* The modern knowledge understanding of heredity has provided great insight into evolution, examples including the development of color vision systems in primates; the presence of broken or "fossil" genes in organisms that clearly indicate functions lost during their evolutionary past; and evidence for the convergent evolution of distinct species. The genetic evidence has also provided intriguing evidence for some facets of human evolution, including the development of dark skin color, lactose tolerance, and resistance to malaria.
One particularly important discovery in modern genetics is the realization that organisms include a kit of "developmental genes" that provide high-level control over their general organization. Much remains to be learned about the genome, however, since there are large sections of it whose function remains mysterious.
* One of the interesting examples of evolution in genetic terms is human color vision. Humans have three types of color receptors: red, green, and blue. Apes and most Old World monkeys are also "trichromats" -- but most other mammals are "dichromats", only able to see yellow and blue, unable to tell the difference between red and green.
At the base of human color vision are a set of visual pigments, each made up of a protein called an "opsin" linked to a small molecule called a "chromophore", which in humans is almost identical to the vitamin A molecule. It is the opsins that provide color sensitivity, the chromophore being the same for all the pigments. Each type of opsin is sensitive to a different wavelength of light, and humans have red or "longwave" sensitive opsins; green or "midwave" sensitive opsins; and blue or "shortwave" sensitive opsins. They also have a fourth and related but distinctly different opsin, "rhodopsin", operating in the blue-green range, that is more sensitive to light and used for seeing in dim light, at the cost of perceiving much in the way of color.
The retina of the eye is carpeted with "photoreceptor" cells, each crammed with pigments. There are "rod" and "cone" photoreceptors, of course named for their general configurations, packed with pigments -- rhodopsin in the rods, and longwave, midwave, or shortwave pigments in the red, green, or blue cones respectively. The rods provide monochrome vision in low-light conditions, while the cones handle color vision in normal light conditions. There are about 120 million rods to about 7 million cones -- our color vision is much lower resolution than our grayscale vision.
Humans and apes have three different opsins, while most mammals only have two. Each opsin is encoded by its own gene, and so the presence of different numbers of opsins in different sorts of animals unsurprisingly reflects genetic differences between them. These genetic differences suggest an evolutionary relationship -- for example, that mammals in general started out as dichromats, but the branch of primates that turns off to apes and humans became trichromats. The diversification of opsins reflects the action of gene duplications.
* A taxonomic tree of primates can be built by selecting a set of SINEs from particular parts of the human genome, and then checking for the presence or absence of SINEs in other primate genomes. It's simple to see if a SINE isn't present -- SINEs are about 300 base pairs long, and if the SINE isn't in a particular gene, that gene is about 300 base pairs shorter. An analysis on this basis using 100 SINEs showed, to no surprise, that chimps were the most closely related to humans, with successively more distant relationships to gorillas, orangutans, gibbons, and green monkeys. The nocturnal New World owl monkey did not have any of the 100 SINEs in common with humans.
Humans, apes, and Old World monkeys are all trichromats; as noted, most other mammals, including most New World monkeys, are dichromats. That suggests the third opsin gene in Old World monkeys arose after the split between the New World and Old World monkeys, and that early mammals were all dichromats.
Incidentally, if the fact that we are trichromats and most other mammals are dichromats seems an indication of our "advanced" nature, many birds, fish, and reptiles have four opsin genes, and stomatopods -- mantis shrimp -- have eight. It seems plausible that our trichrome vision is a re-invention of a capability lost in the distant past -- apparently because early mammals were generally nocturnal, and had little need for color vision.
Most mammals have a long-midwave opsin and a shortwave opsin. Humans, as noted, have long, midwave, and shortwave opsins. The hint that the human long and midwave opsins were derived from the older mammalian long-midwave opsin is the fact that the human long and midwave opsins are right next to each other on our X chromosome, and that their codes are about 98% identical -- in other words, the old opsin gene was duplicated, and then the two new genes evolved to be sensitive to separate bands. This is not genetically problematic; the proteins produced by the two genes only differ in 15 amino acids, and only three seem to be involved in shifting the spectral response of the opsins -- the others may just be simple mutational noise.
The gene duplication also supports the neutral theory of evolution. Initially, the duplicated genes provided exactly the same opsins and gave little or no selective advantage. However, they did no harm and so were not lost. Once mutations began to set in, shifting the spectral response of the opsins, the genetic variability created by the duplication mutation began to make itself felt.
The New World and Old World monkeys split into separate families about 30 to 40 million years ago. That was, incidentally, well after the African and South American continents split apart, but the two land masses weren't so distant in those days; it is generally believed that early primates came west by rafting events, possibly migrating from one island to another. In any case, that puts a time limit on when the duplication event occurred. Color vision proved an important adaptation, permitting primates to identify more nutritious foods. It seems particularly important in leaf-eating monkeys, such as the African colobus monkey and the Indian langur monkey. Leaves are common but not very nutritious, so the ability to spot the most nutritious leaves provided a significant survival advantage.
