Three old news items: from molecular systematics to nanotechnologies and genetic engineering

Paradoxes of Systematics The first task of the first human remains unfinished to this day. According to the Bible, before the fall (which determined the need to earn one’s daily bread by the sweat of one’s brow) Adam invented names for animals. Today more than a million species have been named, and the queue of the unnamed still hides beyond the horizon. Classifying the named species allows us to sort through a million names and make information about their similarity and difference more compact. Systematists still argue whether a single, correct classification exists. Optimists believe that this classification would accurately reflect phylogeny—the evolutionary history. Then, using molecular methods, we would learn how evolution proceeded and put everything in its proper place… Unfortunately, evolutionary changes are multidimensional, and projecting them onto a hierarchical system inevitably causes us to lose a significant portion of information. Which part? The part we deem less important. Do you think “objective” methods can determine which portion of information is most important? Abandon those illusions! Interpret, for example, this fact. Since the evolutionary paths of humans and chimpanzees diverged, humans have acquired 154 new genes, while our “backward” relatives, chimpanzees, have acquired 233! How to measure and compare these changes? By number of genes? By length of DNA sequences? By changes in lifestyle? One influential school of systematics says: if species change cannot be assessed “objectively,” it should not be taken into account at all, and only the order of branching in the evolutionary tree should be reconstructed. A straw‑man solution: why have a classification that ignores the main result of evolution—the change of species? On the other hand, difficulties in interpreting some results do not mean that those results are useless. Often the kinship (or its absence) of different groups of organisms established by molecular methods turns out to be so evident that established classification must be revised. Ornithologists have long separated two groups of vultures: Old‑World (the true vultures) and New‑World (Cathartidae). Although it was clear that these groups are not closely related, DNA analysis yielded unexpected results. American vultures are actually stork‑like. Their ranks include modern condors and the largest birds ever to have flown. We are talking about teratorns (“terrible birds”), “vultures” that in the Neogene fed on the remains of gigantic mammals. One of them, Argentavis, had a wingspan of 7 m and weighed 120 kg! Remember in Jules Verne’s *In Search of the Castaways* the condor that seized and carried a boy through the air? Real condors are not capable of such feats. Yet in our folklore European storks carry children in their beaks (holding the swaddling cloth), while American ones do it with their claws! The latest molecular data concern primitive groups of winged insects. It turned out that termites should not be placed in a separate order, but regarded as a family within the order Blattodea. It does not matter that, in terms of social organization, termites have surpassed all animals except humans. The social perfection of termites is a consequence of their ability to break down cellulose, the main component of wood. In termite guts lives a complex endosymbiotic consortium. Its core consists of highly specialized flagellates (long thought to be ciliates because under the microscope they appear covered with numerous motile cilia, like ciliates). What was considered cilia turned out to be spirochetes—elongated bacteria capable of twisting. The spirochetes inhabiting the termite gut line the surface of the flagellate, synchronize their movements and travel together as a single unit. Flagellates themselves cannot degrade cellulose, but they host symbiotic bacteria that have mastered this reaction. Swallowing tiny wood chips, flagellates feed them to their internal bacteria, and the processing products are shared with the motile spirochetes that provide them with movement. Termites, therefore, feed both on the products of their internal “zoo” and on its inhabitants. Despite all the wonders of endosymbiosis, cellulose digestion for termites is not a simple process; it cannot be completed in the gut of a single insect. Consequently, the same portion of food passes through the digestive tracts of many insects that eat each other’s feces. Ultimately, the resulting pellets of processed material are used to build termite mounds. These structures, sometimes reaching majestic sizes, provide protection and a favorable microclimate for collective wood degradation. And now it turns out that all this is done by cockroaches?! Imagine what a triumph of genetic engineering and other biotechnologies would be to create a strain of cockroaches containing a symbiogenetic complex capable of breaking down cellulose. Such cockroaches would consume not only food waste but also furniture and books. The scope of application of molecular systematics is expanding. The latest news: from soft‑tissue remains of a Tyrannosaurus found a few years ago in Montana, fragments of protein molecules (collagen, the basis of connective tissue) were extracted. Analysis of these fragments has so far yielded only a trivial result: the tyrannosaur is more closely related to a chicken than to frogs and newts. Was it worth disturbing remains that had waited 68 million years for this? Yes! Because a bad thing is a beginning. We will understand in which macromolecular matrices preservation is better, learn to search for them more efficiently and interpret them more insightfully, and in time discover something new. We shall live—see what comes… Nanotech Infection The cutting edge of modern engineering art is considered to be nanotechnologies. In recent years humanity has made considerable progress in this field. We have reasons to be proud of our inventiveness, but we must not forget that, besides us, all biosystems employ engineering solutions at the molecular level. Despite all our talents, in the few years of nanotechnology development we have not even caught up with the