Four news about not quite classical genetics

Genetics: Between Victory and Defeat Scientific news agencies reported the successful completion of a large-scale study in human genetics, which can rightfully be considered a triumph of modern science. On November 23, the journal Nature published the results of a comparison of genetic texts from various individuals, carried out by an international, but primarily American, team of researchers. As everyone who studied biology in school knows, each gene occupies a specific location on a chromosome—a locus. Since, under normal conditions, human cells (except gametes) have two sets of chromosomes (one from the father and one from the mother), they contain two copies of each gene—one on each chromosome. An exception is made for genes located on the sex chromosomes; more precisely, those that are present on the X chromosome but absent from the Y chromosome. Genes can exist in different states—alleles. Thus, for a given gene one can have a pair of identical alleles or a pair of different ones. Allelic variation has been considered the main cause of intraspecific diversity. Of course, it was known that sometimes a fragment of DNA is lost or duplicated. Seventy years ago, experiments on Drosophila demonstrated the significance of changing the amount of genetic information when one of the eye‑development genes was duplicated. However, such data seemed exotic. A reasonably educated person understands that a gene set is a species‑specific trait, and people differ from each other by alleles of genes located in their proper chromosomal positions. Deviations are known, but they are rare and often accompanied by serious impairments… And now the new study. In its course, researchers searched the human genome for so‑called CNVs (copy number variations)—sequences longer than a thousand nucleotide pairs that exist in different copy numbers among individuals. Genomes of 270 people belonging to four groups were examined: members of the Yoruba tribe from Nigeria, white (European‑origin) citizens of Utah, Japanese from Tokyo, and Chinese from Beijing. To identify DNA sequence differences, proliferating cells were required. For this, donor cells were treated with a virus that induced their transformation into tumor cells¹. Special measures helped researchers distinguish genetic consequences of this transformation and exclude them from analysis. Then they applied two independent methods of DNA sequence comparison to register fragments of genetic text that are present in some people and absent in others. Result: 1 447 CNV sequences were found in the genomes of the studied individuals. They occupy about 12 % of the total genome size, affecting roughly the same proportion of all genes. By studying the chromosomes of relatives, the researchers were able not only to demonstrate that the recorded differences are transmitted from generation to generation (in accordance with Mendelian laws) but also, in one case—when comparing a mother and her daughter—to determine the time of origin of one DNA‑quantity variation. Such phenomena may result from unequal exchange between homologous chromosomes. Alongside allelic diversity within a particular gene set, the gene set itself turned out to be a powerful source of individual variability! One of the outcomes of the research team’s work was a map of CNV distribution across the human genome (see figure). The length of the red lines on this scheme reflects the frequency of each CNV among different people; the length of the green and blue lines indicates the number of nucleotide pairs in such sequences; and the green or blue colour denotes the presence or absence of association with segmental duplications of chromosomes. How this picture contradicts traditional notions of “normal” chromosome structure! [IMG_1] For those who continue to view genes as a program instantiated in an organism, the following analogy may be interesting. Imagine a program installer in which one copy differs from another by more than one‑tenth of the code. Some fragments are added, some are changed, some are discarded! Such a solution would be completely non‑functional, as it would destroy the program’s integrity. But if development is governed not by the genes themselves but by something that reads them (if you like, an epigenetic system), such changes become permissible. This situation corresponds to a novel whose different editions differ from each other by one‑tenth of their volume. Some episode is repeated, some is lost or