ScienceHub # 03: Synthetic Microbiology
Continuing to visit the laboratories and look at how domestic scientists go to the future, we looked in on a microbiologist, genetics, Konstantin Severinov, and he told us about what the most active trends in biology are now, what scientists will soon need in this area and what kind of tasks they will decide.
Since the topic of the conversation, indicated in the title of the post, sounds like synthetic microbiology, we will start with it. There are many ways to define this science, it is important that all professions and areas of knowledge are intertwined in it, as it was in click chemistry . But it’s not even about interdisciplinarity, but the fact that physicists and mathematicians can now bring much more into biology than “wet” biologists. What do they want: to answer the question of how the genes in the cell are controlled. To do this, they began to model the processes occurring in the genes artificially.
Another area of ​​microbiology is that you can synthetically create a DNA molecule yourself, and then put it in a cell in which its genetic information is not. This is how a new cell will arise, which is programmed in the same way as its creator, in this case the scientist.
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Konstantin Severinov: “Synthetic microbiology arose when a certain number of physicists and mathematicians of the old memory decided to take up microbiology. Whenever a crisis begins in physics or mathematics — they have nothing more to look for — neither prove Fermat’s theorem, nor the Higgs boson, they go to biology and start doing something there. It's good. And the result of this kind of activity was that physicists wondered how exactly the work of genes in a cell is controlled. Biologists also did this, but physicists approached it on the other hand, they began to model these processes, to use various methods, up to differential equations, to look at the process of gene work in a cell. It turned out that in some cases it is possible, depending on a number of conditions that they themselves control, to change the spectrum of genes working in a cell, biologically active substances that the cell produces, and so on. This is part of synthetic biology. Another synthetic biology of a very high technological level is the science that Craig Venter continues to develop - a man who sequenced the human genome of himself. And this science consists in this: if we can determine the genome, that is, the set of sequences of the whole gene of the organism, and this is DNA, then no one prevents us from creating such a DNA molecule synthetically in principle. It will be very long, but we did it ourselves. ”
When the human genome was fully identified in the early 2000s, and they were able to read all three billion "letters" of which it consists, a new field emerged - bioinformatics. It is designed to store and analyze the information that genetics have managed to obtain. And now, when there is a lot of data, we need serious technical support. We must at least understand how and where all this data is stored, what technologies are needed for this. And bioinformatics should analyze, identify some interesting sequences with which one can experimentally work further. This is one of the most promising areas in biology right now.
The fact is that synthetic microbiology is an ideal model of the science of the future, so for now there are only projects, and you cannot touch the results of scientists. But in what areas it is applicable. This applies, for example, biofuels. If we still stop pumping hydrocarbons from the earth, then they must be produced by bacteria, which will be created by scientists specifically for this. They can do this on a large scale and much cheaper.
K.S .: “An article appeared in the October issue of Nature magazine, where it was shown that ordinary E. coli, the bacterium of which lives in our intestines, was made a factory for the production of oil, or rather not oil, but oil degradation products, which can be used as petrol. And this was due to the fact that using various methods of analysis, sets of enzymes were developed that can build an aliphatic chain, aliphatic substances - this is what oil consists of, of a certain length, from simple precursors such as carbon dioxide, ammonium, etc. and it turned out that E. coli, in which such genes are introduced, actually produces hydrocarbons. From here to the time when the corresponding hydrocarbons appear at the gas station, there is still a long way to go, but the first steps are certainly impressive, at least for venture investors. ”
The second important point on which the enormous powers of biologists are now thrown is the creation of new antibiotics. If this problem is not resolved in the near future, then humanity can return to the situation of the 19th century, when people died of the diseases that we now seem to be able to treat, such as tuberculosis and cholera. Now there are bacteria that are resistant to the forms of antibiotics that scientists have created. That is, the situation turns out, quite according to Darwin's theory, because in hospitals where antibiotics are used a lot, antibiotic resistant bacteria have been selected. And now they live and multiply there, but antibiotics do not affect them. Accordingly, in the future, the situation may turn out when we come to the hospital, pick up a frivolous bacterium there by modern standards, and die.