simplest biological systems. The cunning of our mind is opposed by the experience of evolution lasting almost four billion years. The price of error in this game has always been death. Those who could not solve the adaptation challenges were eliminated. Cellular life is based on finely tuned interactions of individual molecules. Chemical recognition is ensured by an extremely precise match of shape and charge distribution on molecular surfaces. One of the main ways to regulate the activity of cellular robots—enzymes—is through changes in their conformation (spatial arrangement of parts). The cytoskeleton, sensibly assembled from standard blocks, provides transport and interaction of molecules… We have not yet reached the technological level of the cell as a whole, but viruses and other molecular‑genetic infectious systems already attract the interest of nanotechnologists. In fact, a virus is a nanorobot. Some of its functional modules ensure attachment to required targets, others control its synthesis and self‑assembly. Imagine making viruses perform the nanotechnological processes we need! One of the first results of this kind was obtained at the Massachusetts Institute of Technology by a group led by Professor Angela Belcher. So far, viruses have been adapted to create high‑quality yet homogeneous surfaces—electrodes for lithium‑polymer batteries. The viruses were genetically modified to give their surface receptors affinity for the required molecules (in particular, cobalt ions). These viruses were deposited on electrolyte plates and immersed in a cobalt‑salt solution. As a result, the “builders” formed a porous layer of cobalt oxide with an exceptionally large specific surface area. The energy density of a battery built with such electrodes will be significantly higher than standard values. A bad thing is a beginning. The significance of this news lies not only in the emergence of a new technology for producing (at room temperature!) surfaces with prescribed properties. By placing on the virus surface receptors for two different molecules (which is relatively easy to achieve with genetic‑engineering methods), one can make it join those molecules with nanotechnological precision. Professor Belcher’s group also has viruses that coat themselves with semiconductors and then settle on gold electrodes. After obtaining the first samples of these nano‑tools, their production poses no difficulty—they replicate themselves in a suitable medium (cells). The principal obstacle that remains for assembling microchips is the development of methods for precise positioning of the attachment sites of the virus “builders.” By indicating to the virus, which carries various molecules, its location on the assembly surface, one could create circuits according to a predetermined plan. Various methods can be used to obtain such patterned surfaces. Probably the ideology of a “nanotechnological contagion” best corresponds to using a membrane of a genetically modified living cell. So, we will await further news and hope that virus builders will not turn out to be contagious to us. Gene Engineering of Counter‑Intelligence News agencies enthusiastically repeat a story about an alleged victory over cancer. Unfortunately, the victory is still far off, but any progress in this area is encouraging… Cancer is considered such a formidable disease precisely because cancer cells are the body’s own cells whose interaction with the surrounding environment has been disrupted. The result: removal of the brakes on proliferation and ease of dissemination throughout the organism. Moreover, in the “reborn” cells the block responsible for self‑destruction in case of damage is switched off. The diversity of cell types that can undergo this transformation is one component of tumor heterogeneity. Thus, melanoma (a widespread form of cancer) arises from the transformation of highly proliferative skin cells. The phenomenon of tanning is well known. In response to increased ultraviolet (UV) exposure, skin cells (melanocytes) increase synthesis of the black pigment melanin, which protects against excess UV. Why is melanin synthesized only after exposure? This is due to the dual effect of UV. Its high‑energy quanta are used for synthesis of vitamin D, an important regulator of calcium ion metabolism. Therefore, the skin of Europeans, who evolved in conditions where UV may be insufficient, is permeable to this radiation. However, excess UV is dangerous because it causes DNA damage. The immediate effect of UV (photodimerization of adjacent thymine bases) is repaired by cellular restoration systems, but they introduce errors that can impair cell function. Hence melanoma (cancerous transformation of melanocytes) is a common disease among Europeans and light‑skinned Americans. Nevertheless, melanoma is not considered the worst type of cancer. It is not only that the primary tumor is on the body surface. There is a well‑documented series of cases in which melanoma progression halted and reversed under the influence of the patient’s immune system. The properties of signaling molecules on cell surfaces change somewhat in melanoma, and immune “guards” that detect “alteration” may respond to this difference. In practice, they often do not respond… Researchers at the U.S. National Cancer Institute worked with a rapidly growing form of melanoma. They took immune cells (T‑lymphocytes) from a patient who managed to defeat his own tumor. Transferring them to other patients was impossible: the immune system would immediately launch a war against them. Therefore, the T‑lymphocytes of other patients had to be trained to acquire what the successful pioneer’s cells could do. The first step was identifying the receptor by which the recovered patient’s lymphocytes recognized tumor cells. This allowed determination of the gene structure encoding this valuable property. To transfer the gene into cultures of other patients’ T‑lymphocytes, retroviruses were used. Retroviruses employ a “backdoor” for transmitting molecular‑biological information. Using the enzyme reverse transcriptase, they synthesize DNA from an RNA template (the main information flow runs in the opposite direction). The resulting DNA fragment can integrate into