becomes incomprehensible, yet the overall meaning for the reader likely remains the same². Thus, a powerful source of hereditary variability, previously underestimated, has been recorded. Experiencing joy over this major discovery, one can also look at the problem from another angle. Where did geneticists worldwide look before? What is today’s justification for the elaborate scientific theories according to which biodiversity is determined and calculated as a function of the observed set of allelic genes in a population? Is the current victory in knowledge not merely one side of the inheritance mechanism, a result of the defeat of chromosomal genetics methodology, which has been glorified as one of the pinnacles of human understanding? …Read a good exposition of the fundamentals of classical genetics. How simple and logical everything seemed! A Kinship View from the Shell Recently (“KT” #649) the author of these lines, calling sea urchins our close relatives, had to explicitly convince the editor that this was not a mistake. At that time a link was made to the similarity of early embryonic stages of humans and sea urchins. A new argument was presented this month in the journal Science. In an article by two hundred twenty‑eight (!) authors, the results of decoding the genome of the sea urchin Strongylocentrotus purpuratus are reported. The most striking conclusion is that the urchin is 30 % human (and, incidentally, a human is roughly the same proportion sea urchin). How can this be, when we are so different! A sea urchin is an organism enclosed in an egg‑shaped or disc‑shaped shell, studded with more or less developed spines. The main filling of the shell consists of gonads. The most complex organ of this animal is a structure of 35 mobile, articulating calcareous plates called the Aristotle’s lantern. At the top of the lantern are five teeth with which the urchin cuts food. The urchins move by “walking” with their spines. On the side of the body opposite the mouth are simple eyes and pigment spots… It is all the more surprising that a substantial portion of genes in us and this animal coincide. But what do these coincidences mean? Is some part of the human essence truly “locked” inside the urchin? It is not that simple. The genes that “account” for visual perception in us are also present in the sea urchin. Does this mean the urchin has visual‑information‑analysis mechanisms similar to ours? Of course not! Genes are a collection of switches that, together with other factors, influence the course of individual development. During evolution, the regulatory mechanisms of gene function can be reprogrammed. Buttons on a television remote and on a mobile phone may look very similar (sometimes even bearing the same digits), but that does not mean that pressing them yields identical effects. The effect depends not on the switches themselves but on the architecture of the system. Humans and urchins have different “systems,” and activation of similar genes produces different outcomes. In fact, the essence is not in the genes! And how well it all began… Recall the triumphant relays of molecular geneticists when they embarked on decoding the human genome. Let us bring our work to completion, learn how our development is governed, and be able to change it at will! Done. We obtained a massive amount of information. The significance of most of it remains unclear. We learned that besides genetic texts there are other developmental control tools that defy linear description. We confirmed that computational techniques are fundamentally insufficient to describe interactions even in moderately complex genetic (and non‑genetic) networks. And it is not only a technical issue. Our logic, the very features of our thinking, are not adapted to solving such problems. By origin, our psyche is an adaptation of an African savanna animal that had to evade predators, find food, and attract a mate. Our brain is poorly suited for quantitative analysis of interactions in a complex network of intertwined causes and effects! But what makes us – us, and the sea urchin – a sea urchin? Primarily, the structure of the oocyte. Also, the systemic complexity of the multitude of developmental control mechanisms that shape the epigenetic landscape—a set of permissible developmental trajectories—as well as unpredictable randomness that leads to the selection of one trajectory over another. What, then, is our true essence? We would like to understand. But the search must go beyond the gene level.

