Rapid and slow evolution, body remodeling of pythons, and the selfish DNA of infusoria

Evolution in action, or Don't open your jaws for someone else's loaf The fact that evolution cannot be seen with one's own eyes upset many generations of biologists. For example, when Napoleon's army brought ancient Egyptian mummies of cats and crocodiles to Paris, the French Academy of Sciences created a special commission that was to determine whether evolution was occurring or not. Given that the age of the Earth was then estimated at six thousand years and a bit, the relative age of the mummies seemed very respectable. Unfortunately, no fundamental peculiarities could be found in the ancient animals. It is only from our point of view that the ancient Egyptian cats belonged to a special breed; the French were interested in their general structure. However, one member of the commission — Jean-Baptiste Lamarck — recorded in the report a dissenting opinion: that these results do not refute the very possibility of evolution. He was right. Since Lamarck's time much evidence of evolution has accumulated, although there is still less of it than one would like — it is extraordinarily difficult to study this phenomenon. One of the most graphic examples is the change of bivalve molluscs in the Aral Sea as a consequence of its drying out and pollution. The disruption of the conditions for the development of mollusc larvae caused an explosion of their variability. Some of the new forms adapted to a manner of life unaccustomed for them. In various parts of the former sea the molluscs Cerastoderma moved from life in the thickness of the bottom sediments to existence on the surface of the bottom. The result was a change of the shell that took it beyond the bounds of the norm characteristic of the genus and even the family. Recently the results of yet another study, documenting the course of evolution, were published. It is connected with the consequences of the spread of the cane toad across Australia, mentioned in the previous issue of "CT". In those regions that the cane toad has occupied, it proves a powerful factor of selection for predators that die of poisoning by its venom. Australian scientists studied museum collections of snakes assembled before the cane toad's appearance and compared them with modern specimens. Four species of snakes were studied; in two of them (precisely those that can feed on cane toads and suffer from their venom) a reduction of the head was recorded. The larger a snake's head, the larger a cane toad it can eat, and the more it will suffer from poisoning by the toad's venom. Under these conditions small-headed snakes have an advantage, and their share in the population grows. Of course, the recorded phenomenon is an example only of short-term adaptation. Sooner or later the surviving snake species had either to learn to avoid the toads or to neutralize their toxins. For example, the Central Asian cobra is a predator that feeds mainly on green frogs. And the larger the frog eaten, the more pleasant for the cobra. Slow immortality At the end of winter Cardiff University (Great Britain) became the source of two scientific sensations at once.

Astrophysicists coordinated from Cardiff discovered a whole galaxy of dark matter (see "CT" #581), and a professor of the university, the palaeobiologist John Parkes, reported the discovery of almost immortal organisms in the bottom sediments of the ocean. As is known, a substantial part of the products of the weathering of rocks, together with the remains of organisms, moves across the Earth's surface until it ends up on the bottom of water bodies. By human notions, sedimentary rocks form infinitely slowly; yet on the scale of the planet this is a fairly intensive process. In time the rocks from the bottom sediments appear again on the surface (sometimes in a metamorphic form), are destroyed by the forces of weathering, and the elements contained in them are again drawn into the biological cycle. But can life use the substances contained in sedimentary rocks before they are raised to the surface and destroyed? Until recently it was thought that practically no. Living systems require a flow of substances and energy to pass through them (to these two "pillars" a third can be added — information). And all processes in the sediments proceed extraordinarily slowly: time in them is, as it were, preserved. Until now scientists believed that the lower boundary of the distribution of life lies a few metres beneath the surface of the bottom. Parkes's group established that the substances located in the sediments are processed by bacteria buried together with their habitat. The rate of their metabolism is extraordinarily low, while their biomass, on the contrary, is large. By Parkes's estimates, the larger part (60–70%) of the bacteria inhabiting our planet live in the bottom sediments! Viable microorganisms have been found at a depth of over eight hundred metres beneath the surface of the bottom. However slow the chemical processes there may be, they can provide energy for redox reactions and, therefore, for life. An important source of energy for the "deep bacteria" is the hydrogen released from decaying organic matter. But the most fantastic thing is not this. The sediments located at a great depth were deposited very long ago. The bacteria immured in them have the same age as their environment. The age of the layers in question is measured in millions of years! The discovery of cells in such sediments was announced four years ago already, but until now it had not been possible to present convincing data that these bacteria are alive. Today Parkes reports that bacterial cells extracted from a depth of over four hundred metres beneath the surface of the bottom are alive and well. Their age is 16 million years. These cells (not cell populations, but precisely cells) were already living in the Miocene, in the epoch of the formation of our ancestors shared with the hominids. However, the existence of immortal bacteria immured in the sediments hardly brings them much joy: the rate of their life processes is reduced to the limit. And is immortality possible at all, even at very low rates of metabolism? At any temperature differing from absolute zero, ionizing radiation and thermal motion lead to changes in the cell's vitally important macromolecules. When a cell is in an active state, it continuously repairs these damages. It is generally accepted that, over millions of years, important information can be preserved only by selection — the preservation across generations, or culling, of the carriers of its various versions. In the case of "bottom" life, the activity of repairing breakdowns cannot be high, and selection is practically impossible. Even selection for the fixing of useful changes (which allow the bacteria to survive in the bottom burials) must be hindered. A microorganism that has lived for millions of years has almost no chance of leaving descendants: for this the thickness of the sediments must be destroyed and the bacteria released from imprisonment. The English discoverers of the new world assert that life on Earth must have arisen precisely in such conditions, in the thickness of the sediments. The earliest organisms known to us that inhabited the water column are 3.8 billion years old¹. In them, traces of cells have been found — carbon lumps with an altered ratio of the isotopes ¹²C and ¹³C, characteristic of photosynthesizing organisms. In the sediments photosynthesis would be impossible — so the organisms existed in the water column². So did life appear in the sediments even earlier? But how could it have evolved under conditions of hindered reproduction? Parkes's finds are too incredible to be believed at once. Healthy scepticism is never out of place when considering sensations. At the same time one does not want to insist that such a thing cannot be, because it can never be. It's hard to believe, but let us await new data… Why do you need such a large liver? Looking at any organism, we are inclined to perceive its form as something immutable. It is not so simple to learn to perceive structure as a process. Recall, for example, the effect named after the Polish zoologist A. Dehnel. The volume of the skull and the size of the brain in shrews undergo seasonal changes: in winter the braincase becomes lower, and in summer it again changes proportions, rising.

