One of the most interesting results over the last couple of decades has been the applicati

---
Master Index Current Directory Index Go to SkepticTank Go to Human Rights activist Keith Henson Go to Scientology cult

Skeptic Tank!

One of the most interesting results over the last couple of decades has been the application of molecular biology to the question of evolution. One considers molecules from different species that are functionally equivalent. If organisms are "perfectly" adapted, then all such molecules would be identical. But they are not. And the differences are such that one can construct a family tree of molecules. And (surprise, surprise!) the molecular family trees agree with family trees derived by traditional methods (at least when such family trees are well-established). The vertebrate fossil record is very good, because the preserved parts of backboned animals -- the bones and teeth -- are very revealing about their former owners and their way of life. The major outlines of vertebrate evolution have been clear since at least the late nineteenth century. So, biologists examine such molecules as fibrinopeptides (the clotting-system equivalent of the glass to be broken on certain fire alarms), hemoglobins (which trap oxygen when the carbon dioxide level goes down and release the O2 when the CO2 level goes up again), and cytochrome c (which transfers electrons from one enzyme complex to another in the "respiratory chain" between food molecules and O2). Alternatively, biologists can compare large quantities of DNA by finding out how difficult it is to separate two strands from two different species ("DNA-DNA hybridization") -- the more difficult to separate, the more matching (in a complementary sense) of the two molecules. They find that the branch lengths in these trees are approximately proportional to the time deduced for evolution along those branches, which suggests the existence of a "molecular clock". This clock seems to tick at an approximately constant rate, but with some interesting variations. This rate is highest for molecules with little selective constraint -- like fibrinopeptides. When there is more constraint, there is slower evolution, as in the case of hemoglobin. Great constraint means even slower evolution, as for cytochrome c. Thus, fibrinopeptides are good for the last 70 million years, (the divergence of mammals after the extinction of the dinosaurs) hemoglobin is good for up to 500 million years (the divergence of lampreys -- a jawless fish -- and the jawed vertebrates), and cytochrome c is good for at least 1200 million years (the divergence of the animals, plants, and some fungi, such as yeasts [_Sacchromyces_] and molds [_Neurospora_]). How does this happen? Some mutations produce bad effects, and are not preserved for obvious reasons. Other mutations produce good effects, and are clearly selected. And still other mutations produce no change in function. These cause a random walk of the resulting molecule's structure at an approximately constant rate. This effect is sometimes called "neutral selection". Some have labeled this mode of evolution "non-Darwinian", but that only means that this is an aspect of evolution uncontrolled by natural selection. And what are the results? Here is one out of many. Humans and chimpanzees have about 98-99% similarity in their genes The remaining 1-2% must contain some critical control genes, which account for the very noticeable differences in outward form. There is no body part possessed by either us or the chimpanzees that the other does not have, which implies that the differences are all a matter of size. Interestingly, we resemble baby chimpanzees much more than adult chimpanzees, which suggests how our large brains must have evolved -- by not growing all the way to the adult-chimpanzee form but only to the baby-chimpanzee form, a process sometimes called neoteny. This correspondence is not complete; our leg length and related features are an adaptation to walking, while our reduced toes are almost a rudimentary feature. Here is a table of organisms that branch off from the human-ancestry line, in the order determined from molecular comparisons: Chimpanzees (the closest) Gorillas (very close behind) Orangutans Gibbons and siamangs Old World monkeys New World monkeys Carnivores, rodents, ungulates (even- and odd-toed), elephants, whales Kangaroos Turtles, birds, etc. Frogs and toads Bony fish Sharks Lampreys Insects and other invertebrates Plants and certain fungi Does all this look familiar? It should. Since molecular methods agree well with the results of traditional methods in determining family trees, molecular methods can be used in circumstances where traditional methods are ambiguous (convergent evolution can sometimes obscure relationships). Some interesting work has been done in unraveling the evolution of birds, for instance. Indeed, I predict that, by the end of this century, many evolutionary riddles will be resolved with the help of molecular methods. Closer to home, it was molecular evidence that was used to establish that the human-chimpanzee/gorilla split did not happen about 15 million years ago, as was earlier believed, but only about 5 million years ago. The previous result was based on some rather