K.S .: “But now with the development of genomics, an understanding has arisen that the number of bacteria in the world is enormous, and the number of bacteria that we can cultivate, that is, grow in a cup, is very small, that is, 99.9% of all bacteria are dark matter - we cannot cultivate them, therefore we cannot touch them and isolate pharmacological substances. But the development of these methods for determining genomic sequences, which allow us to force a gene to work in a model organism, and not in its natural environment, suddenly reveals a range of possibilities in terms of the achievements of new genes and complexes encoding new antibiotics. Bioinformatic predictions must be made, genes that can give something interesting are identified, and then someone must appear who will make these genes work. ”
The education that biologists receive in modern universities is not enough to solve these problems. “Wet” biologists dealing with test tubes and experiments will become a thing of the past, as future specialists should be able to analyze the data obtained. Moreover, now in the USA and Europe there are companies that are doing all this “wet” work at outsourcing. It is not so expensive and is much more effective than a situation where scientists in the laboratory are doing the same. That is, there is a specialist who comes up with some concept based on the existing database, and in order to check it, he orders the company to prepare some genes, strains or organisms, thanks to which he then checks his predictions.
Ideally, of course, the scientist of the future should combine the skills of both a microbiologist and bioinformatics, but more likely there will not be firms taking orders soon, and there will be robotic stations performing all the necessary procedures. That is, the number of scientists in the modern sense who can and do something with their hands will fall, and people who can think, put forward concepts and theories on the basis of data obtained by robots will be in demand.
Where such people come from. Now you can only retrain existing specialists, but the question arises, who to retrain. Konstantin believes that it is not biologists, but mathematicians who can correctly raise a biological question and create an experiment scheme, but not to engage in the experiment itself. He believes that teaching mathematics to experimental biology is easier than teaching a biologist to understand data that is not associated with fluid transfusion and or microbe research.
K.S .: “Apparently, part of the work force could be engaged in computer analysis. This is similar to Borges’s Babylonian library — a huge number of texts — it’s so large that it contains all the texts that existed, will exist, and will exist, but they cannot be found. And we find ourselves in a similar situation, because the machines that sequence the genomes do it every day. Right now, millions of genetic texts fall into some kind of database. They contain information about everything alive. There is, for example, information on how to beat cancer - the only question is how to find it, how to systematize, what to look at, what questions to ask. But how far it is capacious activity in terms of the number of people I can not imagine. Bioinformatics is a popular profession, and a molecular biologist is smaller. It turns out that these are people with talents. ”
Those who are too lazy to read, can watch the video with Konstantin Severinov here.
Synthetic Microbiology. To the background
Since the topic of the conversation, indicated in the title of the post, sounds like synthetic microbiology, we will start with it. There are many ways to define this science, it is important that all professions and areas of knowledge are intertwined in it, as it was in click chemistry . But it’s not even about interdisciplinarity, but the fact that physicists and mathematicians can now bring much more into biology than “wet” biologists. What do they want: to answer the question of how the genes in the cell are controlled. To do this, they began to model the processes occurring in the genes artificially.
Another area of ​​microbiology is that you can synthetically create a DNA molecule yourself, and then put it in a cell in which its genetic information is not. This is how a new cell will arise, which is programmed in the same way as its creator, in this case the scientist.
')
Konstantin Severinov: “Synthetic microbiology arose when a certain number of physicists and mathematicians of the old memory decided to take up microbiology. Whenever a crisis begins in physics or mathematics — they have nothing more to look for — neither prove Fermat’s theorem, nor the Higgs boson, they go to biology and start doing something there. It's good. And the result of this kind of activity was that physicists wondered how exactly the work of genes in a cell is controlled. Biologists also did this, but physicists approached it on the other hand, they began to model these processes, to use various methods, up to differential equations, to look at the process of gene work in a cell. It turned out that in some cases it is possible, depending on a number of conditions that they themselves control, to change the spectrum of genes working in a cell, biologically active substances that the cell produces, and so on. This is part of synthetic biology. Another synthetic biology of a very high technological level is the science that Craig Venter continues to develop - a man who sequenced the human genome of himself. And this science consists in this: if we can determine the genome, that is, the set of sequences of the whole gene of the organism, and this is DNA, then no one prevents us from creating such a DNA molecule synthetically in principle. It will be very long, but we did it ourselves. ”
When the human genome was fully identified in the early 2000s, and they were able to read all three billion "letters" of which it consists, a new field emerged - bioinformatics. It is designed to store and analyze the information that genetics have managed to obtain. And now, when there is a lot of data, we need serious technical support. We must at least understand how and where all this data is stored, what technologies are needed for this. And bioinformatics should analyze, identify some interesting sequences with which one can experimentally work further. This is one of the most promising areas in biology right now.