The selective advantage of trichrome vision is apparently considerable. While color blindness is common in relatively coddled humans, with up to 8% of white males being color-blind, it is very rare in wild trichrome primates, well less than a percent. Color-blindness makes life so much more difficult for them that they don't reproduce well enough to carry the trait on.
* The evolution of trichrome vision in Old World primates provides an intriguing example of evolution at the genetic level. There are other interesting examples of evolution in animal visual systems. Consider deep-sea creatures. While coral reefs are famously brilliant in their colors, in the deep sea, a few hundred meters down, the light fades into dim dark blue -- the shorter the wavelength of light, the deeper the penetration of light into the sea. Under such dim light conditions, the sensitive rhodopsins become very important to vision.
The interesting thing about the rhodopsins of deep-sea creatures is that their rhodopsins are modified to be sensitive to even shorter blue wavelengths than those picked up by surface creatures. Bottle-nosed dolphins have rhodopsins that are sensitive to wavelengths of blue light about 2% shorter than the rhodopsins of surface mammals. That isn't a big difference, and it might be simply written off as a random variation -- except for the fact that deep-sea eels have rhodopsins sensitive to wavelengths of blue light about 2% shorter than those of shallow-water eels.
The clear implication is that dolphins, descendants of surface mammals with the longer-wave rhodopsins, acquired the same modifications under natural selection as the deep-sea eels. In fact, they are the exact same modifications, with the same three amino acids tweaked in the rhodopsins. That might seem extremely coincidental, but what it suggests is that those modifications are the most likely or even only avenue available that leads to deepening the blue sensitivity of the rhodopsins, and both eels and dolphins took that main road.
While researchers long believed that creatures of the very deep sea would have very rudimentary vision, genetic examination of a number of deep-sea fish showed that they had an unusually large number of different genes for rhodopsins -- notably the silver spinyfin, which lives thousands of meters below the surface, having 38. In addition, some of its rod cells are well longer than normal, and sometimes the rod cells are stacked on top of each other.
Although no light at all penetrates to such depths from the surface, organisms at such depths generate their own light through bioluminescence. The rhodopsins of the silver spinyfin are tuned to the blue and green wavelengths produced by bioluminescence, with the number of different rhodopsin genes suggesting it has exquisite color discrimination, and features like stacked rod cells suggesting the ability to pick up very faint light.
It appears that the ecology of deep-sea organisms is, to a degree, dependent on identification from bioluminescent signatures, for example in reproduction or symbiotic interactions; it's difficult to know exactly what's going on, since it's so hard to observe the behavior of organisms at such depths. What is clear is that evolution is always full of surprises.
* As a footnote to the utility of duplicated genes to evolutionary science, consider the story of the globins, the subassemblies that make up the hemoglobin molecule. To make the story simple -- a full consideration of details is complicated -- our hemoglobin molecule is made up of four globins, with two of them being "alpha globins" and two of them being distinctly different "beta globins". On investigation, this split between alpha and beta globins proved to be common among every vertebrate species examined.
What seemed to have happened was that at sometime in the distant past, there had been a globin gene duplication that had evolved into the distinct alpha and beta globins. The interesting question was of when this might have happened; since it was common among vertebrates, it was obviously in the early days. That quickly turned attention to one of the oldest branches of the vertebrates, the jawless lamprey. Sure enough, examination showed that lampreys only had globins, not distinct alpha and beta globins. The gene duplication that produced alpha and beta globins dates back to just after the line that leads to most vertebrates split off from the line that leads to modern lampreys.
BACK_TO_TOP* Immortal genes are mirrored by "fossil genes" -- genes that remain in an organism's genome even though they have been mutated into uselessness, as discussed in the evolution of the icefish. As mentioned, dolphins have rhodopsins fine-tuned to short blue wavelengths. What about their opsins? It turns out that they, and in fact all the members of the whale family, can only produce the long-midwave opsin, which means that they have no color vision. Their ground-living mammalian ancestors no doubt had both the long-midwave and shortwave opsins. What happened to the shortwave opsin?
The gene for it is actually still there, it's just broken. The gene is missing a few bases, resulting in a catastrophic frame-shift error that breaks the gene. The dolphin and its other family members all carry evidence of their ancestry from mammals with dichrome vision. Creatures who spend most of their time in the deep dark sea can do without color vision, losing it does not impose a selective disadvantage on them, and so once the gene broke, there was nothing to prevent the broken gene from propagating through the entire whale family tree.