flimsy evidence: some teeth of _Ramapithecus_ showed features more like human teeth than like ape teeth. However, in more recent years, more complete skeletons of _Ramapithecus_ have been found, and these show these apes to have been ancient relatives/ancestors of orangutans. Closer to our own time, there are some interesting results on the divergence of the various present-day human populations. Studies of variations in mitochondrial DNA reveal present-day human populations to be the result of divergence from some ancestral population that took place about 200,000 years ago. Additionally, there is an early branch in the mitochondrial family tree -- between Africans and the inhabitants of other continents, with Africans showing the most diversity. This suggests that _Homo sapiens_ evolved in Africa from a relatively small population and that present-day humanity has had little, if any, genetic contribution from (say) Neanderthals, a Eurasian human offshoot. That is why a population of present-day-like humans can be found 100,000 years ago (as was recently found in a cave in Israel), at a time when the Neanderthals were still alive (they apparently went extinct about 50,000 years ago). In the opposite direction, molecular evidence is helping to give a glimpse of the common ancestor of all Earthly life. Fundamental biochemical similarities -- such as a common genetic code and use of the same molecular building blocks -- suggest that there was only one such common ancestor for every organism known to exist. However, it is entirely possible that an organism with (say) a different genetic code or a genetic-material molecule other than a nucleic acid may be discovered. Research by Carl R. Woese and his colleagues (_Science_, v209, p457, 25 July 1980; _Scientific American_, middle 1981; _Microbiological Reviews_, v51, p221, 1987) has unraveled some of the earliest evolutionary patterns. They use a ribosomal RNA molecule (critical for protein synthesis) that is 1200--1400 bases long, thus reducing the statistical effects involved with comparing short molecules. Being involved in protein synthesis, this molecule has an important and constant function, and one expects it to be strongly selected for this single function in almost all times in almost all lineages. This makes it very good for probing evolution over long timescales. Which is what Woese et al. have done. Constructing a family tree of all organisms examined by this method, they find a range of interesting results. They find that (for example) lineages of aerobic bacteria (which combine food molecules with oxygen -- respiration) are surrounded by lineages of anaerobic bacteria (which break up food molecules -- fermentation). This suggests that oxygen metabolism independently evolved several times. This is consistent with the actual nature of oxygen use, which is always a last step in an otherwise anaerobic process, as if it was some evolutionary add-on. This is consistent with the contention that our atmosphere did not always have significant amounts of oxygen, and that when oxygen appeared, a variety of different organisms evolved ways of utilizing it. Looking further, they find that many Gram-negative bacteria (but not all) are mixed in among lineages of purple photosynthetic bacteria, which do not release oxygen and use a simpler photosynthesis process than do plants. This suggests that many purple bacteria have lost photosynthesis, but have kept parts of the photosynthetic electron-transfer chain for use in respiration (there are remarkable resemblances amongst these chains). Mitochondria, respiration organelles in eukaryotic cells with their own genomes and protein synthesis systems, also appear to be descendants of purple bacteria. Interestingly, they also find that the chloroplasts of plant and alga cells are closely related to cyanobacteria, the "blue-green algae", and that plastids (the general term) of red algae and plants are mixed in among various cyanobacterium lineages. Exploring more distant relatives, they find that lineages with photosynthesis diverged very early, suggesting that photosynthesis evolved very early among the "eubacteria", and was lost many times, notably amongst such groups as the clostridia, sometimes cited as primitive from their fermentation. The earliest eubacterium appears to be autotrophic, not needing any organic molecules, only sulfur or metal ions as a reductant (By comparison, cyanobacteria and plants use water as a reductant for carbon dioxide and nitrogen for making organic molecules). At least one early-diverging lineage appears to be thermophilic, having bacteria that live in hot springs and hydrothermal vents on the ocean floors. There seem to be three very early branches, judging from this ribosomal RNA molecule's tree: the "eubacteria", the "archebacteria", and the nuclei and cytoplasms of eukaryotic cells. Inside of each group, the sequences are at most about 20-30% different, while between the groups, the sequences are 40-50% different. And the "secondary structure," the pattern of self-helices, is nearly identical among the three groups. This clearly points to both common origin and strong structural conservation. The early divergence of the eukaryotic nuclei+cytoplasms from the eubacteria