Fit today, maybe fit yesterday, but fit tomorrow...?

kw: book reviews, nonfiction, science, biology, evolution, natural selection

A Creationist would view the appeal of the book as, "Come into my parlor, said the spider to the fly." It won't convince many. That is a pity, because Sean B. Carroll's new book is an outstanding presentation of the best material that shows how evolution by natural selection is such a powerful theory.

The book is The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. Dr. Carroll believes in "Tell 'em what you're gonna tell 'em, then tell 'em, then tell 'em what you told 'em." The opening chapter explains the purpose and structure of the book, and the closing two chapters, which he coyly calls "an after-dinner conversation", reiterate the main points and emphasize that "fittest" is a moving target.

It is a pity that so many use the phrase "survival of the fittest" without giving it much thought. If "the fittest" meant what we commonly mean, there would be but one superorganism on Earth, consuming inorganic material as it grows, subject only to the limits the planet can sustain. But with a little thought we realize that "the fittest" refers to a population of organisms that take best advantage of the resources offered by a particular ecological niche in one restricted ecology or other...or a limited set thereof. (Generalists like H. sap. can thrive in a large number of ecologies, but by no means all).

A knowledgeable person means a lot by the term "natural selection". Selection by itself just narrows the range of variation within successive generations of a population. Should the characterisics of the niche that population is adapted to change too much, it will die out. Selection implies that something supplies a range of possibilities from which to select. That "something" is mutation, a catch-all term for several mechanisms that change DNA. In brief, single "letters" (bases we label A C G or T) in the long "text" of a genome may be exchanged for other letters; one or more letters may be deleted; one or a few letters may be inserted; and bigger blocks may be duplicated.

The last item on the list is facilitated by certain sequences that say "cut here", which happen to occur about every 10,000 bases. "Restriction" (i.e. DNA-cutting) enzymes—used by viruses that need to insert their DNA into ours—cut apart DNA at such points, and other enzymes re-seal the cuts. Such a mechanism can copy a gene right next to itself. Then you have two copies, and further, smaller, mutations followed by selection (i.e. death of offspring for which a mutation is deleterious) will change one of these copies over many generations. New functions, new proteins, and perhaps new physiology arise by this mechanism.

One consequence of this cut-and-copy activity is that a copied gene is typically accompanied by some extra stuff that surrounded its original. Pieces of noncoding DNA (often called "junk") are also often copied to new places. These are called "interspersed elements", or INEs; long and short ones are called LINEs and SINEs, respectively. SINEs that precede genes can be easily extracted from DNA, and their presence in various organisms give us a good idea how closely they are related. They are easy to tell apart because they differ in length if their original source is different. Also, because they do not affect one's life or that of one's offspring, there is no selection pressure on them; they stay put over long stretches of time, slowly degrading as smaller mutations occur, but very rarely eliminated.

One of Carroll's illustrations (Fig. 4.3, p 100), shows the SINEs associated with three genes common to eight primates: Human, Bonobo, Chimp, Gorilla, Orangutan, Siamang, Green Monkey, and Owl Monkey. The SINEs for one gene are just over 500 bases long in Humans, 200 in all other apes, and quite a bit longer for the two monkeys (too long to show in the illustration; not present visibly). Another SINE of length ~750 bases is common to Humans, Chimps and Bonobos, ~450 for other apes, and again not shown for the monkeys. A third is ~475 bases long for all apes, and ~125 for the two monkeys.

Let's call these three SINE varieties alex, barb, and chip; and use -long to denote the longer version of each. Alex-long is found only in humans, so the gene in question was greatly modified in humans, but not in other apes. Barb-long must have been inherited by humans, chimps, and bonobos from their common ancestor, and chip-long from the common ancestor of all apes. The copy of some noncoding DNA that produced alex-long happened only after humans split off from the chimp-bonobo line. And so forth.

The SINEs and LINEs that we all carry, by the thousands, last lots longer than some genes. However, the longest-lasting features of our genome are seemingly immortal genes, the subject of Chapter 3. There is a protein called "elongation factor 1-alpha" that is used in every cell of every living creature yet studied. The DNA that produces it is one of about 500 immortal genes that are almost identical in every living being. Here is a portion of the amino acid (AA) sequence of this 1-alpha protein (we use capital letters for the twenty amino acids in proteins), for five very different organisms:

DAPGHRDFIKNMITGTSQADCAVLIV Human
DAPGHRDFIKNMITGTSQADCAVLII Tomato
DAPGHRDFIKNMITGTSQADCAILII Yeast
DAPGHRDFVKNMITGASQADAAILVV Archaea
DCPGHADYVKNMITGAAQMDGAILVV Bacteria
D-PGH-D--KNMITG--Q-D---L-- "Immortal" letters

Those that differ from the Human sequence are bolded (Although there is an A that doesn't change here, it does change for other organisms not shown. The "immortal" ones never do). The KNMITG is particularly interesting. These six AAs fold into a shape that is critical to the operation of the protein. Any change to any of them is invariably fatal. Thus, natural selection has preserved them, because every cell in which any of them was changed by a mutation has died straight off.