Incidentally, while mammals typically have five different taste receptors -- sweet, bitter, savory, sour, and salty -- whales can only taste salty, the genes for the other taste receptors having broken. This is due to the fact that whales tend to swallow their prey whole, meaning they wouldn't taste them anyway. Why salty has been retained is a bit mysterious, the suspicion being that it helps maintain a whale's salt balance.
In any case, the story concerning dichrome vision in sea creatures gets more interesting. The discovery of the lobe-finned coelacanth fish in the 1930s was a big surprise to biologists since it had been thought to have been extinct for so long, when it was still alive and well in the deep waters of the Indian Ocean. The mention of "deep waters" immediately pops the question: do coelacanths have functional shortwave vision? The answer is no, but like dolphins they do have a fossil shortwave opsin gene -- though the way in which it's disabled is different, with a single nucleotide mutation jamming a STOP signal into the gene, telling the protein expression system to STOP expression and shutting down the gene. Like the dolphin, the coelacanth's ancestors had the shortwave opsin, but the coelacanth has lost it. It doesn't need it in its deep-water environment, and its loss didn't do the coelacanth any harm.
The evolutionary rule is simple: "Use it or lose it." The creationist notion of "genetic entropy" is, as noted earlier, not entirely wrong: left to themselves, genomes have a clear tendency to degrade and break. It is only selection that keeps the genome in good operational shape. This is what makes the notion of genes in "cold storage" absurd: if genes are not being used, they're certain to break sooner or later; and if they're not being used, there's nothing to prevent the breakage from propagating through populations.
In any case, to add to the intrigue, the coelacanth doesn't even have a long-midwave opsin -- it only sees with rhodopsins. There is no recognizable remnant of the long-midwave opsin in the coelacanth's genes. While fossil genes can be used to trace the genealogy of organisms through the patterns of cumulative breakages, in time the breakages will scramble the fossil gene to the point where it can no longer be recognized. It seems that the coelacanth lost its long-midwave opsin gene so long ago that mutations have completely scrambled it. Eventually, mutations are likely to erase the shortwave opsin gene completely in whales as well.
The same sort of loss of an unused function is also seen in the blind mole rat, a colonial burrowing rodent that doesn't seem to have eyes. Actually it does, but they're buried under skin and fur. Their only function appears to be to determine night versus day to help the animal maintain a regular activity cycle. The blind mole rat has functioning rhodopsin and long-midwave opsin genes, but the shortwave opsin gene is broken. The vestigial eyes of the blind mole rat are also a good example of evolution in action at a higher level, amounting to camera-type eyes that don't function any better than a simple eyespot.
The tale of the blind mole rat leads to the tale of the Australian marsupial mole. It has vestigial eyes, but they are completely nonfunctional, lacking even the optic nerve to connect them to the brain. Fossil genes have a tendency to parallel vestigial structures, and this is seen very clearly in the marsupial moles, with a gene fundamental to vision being completely broken.
Yet another example of the loss of an unused function is seen in the owl monkey, a New World monkey and the only nocturnal monkey. Its shortwave opsin gene includes a STOP code mutation, disabling it, though the owl monkey does retain a functional long-midwave opsin gene. Similarly, among the lemuroids, the nocturnal bushbabies and slow lorises both have broken shortwave opsin genes. For these two creatures, the gene is broken in exactly the same way in both animals, implying they were derived from a common nocturnal ancestor with the same broken gene.
* One of the particularly significant features of broken genes is that the odds of a change breaking a gene are much better than the odds of the change resulting in an improvement, and so if the gene isn't subjected to selection pressure, it's going to be broken fairly quickly -- again, use it or lose it. One very good example is the human sense of smell, or more specifically the weakness of it.
Anyone who has noticed how fascinated a dog can be about smells we don't notice knows humans have a poor sense of smell, and this is proven by the fact that about half of our genes for smell receptors are fossilized. We are very dependent on vision, so much so that loss of our ability to smell doesn't do much to compromise our ability to survive. Lemurs and New World monkeys have a good sense of smell; the trichromat Old World monkeys have lost a greater proportion of their smell receptor genes, while the apes have even more broken smell receptor genes. Humans are even worse off in this respect, having the poorest sense of smell of all the primates by a good margin. Incidentally, toothed whales have a very poor sense of smell as well, most of the smell receptor genes being broken -- though some baleen whales like the bowhead have a good sense of smell, apparently for sensing the proximity of swarms of krill they feed on from the smell of the swarm in the air.
