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.

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.