Forum:Isaac Asimov Accurately Predicts Woes Of Bioinformatician
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9.3 years ago

I recently re-read Isaac Asimov's excellent Foundation series. I decided to read them in the order they were released rather than chronological order of the story. I just got to the last book, 'Forward the Foundation', published in 1993 shortly after Asimov's death. I came across an amusing section in which the main character, Hari Seldon, orders the complete genome sequencing of his grand-daughter in order to identify the genetic cause of her mental abilities. His exchange with the biophysicist is quite amusing in its accuracy and foresight. Keep in mind, this was written at a time when the human genome project was just being proposed. He quite accurately predicts that producing a genome sequence will be quick and cheap compared to the challenge of analyzing and interpreting the data. Although, it sounds like we will have better single-cell genome sequencing in the future. The ethical concerns surrounding sequencing and gene therapy are also accurate. Finally, I find it strangely comforting that tens of thousands of years from now, when our origins on earth are a mere legend, we will still be struggling with the under-funding of genome analysis. :-)

Partial excerpt (I strongly recommend you pick up a copy if you haven't already):

… It was not an easy task to obtain a complete genome of Wanda. To begin with, the number of biophysicists equipped to handle the genome was small and those that existed were always busy … And if another difficulty was needed, it was the fact that the process was infernally expensive. Seldon shook his head and said to Mian Endelecki, the biophysicist he was now consulting, "Why so expensive, Dr. Endelecki? I am not an expert in the field, but it is my distinct understanding that the process is completely computerized and that, once you have a scraping of skin cells, the genome can be completely built and analyzed in a matter of days." "That's true. But having a deoxyribonucleic acid molecule stretching out for billions of nucleotides, with every purine and pyrimidine in its place, is the least of it; the very least of it, Professor Seldon. There is then the matter of studying each one and comparing it to some standard. "Now, consider, in the first place, that although we have records of complete genomes, they represent a vanishingly small fraction of the number of genomes that exist, so that we don't really know how standard they are." Seldon asked, "Why so few?" "A number of reasons. The expense, for one thing. Few people are willing to spend the credits on it unless they have strong reason to think there is something wrong with their genome. And if they have no strong reason, they are reluctant to undergo analysis for fear they will find something wrong. Now, then, are you sure you want your granddaughter genomed?" … When it was over, Dr. Endelecki said, "I'll put the scraping under the microscope, choose a decent cell, and put my computerized gene analyzer to work. It will mark off every last nucleotide, but there are billions of them. It will probably take the better part of a day. It's all automatic, of course, so I won't be sitting here watching it and there's no point in your doing so, either. "Once the genome is prepared, it will take an even longer time to analyze it. If you want a complete job, it may take a couple of weeks. That is why it's so expensive a procedure. The work is hard and long. I'll call you in when I have it." She turned away, as if she had dismissed the family, and busied herself with the gleaming apparatus on the table in front of her … Hari Seldon walked into Dr. Endelecki's office, a nervous smile on his face. He said, "You said a couple of weeks, Doctor. It's been over a month mow." Dr. Endelecki nodded. "I'm sorry, Professor Seldon but you wanted everything exact and that is what I have tried to do." "Well?" The look of anxiety on Seldon's face did not disappear. What did you find?" "A hundred or so defective genes." "What! Defective genes. Are you serious, Doctor?" "Quite serious. Why not? There are no genomes without at least a hundred defective genes; usually there are considerably more. It's not as bad as it sounds, you know." ... "The imperfect genes-should we fix them? Can we fix them?" "No. In the first place, it would be very expensive. Secondly, the chances are that they would not stay fixed. And finally, people are against it. "But why?" "Because they're against science in general. You should know this as well as anyone, Professor. I'm afraid the situation is such, especially since Cleon's death, that mysticism has been gaining ground. People don't believe in fixing genes scientifically. They would rather cure things by the laying on of hands or by mumbo-jumbo of some sort or other. Frankly it is extremely difficult for me to continue with my job. Very little funding is coming in.

P.S.: In case you were wondering I didn't type this all out. I found the complete text of the book on a Russian website. I don't condone reading it there. I own paper copies and also the kindle ebook (and audio) versions. I definitely recommend purchasing your own copy. :-)

bioinformatician Forum • 7.5k views
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The bad news is that tens of thousands of years from now, bioinformatics will still be difficult and expensive work. The good news is that they'll be able to write their scripts in perl 6.

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haha. good one.

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I know where the Second Foundation is.

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I liked the very last line - "Very little funding is coming in". It is really amazing that somebody was able to come up with this at that time.

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that is pretty amusing

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Excellent! my favorite -> "The imperfect genes-should we fix them? Can we fix them?" "No. In the first place, it would be very expensive. Secondly, the chances are that they would not stay fixed. And finally, people are against it. " :)

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Great books. Asimov was a biochemist by training, probably explains some of the scientific authenticity.

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9.2 years ago
tayebwajb ▴ 110

I first heard of the word "genomed" during the recent "Understand Your Genome" conference hosted by Illumina #UYG13