Primates also have a fossil gene known as GULO or GLO, which is responsible for production of vitamin C. Most mammals, for example cats and dogs, which rarely eat fruits and vegetables, have a functional GLO gene and so effectively never suffer from a vitamin C deficiency. In primates, fruit bats, and guinea pigs, the GLO gene is present, but it is broken and functionless. It would be nice if we had a functioning GLO gene and weren't vulnerable to scurvy -- due to a lack of vitamin C in the diet -- but our distant ancestors ate enough fruits and vegetables to ensure they almost always had plenty of vitamin C, and so when the GLO gene broke it wasn't missed: Use it or lose it.
Incidentally, the broken GLO gene features more or less the same disabling mutations in all primates. All primates share a subset of the same GLO early mutations, but different primate lineages have different mutations from later ages. The guinea pig GLO, as could be expected, has different disabling mutations. There are fewer ways of getting something right than there are of breaking it.
In any case, the evolutionary progression in broken genes is obvious. If we have a set of pictures of a car with some showing one ding on the windshield; others showing the same ding and a second ding; and still others with the previous two dings and a third ding, we'd have no problem figuring out the chronological order of the pictures. Similarly, we get broken smell receptor genes in Old World monkeys, add additional broken genes in apes to the list of those already broken, and pile on another set of broken genes in humans.
It should be noted that the basic assumption being used so far is relaxed selection, that these fossil genes broke and, not being really needed, were not missed. However, it is also possible in some cases that natural selection could actually select for the broken gene. If a certain trait became a liability due to a change in circumstances, organisms with the broken gene would gradually displace their comrades with the active gene. Again, whether a trait is "good" or "bad" can depend on circumstances.
BACK_TO_TOP* It was noted earlier that New World monkeys are generally dichromats. That is a true statement, but the "generally" condition is important. New World monkeys have genes for two opsins, with the two genes on different chromosomes -- one gene, the gene for the shortwave opsin, is on an autosome, while the other gene is on the X chromosome. This is where it gets tricky, since the gene on the X chromosome has alternate midwave and longwave alleles. That means that male New World monkeys are as a rule dichromats, but they have two different patterns of dichromat vision. Since females have two X chromosomes -- sex determination is the same as it is in humans -- they may end up with an X chromosome coding for the midwave opsin and the other X chromosome coding for the longwave opsin, meaning that the females are sometimes trichromats.
This is another arrow in the quiver for MET, since it would certainly seem haphazard under Design. It has been suggested that it also demonstrates natural selection in that a troop of New World monkeys has three different forms of color vision. Colorblind humans can see through some sorts of camouflage more easily than their trichromat comrades, and it is plausible, if not proven, that three forms of color vision give a New World monkey troop an overall advantage compared to a troop with only one form of color vision.
This is something of a digression; the important issue here is that there is one New World monkey, the howler monkey, that is fully trichromat. The howler monkey is noted for its oversized voicebox, which gives it the ability to produce really loud calls. It is also, unusual among New World Monkeys, a leaf-eater, and so it's not too surprising that it's a true trichromat, with genes for both the midwave and longwave opsin on the X chromosome -- which, along with the autosomal shortwave opsin gene, gives full color vision.
The question arises as to whether the howler monkey "re-acquired" the third opsin, or if the other Old World monkeys lost it. The answer is that the howler monkey re-acquired it. First, there's no broken gene for the third opsin in other Old World monkeys, meaning there is no evidence that they had it and then lost it. Second, the duplicated opsin genes that produced trichrome vision in Old World monkeys are clearly distinct from the duplicated opsin genes that produced trichrome vision in the howler monkey. The longwave and midwave opsins in all Old World monkeys both carry a chunk of noncoding DNA 236 base pairs long. Both obtained that distinctive chunk of noncoding DNA from their long-midwave ancestor. The longwave and midwave opsins of the howler monkey also both carry a chunk of similar noncoding DNA, but it's much longer.
Furthermore, due to genetic drift, the longer ago the two opsin genes were produced, the more they will differ. The two opsin genes in Old World monkeys are about 5% different, while the two opsin genes in the howler monkey are about 2.7% different. The implication is that the gene duplication event in the howler monkey was more recent.
What is particularly astonishing about the howler monkey's re-acquisition of trichrome vision is that the howler's longwave and midwave opsins are tuned to exactly the same color bands as those of Old World monkeys, using very much the same critical mutations. This is convergent evolution at work: the specific color bands were "optimum" in terms of selective advantage, and there was no other available set of mutations that could produce them.
* It is possible to describe other interesting examples of convergent evolution at the genetic level. For instance, there are dozens of different populations of the Mexican blind cave fish. As cave fish often are, they are all albinos: their coloration genes broke and weren't missed. Genetic investigation of the same pigment gene in multiple Mexican blind cave fish populations indeed showed that the gene was broken in all of them -- but it was broken in a different way in each of the different populations. Each population became albinos independently.