A Kinship View from the Shell Recently (“KT” #649) the author of these lines, calling sea urchins our close relatives, had to explicitly convince the editor that this was not a mistake. At that time a link was made to the similarity of early embryonic stages of humans and sea urchins. A new argument was presented this month in the journal Science. In an article by two hundred twenty‑eight (!) authors, the results of decoding the genome of the sea urchin Strongylocentrotus purpuratus are reported. The most striking conclusion is that the urchin is 30 % human (and, incidentally, a human is roughly the same proportion sea urchin). How can this be, when we are so different! A sea urchin is an organism enclosed in an egg‑shaped or disc‑shaped shell, studded with more or less developed spines. The main filling of the shell consists of gonads. The most complex organ of this animal is a structure of 35 mobile, articulating calcareous plates called the Aristotle’s lantern. At the top of the lantern are five teeth with which the urchin cuts food. The urchins move by “walking” with their spines. On the side of the body opposite the mouth are simple eyes and pigment spots… It is all the more surprising that a substantial portion of genes in us and this animal coincide. But what do these coincidences mean? Is some part of the human essence truly “locked” inside the urchin? It is not that simple. The genes that “account” for visual perception in us are also present in the sea urchin. Does this mean the urchin has visual‑information‑analysis mechanisms similar to ours? Of course not! Genes are a collection of switches that, together with other factors, influence the course of individual development. During evolution, the regulatory mechanisms of gene function can be reprogrammed. Buttons on a television remote and on a mobile phone may look very similar (sometimes even bearing the same digits), but that does not mean that pressing them yields identical effects. The effect depends not on the switches themselves but on the architecture of the system. Humans and urchins have different “systems,” and activation of similar genes produces different outcomes. In fact, the essence is not in the genes! And how well it all began… Recall the triumphant relays of molecular geneticists when they embarked on decoding the human genome. Let us bring our work to completion, learn how our development is governed, and be able to change it at will! Done. We obtained a massive amount of information. The significance of most of it remains unclear. We learned that besides genetic texts there are other developmental control tools that defy linear description. We confirmed that computational techniques are fundamentally insufficient to describe interactions even in moderately complex genetic (and non‑genetic) networks. And it is not only a technical issue. Our logic, the very features of our thinking, are not adapted to solving such problems. By origin, our psyche is an adaptation of an African savanna animal that had to evade predators, find food, and attract a mate. Our brain is poorly suited for quantitative analysis of interactions in a complex network of intertwined causes and effects! But what makes us – us, and the sea urchin – a sea urchin? Primarily, the structure of the oocyte. Also, the systemic complexity of the multitude of developmental control mechanisms that shape the epigenetic landscape—a set of permissible developmental trajectories—as well as unpredictable randomness that leads to the selection of one trajectory over another. What, then, is our true essence? We would like to understand. But the search must go beyond the gene level.

Wrong Genetics How do widely accepted views change? Old perspectives hold until a critical mass of contradictory facts accumulates. Traditional genetics, based on the ideas of Mendel, Weismann, De Freitas, and Morgan, can no longer explain a wide range of phenomena. Nevertheless, each new result in this line provokes sincere astonishment: how could alphabetic truths be wrong? A recent article in Nature triggered such a reaction again. Robert Pruitt (Robert Pruitt) of Purdue University, Indiana, and his colleagues studied inheritance of a trait in Arabidopsis thaliana³. This weed became the first plant with a fully sequenced genome and therefore turned into a favourite model for genetic experiments. Plants with defective versions of the hothead gene in both chromosomes were examined. Phenotypically this manifests as “gluing” (non‑separation) of petals and leaves. Strangely, when such plants were crossed, 10 % of the offspring had normal morphology, contradicting Mendelian laws. By analysing the gene sequences in parents and offspring, the researchers confirmed that the mutants had “rewritten” the gene, restoring it to normal. To substantiate this, it was necessary to demonstrate that no other gene, foreign material contamination, or other cause could explain the observed phenomenon. It turned out not to be the case. Most likely, the plants decoded RNA molecules synthesized from the genes of their normal parents (and retained in the cells) and repaired the defective gene version present in their chromosomes. This required the use of reverse