th of February (Darwin day). If anyone does not get a copy, please still feel free to contribute. I have also blogged on some of the topics in the book if some back ground reading is required. I will try and do a post roughly once a week on different chapters.

Dennet's Breaking the spell was also a popular choice. Perhaps that can be the next one. If someone else wants to host it too, then that would be OK by me.

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.

Book Club Idea

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

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

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

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

Convergent Evolution Refutes The "Argument" For A Common Designer

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

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

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

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

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

Fig 1

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

The original publication can be found here

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

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

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