As mentioned, the icefish and their relatives in the Antarctic regions have an "antifreeze" in their blood consisting of a simple protein sequence. There are Arctic fish species that have an antifreeze consisting of a simple protein segment in their blood as well. The two groups of fish are not closely related, and it turns out the construction and genetic coding of their antifreeze components are entirely different. They are only functionally similar; unlike the tuning of opsins, there were multiple paths to obtain the equivalent adaptation.
BACK_TO_TOP* Having considered the genetic evidence for evolution by natural selection in various animals, it is worthwhile to go on to consider it for humans. One of the most obvious of variable human features is skin color, and it is also obvious that people from the tropics tend to have darker skin. The darkness of skin color is due to production of a pigment melanin, which acts as a natural sunblock -- dark-skinned people can still get sunburned, but not anywhere as easily as light-skinned people. Light-skinned people will tend to increase production of melanin under sunny conditions, acquiring a tan. However, a degree of sunlight is necessary to stimulate production of vitamin D, and increased production of melanin works against that.
As with mice, melanin production is ultimately controlled by the MC1R gene, and the structure of this gene varies with human populations. In Europeans and Asians, there are thirteen different MC1R codings that produce ten different varieties of MC1R proteins. In Africans, there are five different MC1R codings, and they all produce exactly the same MC1R protein.
This difference would be very hard to explain as a matter of random chance: it is clear that the MC1R gene in Africans is subjected to greater selection pressure than is the same gene in Europeans and Asians. It is unclear if the variability of the MC1R gene in Europeans and Asians is due to relaxed selection -- it isn't critical any more -- or positive selection -- lighter skin is needed to ensure vitamin D production in lands with less sunlight.
* For another example, consider the issue of lactose tolerance in humans. Although all humans can digest milk as children, as they grow older about half the world's population lose the ability and get sick if they try to drink milk. Lactose tolerance is mainly found among Westerners, Middle Easterners, and East Africans, who have a long tradition of dairying. A mutation that would allow adults to keep on digesting milk would be a major advantage in regions where dairying is common -- while being irrelevant to those from regions where dairying was unknown.
Genetic analysis of lactose tolerance has shown that it can be produced by any one of several genetic mutations. The first was found in Finns and other northern Europeans, but this mutation was infrequent among adult milk-drinkers in Southern Europe and the Middle East, and nonexistent in African adult milk-drinkers. Researchers then investigated blood samples from African peoples who were milk-drinkers and found three more mutations, on the same stretch of DNA as where the Finnish mutation had been found. Some Africans had all three mutations. Not only are there three separated populations featuring lactose tolerance, but they don't necessarily have the same mutations, with at least four different mutations available, and sometimes more than one are found in the same individual.
Estimates from the rate of genetic change suggest the most common mutation occurred about 7,000 years ago, about the same time as the domestication of cattle. Examination of genetic samples of stone-age humans from about 5,000 to 6,000 BCE do not reveal a lactose-tolerance gene. Certainly the mutations must have happened every now and then before that, but until humans began dairying, there was no particular advantage to them and such mutations fell by the wayside.
* Another well-known example of human genetic variability is sickle-cell anemia, a hereditary disorder that gives its victims sickle-shaped red blood cells, in contrast to normal donut-shaped red blood cells. The disease was discovered in 1910; once genetic rules of inheritance were sorted out, it was realized that sickle-cell victims inherited the trait from both parents. If a subject only got the trait from one parent, the subject was normally healthy, the symptoms appearing only under special circumstances. After World War II, it was discovered that the sickle shape was due to the fact that the hemoglobin was different in the two forms of cells.
In 1949, a South African-born Briton named Anthony Allison (1925:2014) performed field studies in Kenya, taking blood samples of local tribesfolk. He found that the sickle-cell trait was very common, 20% or more, among tribesfolk near Lake Victoria or the coastal regions, but very rare, less than a percent, for tribesfolk in dry or highland regions. In a flash of insight, he wondered if the sickle-cell trait was linked to the prevalence of malaria in low-lying, moist areas, where malaria-carrying mosquitoes were common.
After obtaining a medical degree, Allison went back to East Africa in 1953 to test out his idea. He determined that subjects with only one sickle-cell trait were more resistant to malaria, and that the map of prevalence of the trait almost precisely matched the map of incidence of malaria. Malaria was selecting for the sickle-cell trait. By no coincidence at all, further studies showed that the sickle-cell trait also showed up heavily in locations in Greece and in Southern India where malaria was common -- in unrelated populations.
The sickle-cell defect is highly distinctive, caused by a specific single-point mutation, which by inference arose in at least three widely-separated human populations independently. Some believe it may have arisen several more times, since the distribution of the defect in Africa covers several distinct populations. It is a vivid demonstration of evolution in action, in particular because it is such a clear and ugly improvisation: it gives an advantage at the cost of a severe drawback.