combined from the close relationship of the mitochondria and chloroplasts to various eubacteria indicates a multiple origin for different components of the eukaryotic cell. This endosymbiosis hypothesis was first proposed in the late nineteenth century, but has only gotten strong support from data collected over the last couple of decades. From a creationist standpoint, it would be hard to explain why an economical creator would create cells with multiple genomes and protein-synthesis systems. Interestingly, there is an evolutionary trend toward a single genome--many genes for proteins of mitochondria and chloroplasts reside in the nucleus, to which they must have moved from the organelles. The archebacteria are perhaps the most interesting group from the origin-of-life standpoint. Most of these organisms are anaerobic, and are often extremely intolerant of oxygen. The earliest branchings among these organisms are among various thermoacidophiles, which live in the hot, acidic environments of hot springs and hydrothermal vents. These are, for the most part, autotrophic, metabolizing sulfur or other inorganic compounts for energy. An offshoot of one TAphile lineage contains the methanogens, which make methane from carbon dioxide and hydrogen. These organisms are very common, living where organic matter is decomposing, e.g., swamps, animal intestines, and the stomachs of ruminants (Again, why would an economical creator come up with such contrived digestion as rumination?). Curiously, the other two branches are more similar to the archebacteria than they are to each other, in ribosomal RNA sequences, DNA-to-RNA polymerase structure, and other criteria. This suggests that the ancestors of the eubacteria and the eukaryotic nuclei may have arisen by rapid evolution from early archebacteria. Since rapid evolution may create the appearance of excessively early branch-off, it is entirely possible that the eubacteria and the eukaryotes evolved from separate branches of the archebacterial tree. In that case, the ancestral archebacterium, most likely a TAphile, was most like the youngest common ancestor of all life on Earth. It is certainly significant that an archebacterial TAphile appears to be the closest present-day organism to the ultimate ancestor's phenotype. The appearance of its habitats is an inevitable byproduct of volcanism amidst liquid water, both of which have existed on Earth for at least 4 billion years, thus allowing these organisms to become the ultimate "living fossils", having changed little in that period of time. It is also significant that this phenotype is well adapted to one proposed location for the origin of life -- the hydrothermal vent. A HV is produced when seawater seeping through cracks in solidified lava comes in contact with hot magma. It gets heated and rushes upward towards the surface, sometimes making a "black smoker" when it emerges from the seafloor. Why the HV as a site for the origin of life? Oparin originally proposed that early oceans were the site, and posited a reducing atmosphere for the early Earth to make that happen. However, more recent work indicates that the early atmosphere was most likely neutral, containing mostly nitrogen and carbon dioxide (The present-day atmosphere is oxidizing, since it contains oxygen). Urey-Miller experiments on the synthesis of organic molecules from inorganic mixtures work well in reducing environments (with an abundance of hydrogen and hydrogenated molecules), but not in neutral or oxidizing environments. So the Oparin Ocean picture is in deep guano, as some might say. Enter HV's. Water reacting with Fe++ (the most common oxidation state of iron in the mantle) makes Fe+++ and hydrogen. If we are to believe Thomas Gold's deep-earth-gas hypothesis, additional hydrogen-rich material will come from the Earth's interior. This reducing environment and the heat now make possible Urey-Miller syntheses and the formation of energetic intermediates, such as cyanides and phosphates. As this heated "soup" flows upwards, it reacts, catalyzed by the rocky surroundings. Being reducing, it can react with the relatively oxidizing unheated seawater, making additional energy available. Thus, there is no shortage of free energy for chemical reactions. If, among all the organic compounds and assemblages that result, a self-reproducing one arises, it will absorb raw materials from its surroundings and make more copies of itself. As these proto-organisms consume the most usable molecules in their surroundings, they evolve ways of making use of less and less usable (but perhaps more common) molecules. Eventually, they will have little or no need for outside sources of organic molecules, having become autotrophic. Since the autotrophic organisms will have as foodstuffs the most abundant molecules, they will tend to dominate the HV environments. All this time, these organisms will be adapted to hot and acidic conditions, thus being much like today's TAphiles. So, working from two directions, we seem to meet somewhere. So, the origin of life may not require the labors of (say) exogenous genetic engineers after all. -- Loren Petrich (a.k.a. Booji Boy) petrich@crnlastr.bitnet petrich@tcgould.tn.cornell.edu

---

E-Mail Fredric L. Rice / The Skeptic Tank