the host cell’s chromosomes. Gene engineers insert the needed genes into retroviruses as “RNA versions,” infect target cells with the viruses, and hope that the required DNA sequence will land where it can function normally. Using retroviruses, the required gene was introduced into immune cells obtained from patients. Then, from the lymphocyte culture, those cells that acquired the necessary receptors were selected and expanded. These modified cells were infused back into the patients. To increase the chances of tumor eradication, patients underwent chemotherapy. The toxic blow affects all rapidly dividing cells, not only cancerous but also immune ones. Against the backdrop of a weakened immune system, the new lymphocyte clones showed sustained growth: they were found in significant numbers in fifteen of seventeen patients. Unfortunately, they succeeded in curing the disease in only two cases; the remaining thirteen patients who received the lymphocytes, as well as the two in whom the procedure failed, died. One and a half years passed; two patients remained alive. One of them required an additional operation. Thus, the essence of the new method is training a patient’s immune cells using molecular findings from individuals who have overcome the disease, with gene‑engineering providing the data transfer. Promoting the result, American physicians present the name and photograph of one of the rescued individuals. Thanks to the described procedure he attended his daughter’s wedding! Naturally, we can only rejoice for him. So, does this result point toward a victory over cancer? Unfortunately, for now it is merely a great stroke of luck for two survivors and a new hope for everyone else, while the proposed technology can still be refined. It is interesting to ask whether opponents of genetic engineering should demand a ban on such research?

The scope of application of molecular systematics data is growing. Latest news: fragments of protein molecules (collagen, the basis of connective tissue) were extracted from the soft tissue remains of a tyrannosaur found a couple of years ago in Montana. Analysis of these fragments has so far yielded only a trivial result: the tyrannosaur was more closely related to a chicken than to frogs and newts. Was it worth disturbing the remains that had been waiting for their fate for 68 million years for this? Yes! Because a bad beginning is a good start. We understand in which rocks macromolecules are better preserved – we will learn to search for them more effectively and analyze them more intelligently, and over time we will learn something new. Time will tell…

Nanoinfection Advanced engineering art is considered to be nanotechnology. In recent years, humanity has made significant progress in this field. We have reason to be proud of our ingenuity, but we must not forget that, besides us, all biosystems use engineering solutions at the molecular level. Despite all our talents, due to the years of development of nanotechnology, we have not even caught up with the simplest biological systems. The reversibility of our mind is opposed to the experience of evolution, which has lasted for almost four billion years. The price of error in this game has always been death. Those who could not solve the adaptation tasks set before them were destroyed. The life of a cell is based on refined interactions of individual molecules. Chemical recognition is ensured by the precise matching of shape and charge distribution on molecular surfaces. One of the main ways to regulate the activity of cellular robots – enzymes – is based on changing their conformation (spatial organization of parts). The cytoskeleton, efficiently refined from standard blocks, ensures the transport and interaction of molecules... We are not yet able to reach the technological level of a cell as a whole, but viruses and other molecular-genetic infectious systems are already of interest to nanotechnologists. In fact, a virus is a nanorobot. Its functional blocks ensure fixation on necessary objects, others control its synthesis and self-assembly. If only viruses could be made to perform the nanotechnological processes necessary for us! One of the first results of this kind was obtained at the Massachusetts Institute of Technology by Professor Angela Belcher's group. So far, viruses have only managed to adapt to create high-quality, but uniform in their properties, surfaces – electrodes for lithium-polymer batteries. The viruses were genetically modified to give their surface receptors affinity for the necessary molecules (in particular, cobalt ions). Such viruses were seeded onto electrolyte plates and immersed in a cobalt salt solution. As a result, the "builders" formed a cobalt oxide film with an exceptionally large specific surface area. The energy density of assembly on such electrodes of the battery will be significantly higher than standard values. A bad beginning is half the battle. The significance of this news lies not only in the emergence of a new production technology (at room temperature!) for surfaces with given properties. By placing receptors for two different molecules on the surface of a virus (and this is relatively easy to do using genetic engineering), it can be made to connect these molecules with nanotechnological precision. Professor Belcher's group has viruses that coat themselves with semiconductors and then are seeded onto gold electrodes. After obtaining the first samples of these nano-tools, their production is not difficult – in a suitable environment (cells), they multiply themselves! Among the fundamental difficulties remaining to be overcome for assembling microcircuits, the main one is the development of methods for precise positioning of attachment points for the assembler viruses. By indicating the position of the assembler viruses carrying different molecules on the assembly surface, circuits could be created according to a specific plan. The methods for obtaining such a patterned surface can be varied. Probably, the ideology of "nanotechnological infection" is best suited by using the membrane of a genetically modified living cell. So, let's wait for further news and hope that the assembler viruses will not be contagious for us.