Incidentally, just how the sickle-cell defect provides a defense against malaria is not clear. The red blood cells of those who obtained the trait from only one parent generally appear normal but will suffer "sickling" at low oxygen conditions such as high altitudes, and other stresses may cause the sickling as well. One interesting, if not universally accepted, idea is that when the red blood cells are attacked by the Plasmodium parasitic protists that cause malaria, the cells sickle and are scavenged up by the human immune system, along with the parasites infecting them.
While the parasites have evolved resistance against antimalarial drugs, such resistance is due to simple mutations that help nullify toxins. Whatever the mechanism of sickle-cell defense, it's obviously not so easily defeated, since the parasites haven't acquired a way around it in thousands of years. Assuming the mechanism of defense is as described earlier, the parasites would have to develop some way to prevent a red blood cell from sickling and calling down the body's immune system -- a far more elaborate process than neutralizing a toxin.
* Malaria has had other impacts on the human species. There is a protein known as "Duffy" that is often found on the surface of red blood cells, as well as in other contexts within the body. It turns out that the malaria parasites exploit Duffy to get into the red blood cell. To no surprise, people from West Africa rarely have red blood cells with the Duffy protein, though it is common on the red cells of human populations in other regions.
Humans produce an enzyme with the designation "G6PD" that is involved in the metabolism of glucose in cells. It is a very common culprit in human enzyme deficiencies, with the deficiency due to one or more of 34 possible mutations. A deficiency of G6PD seems to confer marginally higher resistance to malaria -- and to no surprise, the map of high incidence of G6PD deficiency closely follows the map of high prevalence of malaria. In a particularly interesting study, estimates of the age of G6PD gene mutations shows they took place about 3,200 to 7,700 years ago. This is about the time agriculture became common in human cultures, meaning settlements and cleared fields near sources of water -- and much more exposure to mosquitoes that carried malaria.
Humans have acquired evolutionary adaptations to fight malaria -- and in recent times, tried to fight back more actively, eradicating mosquitoes with pesticides. However, mosquitoes breed rapidly in large numbers and so have quickly evolved resistance to pesticides. Our knowledge of evolutionary science and genetic modification also gives us a Zen approach to fighting back: genetically engineer mosquitoes to resist infection by the malaria parasites. Since mosquitoes are such a nuisance, it seems a bit perverse to try to improve on them -- but if we must be bitten by mosquitoes, we might as well make sure they don't make us sick as well.
The parasites themselves of course have been evolving as well, developing resistance to drugs such as chloroquine. Having become sadder but wiser about the inevitability of the evolution of drug resistance in pathogens, now the practice is to administer combinations or "cocktails" of drugs. The odds of a pathogen obtaining a mutation to deal with one drug are pretty high; the odds of a pathogen obtaining two simultaneous mutations to deal with two drugs are very low.
BACK_TO_TOP* Another topic worth covering in evolutionary genetics is the subject of "evolutionary development" or just "evo devo" for short. It is actually a very big subject in itself, but it is also elaborate, and so it's only discussed briefly here.
Back in the 1950s, when MET was being assembled and DNA was a new concept, the general assumption was that when heredity was finally unraveled in detail, the genomes of different creatures would be as entirely different as their appearance; it was expected that the genes of the fruitfly and the dolphin would have very little in common. It wasn't learned for decades that the logic of the genetic "machinery" underlying organisms actually has strong common elements -- particularly in terms of the genetic switches that control development of a multicellular animal through its embryonic stage.
For example, the development of the eye is dependent on a gene designated Pax-6 -- some other developmental genes are also involved, but they will be ignored here for simplicity. The interesting thing is that the development of the eye in all animals, no matter if the eye is that of a mantis or a spider or a squid or a human, is dependent on Pax-6. Although the eye has evolved independently in many different forms many times, all types of eyes are traceable back through common their common descent from a basic eye biosystem.
There are other "developmental" or "homeotic" genes, the most famous being the Hox genes, which control the arrangement of body parts. The term stands for "homeobox", incidentally, which refers to a distinctive segment of DNA found in all these genes that encodes a protein element, the "homeodomain", that meshes to DNA to regulate its operation. Hox genes are homeobox genes that are homeotic -- not all homeobox genes are homeotic, and not all homeotic genes are homeobox genes.
Hox genes are universal among the animals. These genes don't really construct anything themselves, they just tell other genes in the genome to build the appropriate structure. For instance, developmental genes provide commands to direct the construction of our five fingers, all using the same low-level genetic routine. Sometimes the developmental gene gets it wrong, and the result is six fingers. It's not unknown in humans, and six-toed cats are fairly common -- they can be spotted by their oversized paws. There are also breeds of dogs that are prone to have two noses, side-by-side on the end of the muzzle.
