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When Computers Replace Brains

When Computers Replace Brains

Intermediate

I really hate to admit it, but in certain situations I am old fashioned! In the good old days, biology students were taught about living organisms. We learned the appearance, life cycles and ecological preferences of various groups of plants, animals, fungi and microbes.

Then the interest changed to themes. In graduate school, I took a course on fungi in which we learned about dispersal methods, environmental influences on reproduction, mechanisms of inheritance etc. We were given long lists of organisms exhibiting one characteristic or another, but if we were not familiar with any of these fungi, all we were left with was memorized names, and no understanding.

ankeyboard-dnsThings are ever so much worse today when the trend is to study genomes (the chemical composition of the genetic material). Everyone wants to know the DNA sequence or the order of coding in the DNA molecule for each organism of interest. Then we are told what the differences are between the sequences of species X and species Y.

If you don’t know what Caenorhabditis or Arabidopsis (or other organisms under consideration) are, you will not be impressed by differences in the order of DNA codes in their genetic material. The worry today is that many biologists will run a sample of DNA through a machine and thereby obtain a name. Will they know what the organism looks like or even how it acts? In many cases they won’t.

It was evolutionary assumptions which led to interest in the specific order of information in each organism’s genetic code. Most scientists assume that changes in the details of the genetic code will lead over time to major changes in the appearance and biology of an organism. Descendants which are more recently descended from a common ancestor, for example first cousins, should show more similarity in coding sequences than a population of third cousins once removed. In the same way scientists look for similarities and differences in coding between organisms which they assume have descended from a common ancestor.

Thus there has been a major effort to document the exact sequences of the genetic material in well known organisms. The results have often been a surprise. That means the results have been contrary to evolutionary expectations.

Scientists would naturally expect that ordinary molds, such as one finds on rotting fruit and old bread, would exhibit quite uncomplicated patterns of DNA coding. A recent study of Aspergillus species is a case in point. You have seen such molds many times. These typically are dark coloured as a result of their spores.

aspergillus_sporesAspergillus nidulans is a common nuisance for ordinary people but a popular object of study in the laboratory. Aspergillus fumigatus exploits such good things as vegetable compost heaps, but it also occasionally invades the lungs of individuals with compromised immunity. This naturally is a very serious situation. It also produces a variety of compounds to which many people are allergic.

Lastly scientists recently studied Aspergillus oryzae, a microorganism used by oriental peoples for at least the past thousand years to make soy sauce (through the process of fermentation). The results of the DNA coding exercise were not at all what one might have expected. It turns out that the commercially useful species A. oryzae has about the same number of genes as a fruit fly!

In addition the genome of A. oryzae is 25% larger than either of the other two Aspergillus species. The commercial fungus turns out to have genes involved in the synthesis of numerous compounds not directly needed for normal growth, development or reproduction of the organism. It is these unusual products which make this organism so useful for improving the taste of foods.

Similarly another recent study looked at the genome sequence of the rice blast fungus Magnaporthe grisea, the most destructive agent of disease on rice. This fungus is very similar in its appearance to another common mold called Neurospora crassa and not that different from the Aspergillus molds also. Anyway the interesting point of the study of the rice blast fungus is how different the details of its genetic information are compared to Neurospora. The scientists conclude their study with the remark that the rice blast DNA sequence is as different from that of the presumably closely related Neurospora, as the human genome is from that of a tropical toad (Xenopus)! (Nature April 21/05 p. 985)

This unpredictable and unexpected degree of differences between some similar organisms notwithstanding, biologists have accumulated a lot of data which can be compared by computers provided with suitable software. When provided with a piece of DNA, modern laboratory machinery can produce a report on the order of the nucleotides (DNA code). Computers with suitable software can compare the nucleotide order and rank the DNA samples as the same as a standard or more or less different.

It has occurred to many people that this is an objective way to compare specimens. Here we have hard data evaluated by a computer. Perhaps, some have suggested, we no longer need specialists who can study the appearance and biology of an organism in order to identify it. All we need is a piece of tissue from which DNA can be extracted. Insert the DNA into the machine and let the computer (comparing the order of nucleotides with standards for each species already in the database) then make the identification. No fuss, no muss! DNA barcoding is not here yet, but it is a coming phenomenon.

The Census of Marine Life (see Animal Travel Plans in the Spring 2006 Dialogue) has jumped on the DNA barcoding bandwagon. On a 21 day survey in April 2006, scientists trawled the sea at a depth of 5 km in an area near the “Bermuda Triangle”. They catalogued 500 animal species including 12 new species. Now the scientists are barcoding or producing DNA sequences for the animals discovered.

The hope is that in the future, a water sample containing organisms can be sequenced for its DNA content and the presence of various organisms discovered from a comparison of the results with DNA standards in the database. No scientist needs to squint at any of these organisms again, their presence would simple be recorded by the machine/computer combination.

A consortium to promote DNA barcoding already exists. It consists of museums, herbaria, government organizations and private companies. Indeed a conference on the topic was held at the Natural History Museum in London in February 2005. The technique, it is hoped, will enable technologists to carry out the identifications rather than expensively trained scientists. Even botanical gardens are getting into the act. The New York Botanical Garden for example, is opening such a research centre in May/06 at a cost of $23M.

The question arises, are we moving too far away from an understanding and appreciation of whole organisms? Would barcoding, even if the system were effectively set up, really provide us with anything other than dubious reports of positive or negative occurrences? Some specialists query the wisdom of the barcoding idea (given the expense of setting it up), but the idea seems to be gaining momentum.

What we need rather than barcodes is appreciation and understanding of organisms and their ecology. The mandate of botanical gardens, for example, is to study and preserve beautiful and rare plants. What happens when their major interest becomes genome studies?

We do not advocate the abandoning of genome studies in appropriate venues. These reveal really interesting information (typically contrary to evolutionary expectations) as with the mold studies. But we do not want to see most of biology turned into a numbers/barcode game.


Margaret Helder
July 2006

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