transcriptase: an enzyme that synthesises DNA using an RNA template (Recall that not long ago such a possibility, contradicting the “central dogma of molecular biology,” seemed absurd). Thus, plants appear to possess a “rollback” mechanism (something like a computer “Undo” command) that allows them, when needed, to revert a trait to the normal state characteristic of their parents. Several leading geneticists, commenting on this report, called it sensational, emphasizing that no one could have even imagined the existence of such “incorrect” mechanisms. Unfortunately, the grounds for such suppositions (and the suppositions themselves) existed but were simply pushed to the periphery of the consciousness of specialists firmly convinced that they knew how the inheritance mechanism works. Let us prove our statements. What did we learn from the new results? For example, this case showed that an organism is not merely the result of a “letter‑by‑letter” implementation of an inheritance program. DNA information is not the “cause of the organism,” but merely one of its “tools.” This claim may seem doubtful to most readers. For instance, a programmer does not contemplate how the processor’s property of executing program commands arises. It is given a priori, and the problem is only how to use it optimally. Is inheritance not the same a priori property of life? No, in living organisms inheritance is the result of long‑term selection for the ability of “successful” organisms to produce “successful” offspring⁵. [IMG_2] Arabidopsis thaliana has a very small amount of genetic information, and therefore was the first in line for its complete reading In the 1920s, geneticists first investigated hereditary endowments of individuals from natural populations. The result was astonishing. Externally identical “normal” organisms turned out to be genetically quite different. Among carriers of “mutant” traits, some had altered genes (different ones), while others were genetically normal. However, carriers of altered traits differ from normal individuals by one important circumstance. Their characteristic change did not pass through the crucible of selection for reproductive stability across generations. Therefore, the manifestation of the mutation is often unstable. For example, the author was acquainted with a family carrying a gene that causes fusion of toe phalanges. In this family the full spectrum of the mutation’s manifestations was observed. One person could have completely fused toes on one foot and normal ones on the other! Thus, in our world advantage belongs to organisms capable of normal development (representing the best compromise from the standpoint of all adaptive tasks) even in the presence of certain deviations (e.g., in genetic information). This is the principle of stabilising selection. As a result, a portion of externally normal individuals are genetically mutants (carrying altered DNA that simply does not manifest in their development). Yet the mutant Arabidopsis was not only able to develop normally; its DNA sequences returned to the norm. Was anything like this known before? Yes. [IMG_3] These mutants “remember” the normal state of the gene characteristic of their parents and can, when necessary, correct the mutation Classic experiments showing that gene changes are independent of any need for them were performed on Escherichia coli that, after mutation, lost the ability to hydrolyse lactose (milk sugar). Such bacteria were grown on a medium lacking lactose and then transferred to a medium where lactose was the sole food source. Most of those bacteria perished, but some (those that underwent a reverse mutation restoring lactose utilisation) survived. The experimenters demonstrated that the mutation allowing lactose hydrolysis arose already in the original lactose‑free medium, i.e., it was random and non‑directed. It would seem clear. But in 1988 Nature published a paper by J. Cairns, who slightly altered the conditions of the classic experiment. In Cairns’ setup, bacteria unable to grow on the new medium did not die; they merely lingered in a miserable existence: they remained alive but could not divide⁶. Under these conditions they intensely remodelled their hereditary apparatus, and many quickly acquired the needed trait. Faced with the choice to die or return to normal, the mutant manages to “pick” a reverse mutation and become normal! The described example calls into question one of the cornerstones of modern genetics. We know that hereditary changes arise randomly and are not driven by need! Unfortunately, this postulate has also been challenged, and for a long time. In earlier searches for environmentally induced hereditary changes, the well‑known “Michurinist” Lysenko, on his experimental farm in Gor’ki Leninskiye, fed cows chocolate. The cows produced very fatty milk (as expected!), and Lysenko hoped this trait would be passed to their offspring. It did not. In 1984, Science published an article by J. L. Marx, in which he recalled the “Lysenko ghost.” When flax plants were grown on soil with excess mineral nutrition, they grew tall and robust. However, when their progeny were grown on ordinary soil, they still retained part of the parental