Mutations in developmental genes can often be disastrous and lethal, but they clearly can be useful as well, in the form of "stretched jetliner" modifications: snakes have hundreds of ribs, far more than the legged reptiles that were their ancestors, and it doesn't require much imagination to see how errors in developmental genes gave them their vastly extended ribcage, providing a body that could get around efficiently without legs. Centipedes and millipedes demonstrate a similar modular repetition.
* The impressive thing about the developmental genes is their universality: they are immortal genes common among the animals. In essence, they define a core "machine", established before life ever emerged from the sea, that is manifested in a bewildering range of organisms.
Developmental genes define a hierarchical system, operating at multiple levels, with the higher levels describing a "block diagram" organization in which "modules" are linked together in a particular architecture, with the "modules" then implemented by the lower levels. Minor variations in the genetic specification of the "block diagram" can result in major differences in the configuration of the organism that results. This consideration tends to muddy the argument over micro-evolution versus macro-evolution -- as if it wasn't muddy enough already -- since minor mutations can have major consequences. Organisms that may seem very different externally may be very similar at the genetic level.
From this point of view, the introduction of genes to coordinate the development of multicellular organisms was, like the "invention" of sex, an example of the "evolution of evolution." It is generally assumed that more "core machine" genes will be found, for example that provide high-level influence over instinctive behaviors.
* Incidentally, plants also have distinctive developmental genes, including the MADS box genes, that provide the same sort of homeotic control over their large-scale organization as Hox genes do with animals. The name, is derived from the initial letter of the first four genes of this type to be discovered .... listing them would not be very illuminating.
In any case, MADS box genes are not interchangeable with animal Hox genes, but ironically plants do have homeobox genes, they just don't play any role in plant development. Animals also have MADS box genes, but similarly they don't play any role in animal development. What this reversed symmetry suggests was that the most recent common ancestor of plants and animals, estimated to have lived about 1.6 billion years ago, was a single-celled organism, and when the plant and animal branches of the kingdom of life went their separate ways, each developed a different set of developmental genes, based on preexisting genes.
BACK_TO_TOP* To cap off this discussion of evolutionary genetics, the confusing concept of noncoding DNA needs to be considered in more detail. The fundamental assumption of genetics after the discovery of DNA in the 1950s was that genes produce proteins -- "one gene one protein" was the (not completely hard and fast) rule. The problem to early genomics researchers was that there didn't seem to be any hard and fast relationship between the size of the genome and what might be imagined to be the "complexity" of the organism. Of course, it was very difficult to meaningfully characterize "complexity" -- on what strong basis would we assume that, say, a single-celled organism might not have a larger genome than a human? -- but genomes could vary considerably in size between organisms that were closely related and didn't really seem all that functionally different.
The puzzle simply got worse when it was discovered that only a few percent of the human genome was actually able to code proteins. Not only were there large segments of noncoding DNA between genes, genes themselves had noncoding segments, known as "introns", that were tossed out when the gene was translated by cellular machinery into proteins -- and there was well more DNA, on the average, in the introns than in the genes. What was all this noncoding DNA doing?
It did become apparent that a surprisingly large portion of the genome, at least 8% in humans, consists of either fossil genes or the insertions of viral codes into the genome. These "pseudogenes" no longer perform their original functions, if they perform any function at all -- thankfully in the case of viral insertions, since otherwise we could suffer from spontaneous viral infections -- and were clearly doing not much more than taking up space. Pseudogenes do have a useful function for researchers at least, since as discussed earlier they help trace the genealogy of species.
There have been suggestions that pseudogenes provide an injection of genetic diversity into the genome, and there are a few cases where pseudogene sequences do provide functions in the genome -- the parasitic wasp that produces viral particles from its genome and then injects them into a host has already been mentioned. However, such cases are freakish; most pseudogenes are clearly broken, and nobody has been able to demonstrate that pseudogenes have an evolutionary impact significant in comparison with normal mutational processes.
* In any case, pseudogenes would seem an interesting but not particularly controversial idea, but in 1972 the Japanese-American geneticist Susumu Ohno referred to them as "junk DNA", a catchy name that caught on. Ohno could not have known that the term would end up being such a headache. In the worst case, even in some scientific literature "junk DNA" was played up as synonymous with "noncoding DNA", despite the fact that it wasn't entirely clear that all noncoding DNA was useless.
The result was a long-running argument over whether noncoding DNA was mostly junk or whether it was mostly functional. It wasn't just a Big-Ender / Little-Ender argument among the professionals, either; creationists strongly believe that the genome reflects Design and so it can't, cannot, be mostly junk. The overall result is that the argument has now taken on a tone of antagonism and sniping well beyond that of ordinary academic technical disputes. The term "junk DNA" has become discredited, with some suggesting that "genomic dark matter" or just the "dark genome" would be a much better label: There's something in there, we're just not sure what it's all about.