The brain changes accordingly, now decreasing and flattening, now increasing in volume. The example given is characteristic of animals with a record-high metabolism, whereas the phenomenon recorded by ecologists of the University of California (Long Beach) is, on the contrary, inherent in the most economical — the tiger pythons. Do not hurry to choose a suitable place for ambush. Patiently await the right moment. Gathering all one's forces, deliver an explosive release of energy and immobilize the prey, which may be equal in mass to the attacker. Using the astonishing plasticity of the body, swallow the prey (more precisely, "pull" oneself onto it), spending much strength and time on solving this task. Finally, digest the swallowed food and use the energy contained in it as fully as possible. Such is the feeding strategy of large snakes, in particular pythons. During the short period of struggle with the prey the python uses its white musculature, intended for work in a regime of insufficient oxygen supply. Such muscles are stronger than red ones, which require intensive blood supply, but they tire much faster. Swallowing the prey is a long process, during which one can rest and breathe through the tracheo-air channel located in the corner of the mouth. Far more complex is the digestion of large prey. If the python fails to digest it before it spoils inside its body, it must get rid of the food remains (otherwise it risks being poisoned). Within two days of swallowing a large animal, the python increases the size of its heart by 40%. Its whole body is subordinated to solving the most complex task: the liver triples, the intestine doubles, the intensity of the work of the digestive glands grows many times over. No other animal can so fully use the energy contained in food. Having digested 10 kg of meat, a dog gains about half a kilogram of weight, while a python (having digested even the bones of the prey) — over four. After the completion of digestion the enlarged organs become superfluous for the snake, and they shrink back to the usual state — taking into account the increased size of the whole individual. How the tiger pythons' know-how would help heart patients recovering after a heart attack! It would be good if the structure of our body could be rebuilt not by surgical intervention, but thanks to its own regulatory signals. However fantastic this may sound, pythons show that this is a complex but not hopeless task. A trip-up for selfish DNA Nothing makes a person err so much as overconfidence. Perhaps the theory of selfish DNA, originating with one of the founding fathers of molecular biology, Francis Crick³, is a consequence of the euphoria from the first successes of this science?.. It all began with the fact that geneticists considered genes the primary cause of organisms. Organisms are merely imperfect embodiments of genetic information, which serve to reproduce their masters — the genes. And when it was learned that the predominant part of DNA is not part of genes and codes for no proteins, it was named "selfish". So, a few percent of DNA works, determining the properties of the organism, while the rest of the DNA is responsible for nothing. It exists on its own.