tallness for many generations. As shown in several papers⁷, excess nutrition leads to additional copies of a growth‑accelerating gene being inserted into flax chromosomes and stably transmitted to offspring. What else is new in the Arabidopsis report? That reverse transcriptase may participate in correcting hereditary information in higher organisms. But recall—recently “KT” reported⁸ a well‑substantiated hypothesis that virus‑like particles take part in the inheritance of immune traits. Presumably, they transport information about dangers encountered during an organism’s life into germ cells and, via reverse transcriptase, integrate this information into genes. Thus, new data on inheritance in Arabidopsis continue a series of results gradually reshaping our view of the inheritance system. A drop hollows a stone: what children are taught in schools and what university students learn can no longer be taken seriously. Yet is such a situation now characteristic only of genetics?We will not limit ourselves to paramutations! French scientists have published the results of a study that sparked talk of another crack in the foundation of the proud edifice of modern genetics. In fact, once again only school‑level simplifications, widely spread in the science of inheritance and beyond, have crumbled. Recall the school biology course. You were authoritatively taught that the traits of organisms are determined by genes—segments of DNA. Changes in these segments arise solely as unpredictable “breakdowns,” reflected in cells and organisms—the containers of genetic information. Faithful RNAs help convey information from the majestic DNA to the executing ribosomal machines. Natural selection is said to pick up and copy the consequences of random DNA errors, resulting in the supposed spontaneous appearance of useful traits. Their accumulation gave rise to us and the entire living world in which we find ourselves. These reflections would be endorsed not only by a conscientious schoolteacher but also by the majority of professional biologists who work on other problems. Yet this picture is extremely far from the actual state of science (discussed, re‑examined, dynamic collective knowledge). Most traits important for survival are not encoded in DNA but arise as a result of the individual development of the organism as a whole. Pinpointing a specific cause and its effect amid the tangled developmental interrelations is usually impossible. It succeeds either in cases of a clear malfunction (a gene breaks → an enzyme disappears → the bacterium cannot use the nutrient medium) or in situations where two stable developmental pathways exist and a well‑tuned genetic switch toggles between them (the pea plants with yellow/green and smooth/wrinkled seeds in Gregor Mendel’s experiments). However, for those traits that determine the life success or failure of a given organism, the entire genotype and many additional factors are involved. Even knowing all initial conditions, we cannot precisely predict which trajectory an organism’s development will follow. Unfortunately, a systematic classification of traits by the degree of pre‑determination during development still does not exist. Consequently, conclusions drawn from studies of simple biochemical traits are extrapolated to the whole set of organismal properties. DNA and other carriers of hereditary information are not the causes of cells and organisms, nor their “true essence” (“KT” #567), but rather tools that, incidentally, can be deliberately restructured when needed. Some DNA changes are more likely than others and occur more frequently precisely when there is a demand for them (“KT” #585). The information‑reading system from DNA both writes and modifies the text with which it interacts. RNA produced by this interaction undergoes various rearrangements, the mechanisms of which are only partially understood. The properties of proteins synthesized on ribosomes depend both on their amino‑acid sequences—ultimately derived, through all the intervening steps, from the DNA sequence—and on interactions with other molecules. Contrary to the wishes of simplicity lovers who want a one‑to‑one correspondence between an elementary cause and a concrete effect in every case, complex systems possess holistic properties and often can transmit (inherit) those properties over time. One example: what and how something is done in a particular cellular locale is determined by the cytoskeleton—the network of protein filaments that permeates the entire cell. These filaments transport and sort various cellular components. In ciliates, the cytoskeleton also coordinates the countless cilia on the cell surface. If, by micro‑surgery, a patch of the ciliate’s surface is cut out, rotated 180°, and re‑inserted, the cilia on that patch will beat in the direction opposite to the overall movement. Remarkably, such a patch can persist for several generations of the operated ciliate’s offspring! The architecture of the cytoskeleton is so complex and integrated that it can transmit its properties during cell division. When studying inheritance, we face a knot of interconnections whose complete untangling is a superhuman task. The DNA–RNA–protein–trait chain