I will touch but one other area, one I find fascinating: color vision. The author presents it in detail in Chapter 4, and returns to it frequently in later chapters. First, a study of color vision throughout the animal kingdom indicates that early animals had at least five different color receptors; the lamprey and other very primitive animals have five. Most birds and many fish and reptiles have four, primates either two (New World monkeys) or three (apes and Old World monkeys), and most other mammals and many more primitive animals (but not the most primitive) have two.

Humans actually have a fourth receptor, the "night vision" rods, which do not produce color vision. However, there is a twilight region of near-dark for which the rods begin to work, and the "green" (medium wave) cone still works, though the "red" (long wave) and "blue" (short wave) have quit working. Under a quarter moon, objects that are brightly colored by day take on deep blue-to-yellow/brown hues. It takes near-total darkness to produce entirely monochromatic rod vision. But by day our vision is trichromatic, because of three color receptors...for most of us. For about one man in fifty (but very few women), either the long or the medium cones are missing. It takes both to distinguish colors in the red-yellow-green area of the spectrum. So such men are red-green color blind. They can still distinguish "yellow" from blue.

However, there are three sites in the opsin pigment protein sequence that make most of the difference between the long and the medium (red and green) cones. When all three are one way, we have the green variety, and the other way, the red variety. More than 90% of us have "green" pigment that is "really green" and "red" pigment that is "really red." But for some people, there is a mixed case. One of these sites in particular makes half the wavelength difference in a pigment's peak sensitivity. Mix it wrong, and half of one's color discrimination is gone. For most people with such "anomalous color vision" there is no problem. They are still able to see all the colors, the experience is just less intense.

Now, WHY do we and our closer primate relatives need to tell red from green? Most mammals get along with two colors (dogs and cats included). Why, because we eat fruit. It is a major part of the diet, and ripe fruit is usually red. A dog can't tell a ripe raspberry from a green one, and doesn't need to, because dogs don't eat raspberries...and house pets that have learned to like them can tell more from the smell than the color anyway. Primates have poor noses! (That is another story...)

Old World primates with 3-color vision descended from 2-color ancestors. How? By duplication of an opsin gene, and a gradual shift of one copy to detect redder things, compared to the other. We can tell which came from which by comparing sequences with the long wave opsin in 2-color vision primates. Areas that don't determine color vision, that are primarily structural, are more similar in the more closely related genes. There's lots more here, but that's enough for now.

The author's principal aim is to prove, as closely as one can come to proof, that natural selection is a correct theory. While we know that theories are really only falsifiable, never totally provable, a sufficient mass of favorable evidence coupled with an absence of contrary evidence is as close as one can come. A theory is considered strong, not because it explains phenomena known at the time of its inception, but when it makes correct predictions of observations yet to be made, and even more if unexpected findings are found to fall under its explanatory umbrella. Very few theories currently reign as Very Strong Theories: Quantum Electrodynamics, Special Relativity, General Relativity, and Evolution by Natural Selection are the top four.

His secondary aim it to show that "intelligent design", the latest offshoot of creationism, is not a scientific theory. He actually expends little effort to this end, because ID is an unwitting straw man very easy to demolish, and because Christians have already done a good job of it. Here is part of a statement by Richard Harries, the Bishop of Oxford, as quoted on p. 242: "The theory of evolution, far from undermining faith, deepens it. This was quickly seen by Frederick Temple, later Archbishop of Canterbury, who said that God doesn't just make the world, he does something more wonderful, he makes the world make itself. ... biblical literalism brings not only the Bible but Christianity itself into disrepute." The simple fact is that ID makes no statement that can be scientifically tested, so it isn't science, it is just a myth, not even a biblical one.

This reminds me of a joke I first heard as jibing certain fundamental baptists, but here:

A devout Episcopal appears at the gate of heaven and Peter admits him. He is assigned an angel to show him around. The angel tells him there is just one place he must avoid, and shows him a walled compound, without windows, and a fence far from the wall, guarded by armed angels. "Who is in there?" the gentleman asks. The angel replies, "The creationists. They think they're the only ones here!"