Why perform any functions, if the organism will pass on all the genetic sequences it has received to its descendants anyway? The study of "selfish" DNA showed its extraordinary complexity and diversity. For some types of sequences more or less important functions have been found. Indirect data accumulated, testifying to a certain significance of the whole volume of an organism's genetic information. Thus, species differences unexpectedly proved connected not so much with genes as with genome "junk". However, the discovery of the purpose of some types of "selfish" DNA did not prove that its other types are also occupied with something useful. Nevertheless, faith in "selfish" DNA (which sacrifices the "interests" of the organism for the sake of the possibility of its own reproduction) began to change into the notion of "junk" DNA (not "selfish", but simply meaningless). For biologists with classical thinking such an approach is unacceptable. In their view, heredity is not the cause of organisms, but a means that arises in the process of evolution, which allows the preservation of the adaptive qualities of successful individuals selected by the environment. Any part of an organism, including any part of the genome, is regarded as the result of selection that increases the chances of survival and reproduction of the organism itself. Of course, accidents and breakdowns create useless fragments of the genome, which are selected out over time. Repetitive and regularly occurring sequences, from this point of view, must perform certain functions that explain their existence. And now an unexpected argument in this discussion has been provided by the study of the genome of the ciliate Tetrahymena (Tetrahymena thermophila), the results of which were published by an American-Canadian team of half a hundred scientists. Perhaps the cells of ciliates are the most complex in the world of the living. Some of them are enormous, since even the slipper ciliate can be seen with the naked eye (against a contrasting background with good lighting). In multicellular organisms different functions are performed by different organs. The ciliate's cell carries all of this itself, and also adapts to the difficult life of a very small creature. To control such a complex cell with the usual organization of the nucleus is hard or altogether impossible. Probably for this reason ciliates have two nuclei. The small nucleus (micronucleus) is responsible for storing inherited information and transmitting it to subsequent generations, while the large one (macronucleus) controls the cell itself. In the macronucleus each chromosome may be copied several hundred times, and from each such copy the necessary information is available for reading. During sexual reproduction the macronucleus (the working nucleus) is destroyed, and in the descendants it is formed anew from the material stored in the micronucleus (the archive). Scientific commentators draw attention to the fact that, according to the data obtained, the number of the ciliate's genes (over 27 thousand) corresponds to that in a human. But the most astonishing thing is not this. The researchers of Tetrahymena concluded that, in the formation of the macronucleus, the predominant part of the non-protein-coding sequences is discarded from it. So, the cell may well "wash out the junk"! If nothing similar happens in the micronucleus, there must be its own reasons for this. The preservation of non-coding DNA in the nucleus that ensures the heredity of generations is evidence of its evolutionary significance. And if such DNA is not needed for the cell's daily work, it is cleansed from the working genome. These are not all the news connected with the study of Tetrahymena. It uses a different version of the genetic code than other known organisms. The "meaning" of some codons depends on the context in which they are located (one and the same codon can mean both the end of a protein chain and an unusual amino acid not among the standard twenty). In other words, Tetrahymena acts not as a slave of its genetic information, but as its mistress. Probably the notion of genes as the primary cause of organisms should go to the rubbish heap. Remember Plato's analogy of the world and the cave? The prisoners look at the shadows on the wall (objects, organisms, and so on) and take them for reality, whereas these are only imperfect images of primary causes (Platonic ideas, genes…). Such views are merely a game of the intellect. Our life is connected with objective, not ideal, reality. Our success and failures are determined by the ecological environment in which organisms live. Look for the answers to questions precisely in it. 1 The oldest sedimentary rocks known to us (from the Isua formation in Greenland) are 3.8 billion years old (by radiochronological dating). 2 The Earth itself is estimated to be about 4.5 billion years old. 3 In fact, molecular biology also had a mother — Rosalind Franklin. Franklin's boss, Wilkins, without her permission handed the X-ray images of the DNA structure she had made to Watson and Crick. They quickly published the result, which Franklin herself would inevitably have reached. The resourceful men divided the Nobel Prize among the three of them. D. Shabanov. Evolution in action, or Don't open your jaws for someone else's loaf // Computerra, Moscow, 2004. — No.

47 (571). — pp. 17–18 D. Shabanov. Slow immortality // Computerra, Moscow, 2005. — No. 10 (582) D. Shabanov. Why do you need such a large liver? // Computerra, Moscow, 2005. — No. 12 (584) D. Shabanov. A trip-up for selfish DNA // Computerra, Moscow, 2006. — No. 35 (655)