It is generally agreed that some noncoding DNA is unambiguously functional -- "regulatory sequences", segments of DNA that, by providing binding sites for elements of the cellular regulatory system, control the actual expression of genes. It is true that some of the other noncoding DNA sequences are conserved, being relatively unchanging over time, meaning that they might actually be doing something useful since they're subject to selective "control".
However, to complicate this issue considerably, it has also been observed that functional gene sequences that should be conserved don't actually seem to be conserved, throwing that question into doubt. In addition, researchers have snipped out big chunks of conserved DNA from the genomes of mice, and the mice that were born differed in no perceptible way from their relatives that retained the sequences -- if there was any difference, it was subtle.
That's only the beginning of the ambiguities. There is the class of genes known as "jumping genes" or "transposons" -- too complicated a subject to discuss in detail here, enough to say that they are genes that relocate from site to site on chromosomes, sometimes copying themselves until large numbers of duplicated genes clutter up the genome. Transposons do in some cases seem to have functions, but it's hard to understand why a genome would need such large numbers of duplicated copies of the same gene.
It is known that introns often include small bits of genetic code near their ends that allow genes to be spliced together in different ways, which is clearly a function -- but they're just small bits of code, in no way demonstrating that the much larger remainder of the intron actually codes for anything. One interesting observation in this context is that the human gene for a blood-clotting protein named "Factor VIII" is about ten times longer than the Factor VIII gene for a chicken; both genes actually have about the same amount of coding DNA, they even have roughly the same number of introns, but the chicken's introns are much smaller. If the introns have a function, how does a chicken get by with much less intron code?
There doesn't seem to be any particular correlation between genome size and the taxonomy of organisms -- some organisms that seem to be of similar elaboration have genomes of very different size. Why does an ordinary onion have a genome five times bigger than a human genome? And why do members of the same plant genus as the onion have genomes that vary by a factor of four in size? If the entirety of the oversized genomes of these organisms is functional, then why can their close relatives get by with far smaller genomes?
In one particularly interesting example, genomic analysis of the bladderwort plant has shown only about 3% of its genome is noncoding DNA, the reverse of the ratio in humans. None of this ends up being conclusive one way or another, but that's kind of the point. Researchers think there is a method to the madness, but they just haven't figured out exactly what it is yet.
Advocates of function insist that if there was nonfunctional DNA in the genome, under MET it would be weeded out by selection. There's no strong logic for believing this to be so. Genes have an "evolutionary incentive" to make as many copies of themselves as possible, and so it would be expected that some genes would replicate to the maximum ability of the genome to bear. If the additional genes don't really affect the survival of the organism, selection is not going to toss them in the dumper; without any demonstrable evidence that nonfunctional DNA does any real harm, there's no reason to think it has to be thrown out. It has been observed that genes that get a lot of use tend to have less intron overhead than genes that don't get a lot of use, suggesting that selection will throw out introns if they become a burden.
There does seem to be a clear correlation between the size of the genome of a species and the size of the cells in that species, and the size of the cell does seem to have selective advantages or disadvantages, depending on circumstances. Maybe it's more like finding a piece of wadded-up newspaper in a package and thinking it's supposed to say something, when its only function is as padding. There are some creationists who claim that the dark genome actually contains potentially functional gene sequences left in reserve by an Intelligent Designer for the future use of an organism. That's the "cold storage" notion, which as already discussed, is nonsense.
* The issue of the dark genome led to a scientific flap in 2012 over the issue of a report by a study group titled the "Encyclopedia of DNA Elements (ENCODE)". ENCODE was focused on mapping the functions of the genome, which was all well and good, their work being praised by the science community. What didn't get much praise was the announcement in the ENCODE report that "80% of the genome had a function", which many science publications announced as "the death of junk DNA."
In reality, the ENCODE report did little to shine light into the dark genome, since its definition of "functioning gene" was one that demonstrated any activity at all. By that definition, transposons were functioning genes. Some of the critics of ENCODE said the report had done "tremendous damage". That might be argued, but there's no doubt it got a lot of people really steamed up, and the ENCODE people had to back up a bit.
The whole issue of "junk DNA" is actually irrelevant to the foundations of evolutionary theory. As noted earlier, if cluttering up a genome with dud DNA imposes a penalty on a organism, the junk is going to be gradually discarded via selection, or more correctly the population of organisms that are carrying it around will be gradually discarded. If it doesn't impose a penalty, the junk is going to accumulate. The dark genome remains a fascinating subject of study -- but MET neither stands nor falls on it.
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