What for?
The fact is that synthetic microbiology is an ideal model of the science of the future, so for now there are only projects, and you cannot touch the results of scientists. But in what areas it is applicable. This applies, for example, biofuels. If we still stop pumping hydrocarbons from the earth, then they must be produced by bacteria, which will be created by scientists specifically for this. They can do this on a large scale and much cheaper.
K.S .: “An article appeared in the October issue of Nature magazine, where it was shown that ordinary E. coli, the bacterium of which lives in our intestines, was made a factory for the production of oil, or rather not oil, but oil degradation products, which can be used as petrol. And this was due to the fact that using various methods of analysis, sets of enzymes were developed that can build an aliphatic chain, aliphatic substances - this is what oil consists of, of a certain length, from simple precursors such as carbon dioxide, ammonium, etc. and it turned out that E. coli, in which such genes are introduced, actually produces hydrocarbons. From here to the time when the corresponding hydrocarbons appear at the gas station, there is still a long way to go, but the first steps are certainly impressive, at least for venture investors. ”
The second important point on which the enormous powers of biologists are now thrown is the creation of new antibiotics. If this problem is not resolved in the near future, then humanity can return to the situation of the 19th century, when people died of the diseases that we now seem to be able to treat, such as tuberculosis and cholera. Now there are bacteria that are resistant to the forms of antibiotics that scientists have created. That is, the situation turns out, quite according to Darwin's theory, because in hospitals where antibiotics are used a lot, antibiotic resistant bacteria have been selected. And now they live and multiply there, but antibiotics do not affect them. Accordingly, in the future, the situation may turn out when we come to the hospital, pick up a frivolous bacterium there by modern standards, and die.
K.S .: “But now with the development of genomics, an understanding has arisen that the number of bacteria in the world is enormous, and the number of bacteria that we can cultivate, that is, grow in a cup, is very small, that is, 99.9% of all bacteria are dark matter - we cannot cultivate them, therefore we cannot touch them and isolate pharmacological substances. But the development of these methods for determining genomic sequences, which allow us to force a gene to work in a model organism, and not in its natural environment, suddenly reveals a range of possibilities in terms of the achievements of new genes and complexes encoding new antibiotics. Bioinformatic predictions must be made, genes that can give something interesting are identified, and then someone must appear who will make these genes work. ”
Scientists new type
The education that biologists receive in modern universities is not enough to solve these problems. “Wet” biologists dealing with test tubes and experiments will become a thing of the past, as future specialists should be able to analyze the data obtained. Moreover, now in the USA and Europe there are companies that are doing all this “wet” work at outsourcing. It is not so expensive and is much more effective than a situation where scientists in the laboratory are doing the same. That is, there is a specialist who comes up with some concept based on the existing database, and in order to check it, he orders the company to prepare some genes, strains or organisms, thanks to which he then checks his predictions.
Ideally, of course, the scientist of the future should combine the skills of both a microbiologist and bioinformatics, but more likely there will not be firms taking orders soon, and there will be robotic stations performing all the necessary procedures. That is, the number of scientists in the modern sense who can and do something with their hands will fall, and people who can think, put forward concepts and theories on the basis of data obtained by robots will be in demand.
Where such people come from. Now you can only retrain existing specialists, but the question arises, who to retrain. Konstantin believes that it is not biologists, but mathematicians who can correctly raise a biological question and create an experiment scheme, but not to engage in the experiment itself. He believes that teaching mathematics to experimental biology is easier than teaching a biologist to understand data that is not associated with fluid transfusion and or microbe research.
K.S .: “Apparently, part of the work force could be engaged in computer analysis. This is similar to Borges’s Babylonian library — a huge number of texts — it’s so large that it contains all the texts that existed, will exist, and will exist, but they cannot be found. And we find ourselves in a similar situation, because the machines that sequence the genomes do it every day. Right now, millions of genetic texts fall into some kind of database. They contain information about everything alive. There is, for example, information on how to beat cancer - the only question is how to find it, how to systematize, what to look at, what questions to ask. But how far it is capacious activity in terms of the number of people I can not imagine. Bioinformatics is a popular profession, and a molecular biologist is smaller. It turns out that these are people with talents. ”
Those who are too lazy to read, can watch the video with Konstantin Severinov here.
Source: https://habr.com/ru/post/201008/
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