is only one of many pathways. Naturally, when a simple informational channel was described, an illusion arose that it could explain all organismal properties. Now, fragment after fragment of alternative pathways are being uncovered—for example, protein‑to‑protein information transfer, RNA‑to‑DNA transfer, etc. Each such discovery is accompanied by claims that “traditional genetics has been refuted.” One recent example is the discovery in the model plant Arabidopsis thaliana of the ability to correct mutant genes in its own genotype (“KT” #585). It was assumed that RNA molecules played a key role, “remembering” the gene’s natural state and restoring mutants to normal. So what has been discovered this time? Minoo Rassoulzadegan and colleagues at the INSERM institute in France worked with genetically modified brown hamsters (Scotinomys)9, close relatives of mice. They used a hamster line with an artificially induced mutation in the Kit gene. As you recall, advanced organisms usually possess two copies of most genes, located at the same positions on the maternal and paternal chromosomes. Hamsters with two mutant Kit alleles die; carriers of one mutant and one normal allele display characteristic white patches on their fur, while carriers of two normal alleles have (or should have) a normal appearance. However, it turned out that the external mutation phenotype persisted in genetically normal hamsters whose father, mother, or more distant ancestor carried mutant Kit genes. This phenomenon is called paramutation. Genetically normal but externally altered individuals transmit the anomaly to offspring for several generations (albeit with gradual weakening). What then carries information from ancestors to descendants if not genes? It appears that RNA synthesized from mutant genes is fragmented but retained in the cell (likely bound to some carriers). Especially many such fragments are found in germ cells. In the cells of genetically normal offspring, these RNAs interfere with normal gene function and somehow miraculously reproduce analogous molecules. Consequently, the RNA synthesized from the normal gene becomes abnormal in their presence. This resembles the “work” of prions—protein molecules with altered spatial folding. “Normal” proteins synthesized by a cell in the presence of prions become prions themselves. “Normal” RNA synthesized in the presence of mutant RNA becomes similarly altered. As for the elevated RNA content in germ cells… Charles Darwin, in his later years, formulated the hypothesis of pangenesis. According to it, the body’s cells discharge special “gemmules” into the germ cells. Thus, germ cells accumulate information about the organism’s current state. And how they laughed at the author of this hypothesis10! The peculiarity of the described experiments is that information from an artificially created mutant gene was capable of non‑traditional reproduction. We are dealing not with an exclusive property of that gene but with a “side door” that other informational streams might also use. From this circumstance, serious conclusions can be drawn. Technological advances have predetermined the use of technical analogies in our attempts to understand living systems. How we would like to identify in a cell an information‑storage block, a coded transmission pathway, an execution block, and to write precise algorithms governing interactions among these and other subsystems! Then life would be organized as if created by a mind like ours. In reality, life made itself, passing through countless attempts to solve the problem of adaptation and the memorization of successful choices. In a living cell, the information carrier, its reader, interpreter, and executor are tightly intertwined. Inheritance is not the cause of evolution but its consequence. Billion‑year selection acted simultaneously on organisms’ ability to generate advantageous traits and on the ability to transmit those traits to offspring. Anything that cannot be inherited by any route lacks evolutionary potential. “Normal” genetic inheritance, conformational information transfer between protein molecules (as in prions), cytoskeletal “memory,” paramutations, and likely many other mechanisms are different, complementary solutions to the problem of transmitting survival‑critical traits to descendants. By the way, the main reason that made humans human is the solution of the same problem. We are a species specialized in adaptation through cultural inheritance, the transmission of traits from individual to individual via learning. Our evolutionary breakthrough is a consequence of this informational channel being far more efficient than genetic and other channels. It is a rapid route allowing information transfer between individuals regardless of kinship. It is open to large volumes of transmitted (heritable!) information. Yet, if one probes the informational flows and interconnections in our bodies, many more “side doors” will be found. I bet the French discovery is far from the last in this series! 1 Are you, dear reader, willing to give a sample of your cells so that, by infection with Epstein‑Barr virus, they become lymphoblastoma cells? Something about this idea is repellent Back to text