Two rounds of recursive construction are enough to create a perfect long DNA molecule, enabling efficient biological action
Build perfect structures from imperfect components? It sounds like baking a perfect cake with not fresh ingredients. In other words, it sounds like an impossible task. But this is exactly what scientists from the departments of computer science and applied mathematics, and biological chemistry at the Weizmann Institute of Science were able to do. To do this they used a scientific concept called recursion, which we use, intuitively, to create and understand sentences like "the dog that chases the cat that bit the mouse that ate the cheese that fell out of the man's pocket is black". Using recursion, long DNA molecules can be assembled, hierarchically, from smaller building blocks. But, in the building blocks of artificial DNA, and also in the long molecules themselves, there are various errors scattered in random positions over the sequence. To use these molecules and obtain desired products, these errors must first be corrected.
Despite the fact that the artificially constructed molecules contain errors, it is possible and reasonable to expect that at least some of them will contain long sequences without a defect. These long perfect DNA segments can be identified, removed from the molecule, and used again in another step of recursive construction, where one starts from longer and more precise elements, increasing the chance of getting long perfect DNA molecules.
In the experiments carried out by the team, which was headed by Prof. Ehud Shapira from the Department of Computer Science and Applied Mathematics, and from the Department of Biological Chemistry at the Weizmann Institute of Science, and also included Dr. Gregory Linshitz and research student Toval Ben-Yehezkel, it was found that two rounds of recursive construction are enough to create a molecule Perfect long DNA, which enables effective biological action. However, the researchers say that if it is necessary, it is possible, theoretically, to continue this error correction process until a perfect molecule is obtained. These findings were recently published in the scientific journal Molecular System Biology.
This original repair method may be used for the rapid and precise construction of DNA molecules, as well as for the integration of DNA segments. "Synthetic DNA molecules are essential for biological and biomedical research, and we hope that building them efficiently and accurately through this recursive process can help progress in these fields," says Prof. Shapira.
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Michael,
I believe that in any transfer of a concept from a certain scientific world (such as computers) to another world (such as biology) one should be very careful in wording and clarify their full meaning.
As Hanan said, part of the problem here lies in the vague definition of recursion in the article. Another problem lies in the fact that all metabolic processes in the cell and body are recursive to one degree or another.
In short, these two contribute to confusion. Perhaps the word recursion is appropriate here, but the article itself is not entirely clear and makes me loathe the use of this term.
Roy:
I don't know if you read my last response (on the topic of the mental tool).
As someone who has dealt a lot with computer algorithms, I know that it is a powerful tool like no other.
I also want to point out that due to its being so useful among computer people - none of them consider the word recursion a bombastic word - it is simply an appropriate word in many cases and the case before us is one of them. In my opinion, the word was chosen in this article not because of its bombast but because of its appropriateness. She simply explains what they did better than any other word. I'm pretty sure if they didn't use that word it would be much harder to understand what they did and why it works.
Hanan,
A little late, but I agree with what Michael said. The process is indeed recursive because it receives as input its own previous output. It is difficult in biology to determine the existence of a unique recursion (perhaps because when you think about it deeply, any form of metabolism is actually a recursion), but that seems to be what the researchers did here.
I also agree with you that the researchers could have chosen a less bombastic word for the process, but big words sell articles better.
Roy.
Michael, in this case I am ready to accept the argument you raised, regarding the idea of a mental tool. I wonder if this is also what guided the researchers in determining the wording...
Personally, what bothered me here was the wording itself and not the idea of the research.
Hanan:
Your words are not correct.
Recursion is first and foremost a mental tool.
The diagnosis that if there is a certain process that if performed on the input will create a situation where the output can be used as input for the exact same process and that if you repeat and run the process you will end up with the desired outcome, it has tremendous power and I personally have used it a lot to solve problems.
Just as it is a good tool for solving problems, it is also an excellent tool for explaining the solution.
True Michael, but my question is simpler. It's also a loop, it's also an iteration, it's also a cyclical process, it's a cyclical process and so on...
Why did they choose the term "recursion"? I can't find any specific reason, except to give an inflated name to the idea itself (with all due respect to the development, which is extremely interesting). Anyone who is involved in the computer field immediately understands that there is nothing here in terms of nomenclature, but to give names that will catch the eye. From a practical point of view, this is a cyclical process, of which there are thousands (and also in which the output is the input of the next stage). In computing terms, there is no difference in the final product whether the process is done in recursion or in some other iteration. The differences exist only in the field of computers and are focused solely on the method of computer operation, the memory, the efficiency of the algorithm, the complexity of the running time of the algorithm, etc. From the point of view of the biological world, all of this has no meaning at all.
Hanan Sabat
http://WWW.EURA.ORG.IL
Hanan:
This is by definition recursion because it is a process in which the input at each stage is the output of the previous stage while what is done with the input to get the output is the same in all cycles.
This, by the way, is not surprising at all, both because the image of computer software and data is very suitable for DNA and because Ehud Shapira, who leads the project, is a computer science expert.
A very interesting invention, but I have to ask: why take terms from the computing world and attach them to some cyclical process? After all, most of the processes for building polymers, metabolic pathways, etc. are fundamentally circular, and so are artificial processes - such as the PCR operation.
Why couldn't the researchers simply say that this is an iterative process (similar to a "loop" in programming) and had to flaunt the idea of recursion (which is used in programming and mathematics, but has no advantage or realistic meaning compared to the other terms)??? I did not understand why and what is unusual about the above-mentioned process, which was decided to be called recursive and not simply a circular/looping/iterative/cyclic/cyclical process, etc.???
Roy Tsenza - your stage 😉
Hanan Sabat
http://WWW.EURA.ORG.IL