About the benefits of useless knowledge
The crooked path to the truth
Konstantin Severinov, Professor at the Skolkovo Institute of Science and Technology and Rutgers University, USA, gave a lecture on the role of chance in modern biomedical research.
Photo: Yulia Mayorova
Konstantin Severinov's lecture gathered a full audience of the "library" on the second floor of the hotel "Ukraine". As always happens in crowded classrooms, someone understood everything, and someone only understood something; someone could not get to the lecture at all. Taking into account the interests of the last two categories of the public, we will retell here in our own words the amazing story of scientific research, which Konstantin shared with the audience. It shows how tortuous and unpredictable the path from ignorance to knowledge is, how many times you have to go back along this path, rethink dogmas, move from theory to practice and – what is especially curious – back, from practice to theory.
Chapter one. Darwin vs. LamarckThis story began 70 years ago.
Back then, biologists still knew almost nothing about genes and DNA. But they were well aware of Darwin's teaching that evolution proceeds by natural selection, and the material for selection is small random changes in the hereditary program of the organism. But there was also an alternative hypothesis: these changes may not be accidental, but dictated by the environment. The environment causes the organism to change in a certain way, and then these changes are inherited by its descendants (this idea is known as "Lamarckism").
Take, for example, bacteria. They have a natural enemy – bacterial viruses (bacteriophages). If you infect bacteria with the virus, they will almost all die. But among the disfigured corpses, there will certainly be a couple of cells resistant to the virus. They will pass this stability on to their children.
The question is: did this resistance arise by chance, even when there was no virus around? Or was it forged precisely in the process of fighting the virus (that is, under the influence of the environment)?
It is not so easy to distinguish between these two options in the experiment. Think for yourself: to make sure that the cell is stable, you will have to try to infect it with a virus – and after the meeting has already taken place, how can you prove that this meeting was not the cause of resistance?
How to do this was invented in 1943 by future Nobel laureates Max Delbruck and Salvador Luria. The idea is this. Let's take a hundred bacteria, put them in separate tubes and let them divide so that, for example, 10,000 cells accumulate in each tube. And then we'll add the virus. If, when encountering a virus, some bacteria become resistant – for example, 0.1% – then there will be about ten resistant cells in each culture. That is, an average of ten. Maybe there will be 6 or 17 somewhere, it's a matter of chance. But it is unlikely to be 0 or 50, it is too unlikely.
But if resistance occurs independently of the virus, then in some test tube it could occur even in the very first cell - and then all the descendants will be resistant. And at some point – in the third generation (then a quarter of the cells will be stable).
In any case, the spread of the number of resistant cells will be much larger. This is exactly what Luria and Delbruck observed. For which they duly received their Nobel Prize, even after a quarter of a century.
The conclusion of their work is as follows: mutations – including the resistance of bacteria to the virus – arise spontaneously. Accidentally. Whenever. The virus itself is not needed for this. Genes affect the circumstances of life, but the circumstances of life do not affect genes. Acquired traits are not inherited.
Science remained in this belief for another fifty years.
Chapter two. The science of yogurtThe specialists of the Danish company Danisco, which produces dairy starter cultures, faced tasks not as large-scale as those for the solution of which Nobel Prizes are distributed.
They were thinking about how to deal with biotech piracy. After all, the starter can be bought for money from the manufacturer, or you can borrow it from friends (just like housewives share a tea mushroom) without paying the manufacturer a single era. To bring the pirates to light, it was necessary to figure out how to accurately distinguish the breeds of lactic acid bacteria bred in the company's laboratories.
Fortunately, by this time (the 1990s) a lot was already known about genes and DNA. Scientists looked closely at the genome of their bacteria and saw one curious thing in it: a certain region of the genome was very different even in closely related bacterial lines. It was decided to use it as a kind of "fingerprints" in order to distinguish "their" breeds and bring the kidnappers to account.
This area of the genome looked rather curious: one piece of DNA was repeated many times there, and in the intervals other, unlike anything else, pieces were scattered. Recall that DNA consists of four letters A, G, C and T. The text looked something like this:
HERE YOU ARE, YOU ARE, YOU ARE, YOU ARE, YOU ARE, YOU ARE...
Only the "names" and the refrain separating them were about 30 letters long, and the refrain was written in a "palindrome": from right to left, then from left to right. But the main thing is this: the order and number of "names" made up the individual signature of the starter bacterium, by which it could be easily calculated, no matter into whose hands it fell.
They called this thing CRISPR – Clustered Regularly Interspaced Short Palindromic Repeats – and began to use it for its intended purpose, to identify the starter culture. And why such a thing is needed in nature – no one told the biologists from Danisco to investigate it, because applied science should concentrate on tasks important for practice.
Chapter three. The Nobel Prize is in questionMeanwhile, another important task for the practice of curdled science was the removal of lactic acid bacteria resistant to viruses – to the very bacteriophages, the experience with which Delbrück and Luria once allowed to establish the spontaneity of mutations.
Danisco specialists treated their cultures with different viruses and isolated cells that had acquired resistance.
And then, of course, new sustainable crops were catalogued – including determining their "signature", their "fingerprint", that is, the configuration of the CRISPR site. It was then that it turned out that the "signature" of most resistant microbes changed. In a monotonous series of repetitions, a new link appeared. A new name appeared in the list of names:
...ZDESBYLZAMA...