Genetically Engineered Counterintelligence News agencies enthusiastically repeat the news about a supposed victory over cancer. Unfortunately, victory is still a long way off, but any progress in this area is welcome... Cancer is considered such a dangerous disease precisely because cancer cells are the body's own cells whose interaction with their environment has been disrupted. The result: the removal of reproductive brakes and ease of spread throughout the body. Furthermore, in these transformed cells, the block responsible for self-destruction in case of malfunctions is lost. The diversity of cell types that can undergo this transformation is one of the components of tumor diversity. For example, melanoma (a common form of cancer) arises from the transformation of rapidly dividing skin cells. The phenomenon of tanning is familiar to everyone. In response to increased ultraviolet radiation, skin cells (melanocytes) increase the synthesis of the black pigment, melanin, which protects against excess ultraviolet light. But why is melanin synthesized only after irradiation? This is due to the dual effect of ultraviolet radiation. Its high-energy quanta are used for the synthesis of vitamin D, an important regulator of calcium ion metabolism. Therefore, the skin of Europeans, who evolved in conditions where there might be insufficient UV radiation, is permeable to this radiation. However, excess UV radiation is dangerous because it causes damage to DNA. The direct effect of radiation (photodimerization of adjacent thymine bases) will be corrected by the cell's repair systems, but they will introduce many errors that can disrupt cell function. Therefore, melanoma (cancerous transformation of melanocytes) is a common disease among Europeans and white Americans.

Nevertheless, melanoma is considered not the worst type of cancer. And it's not just because the primary tumor is on the body's surface. A number of reliably documented cases are known where the development of melanoma stopped and reversed under the influence of the patient's immune system. The properties of signaling molecules on the surface of melanoma cells change somewhat, and the immune sentinels searching for "changes" can react to this difference. However, more often they do not react... Researchers at the American National Cancer Institute worked with a rapidly growing form of melanoma. They took immune cells (T-lymphocytes) from a patient who had managed to overcome his own tumor. It was impossible to introduce them to other patients: the immune system would immediately start a war with them. Therefore, it was necessary to teach the T-lymphocytes of patients what the cells of the fortunate pioneer could do. The first step in this direction was the identification of the receptor by which the lymphocytes of the cured patient recognized the tumor cells. This allowed determining the structure of the gene encoding such a valuable property. Retroviruses were used to transfer the gene into a culture of T-lymphocytes from other patients. Retroviruses use a "back door" in the transmission of molecular-genetic information. Using the enzyme reverse transcriptase, they build DNA from an RNA template (the main flow of information is directed in the opposite direction). The constructed DNA fragment can be integrated into the chromosomes of the host cell. Genetic engineers insert the desired genes into retroviruses in the form of "RNA versions," infect target cells with the viruses, and hope that the desired DNA sequence will end up where it can function normally. Using retroviruses, the desired gene was introduced into immune cells obtained from patients. After that, cells with the necessary receptors were selected and propagated from the lymphocyte culture. These cells were reintroduced into their hosts. To increase the chances of overcoming the tumor, patients underwent chemotherapy. The toxic impact affects all rapidly dividing cells, not only cancer cells but also immune cells. Against the backdrop of a weakened immune system, the new lymphocyte clones showed stable growth: they were found in significant numbers in fifteen out of seventeen patients. Alas, they were able to correct the situation in only two cases; the remaining thirteen individuals, to whom lymphocytes were successfully transferred, as well as the two in whom the procedure did not work, died. A year and a half passed; two patients remained alive. One of them required additional surgery. Thus, the essence of the new method lies in training the patient's immune cells, using molecular findings from people who have overcome the disease as a source of information, and the genetic engineering procedure ensures data transfer. When advertising the obtained result, American doctors cite the name and photograph of one of the saved patients. Thanks to the described procedure, he attended his daughter's wedding! Naturally, one can only be happy for him. So, does this result count as a victory over cancer? Alas, for now, it is just great happiness for two saved individuals and new hope for all others, as the proposed technology can be improved. It is interesting, should opponents of genetic engineering demand a ban on such research?

D. Shabanov. Paradoxes of Systematics // Kompyuterra, M., 2007. – No. 16 (684) D. Shabanov. Nanoinfection // Kompyuterra, M., 2006. – No. 15 (635) D. Shabanov. Genetically Engineered Counterintelligence // Kompyuterra, M., 2006. – No. 33 (653)