This added piece was different for different resistant microbes. But for all of them, it exactly corresponded to different pieces of the chromosome of the very virus to which resistance arose!
Isn't this the mechanism of bacterial immunity to the virus? It's easier to check this than a turnip: we take a piece of viral DNA, insert a bacterium into the chromosome between two fragments HERE and look: has resistance appeared?
Appeared.
Thus, the mechanism of acquired immunity in bacteria was discovered. Not only in lactic acid: the described thing, as it turned out, is ubiquitous in nature. It turns out that what happens is this: some bacteria infected with the virus manage to insert a piece of the viral genome into their CRISPR site – and immediately acquire an unknown weapon against the virus, which they pass on to their descendants.
And while there is no virus – naturally, there is nowhere to take a piece of its genome.
But let me! Delbruck and Luria seem to have proven a long time ago that resistance does not depend on the presence of a virus! So their experience was a mistake? We take away the bonus, we divide the money?
No. There was no mistake, it was an accident. Delbruck and Luria worked with a laboratory cell line, pampered and pampered. For some reason, the described mechanism of immunity did not work for her. This is what allowed scientists to establish the presence of spontaneous mutations. And the fact that in addition to spontaneous mutations, there are also directed adaptations to the environment is an additional complexity that biology is so rich in. This does not refute Darwin at all.
Chapter four. About the benefits of useless knowledgeThe case of inheritance of acquired traits is not yogurt for you: of course, serious scientists from university laboratories immediately became interested in the acquired immunity system and soon figured out how it works.
It turns out that short RNA molecules are read from all the unique DNA fragments of the CRISPR region, that is, from all the "names" of the guys who were "here". When one of the pieces of RNA matches a section of the DNA of the virus that infected the cell – and it will certainly match if the virus has already visited the cell and left its signature there – a special system comes into play. Her work begins with an incision being made into the viral chromosome. And then – a matter of technology: cellular enzymes spread the alien to smithereens. If anyone is interested in the details, then here they are http://elementy.ru/news/431989 .
A scientist who is only interested in the structure of nature – and who is not too concerned about the happiness of mankind – would stop there. But, thank God, there are not so many of them. And the others in this story were intrigued by an insignificant, at first glance, fact. The length of the "names" of the defeated alien viruses in CRISPR repeats is not so great – only 30 letters. In the real genome (both bacteria and humans), a piece of this length statistically occurs only once. But if we allow the possibility of at least one typo, the coincidences immediately become much more. In other words, if this system allowed typos, the cell would find similar "names" even where there are none, and in the end would blow its own chromosome to smithereens. That is, she would have died. This means that the system works absolutely accurately.
And if so, it can be used to find errors in a single letter in the genome. By the way, sometimes the life and death of a person depends on such mistakes.
Chapter five. Questions of life and deathA single typo in DNA can be the cause of severe and even fatal diseases – for example, sickle cell anemia or some types of blood cancer.
The patient's bone marrow produces cells containing the error. The only hope is to replace such a bone marrow with a donor one, in which there is no mistake.
But there is another option. We take his stem cells from the patient and correct the error in them artificially, in a test tube. And then we inject him back. And the diseased cells are gradually replaced by healthy, edited ones. There is no problem of rejection: the cells are their own.
But how to fix a mistake in many cells at once, how to find it among billions of letters of DNA? That's where the CRISPR enzymes come to the rescue. We already know that they can do it. And they can do something else: finding an error (in a single letter), they make an incision in the chromosome.
No one will allow them to do the rest of the destructive work. And the chromosome section is exactly the event that begins the exchange ("crossing over") between two homologous chromosomes, dad's and mom's, present in all cells of the body. An error on one chromosome is corrected according to the pattern of another, healthy one. The cell is recovering. Then it shares. And then he returns to the patient to make him healthy.
This is not a fantasy, this is the future. In this way, they have already learned how to treat mice. They will soon learn how to save people, because that's what everything was started for.
And you said: ugh, Darwinism, abstract theory! Fie, curdled milk, mundane practice!
ConclusionTwo conclusions can be drawn from this fascinating story.
Firstly, the complexity of life cannot be reduced to any dogmas, and even the most indisputable discoveries may need revision and additions. All biology students still go through the experience of Delbruck and Luria, but they also do not forget to warn them that life is more complicated than any theory.
Secondly, instead of a direct path "from theory to practice", cognition sometimes moves in tortuous and unpredictable paths. No one knew what an attempt to figure out one part of the chromosome of a dairy starter would lead to. Just at the time when modest corporate researchers in Copenhagen were poking at an uninteresting repeat of CRISPR, billions were allocated in the United States for a cancer control program. And where are those billions, and where is this cancer. And the solution to the problem – a small solution to one particular problem, but still – came from an unexpected side.
This example can teach fans of all kinds of "targeted programs" something, when all resources are thrown in one direction and they are waiting for an inevitable breakthrough there (and if there is no breakthrough, it means either sabotage or money has been cut). It doesn't happen that way, guys, you won't have a breakthrough. Science can develop only as a whole – or not at all. There is no need to tell science where to go: to find out the exact path to the truth, you must first go through it.
And then look back and say, "Wow!"
Portal "Eternal youth" http://vechnayamolodost.ru02.09.2014