The powerful world of bioinformatics

The computer is increasingly being used to decipher, manage and organise the vast genetic information that is the raw resource for the emerging biotech economy. DEEPAK SHIKARPUR describes the exciting convergence of IT and biotech and analyses the potential impact on both these fields as well as the ramifications for humanity

After more than 40 years of running on parallel tracks, information technology and biotechnology are slowly beginning to fuse into a single technological and economic force. The computer is increasingly being used to decipher, manage and organise the vast genetic information that is the raw resource for the emerging biotech economy. Scientists working in the new field of bioinformatics are beginning to download this vast genetic information, creating a powerful data warehouse—a Biological Data Bank. The rich genetic information in these biological data banks is being used by researchers to simulate the natural world on the computer.

The industrial age would not have been possible without the invention of the printing press. Print technology provided a new means of communications to manage the fast-paced, complex world of coal and steam power. The print medium also redefined the way human beings organise knowledge. It introduced charts, lists, graphs and other visual aids. But today print technology is being augmented and increasingly subsumed by computer technology in the organisation and so is management of production, commerce and telecommunication. The primary role of new communication technologies will be to manage the genetic information of the new biotech marketplace just as print was used to manage the industrial marketplace built on fossil fuels.

Information technology is not so much an economic resource as it is a ‘language’ of management and coordination. Its destiny is intimately linked to the raw genetic resources that it will isolate, download, organise, interpret, edit and program in this ‘Biotech Century’. The computer and accompanying telecommunication technologies are the extension of the human nervous system into the world. In the coming years we will all come to terms with usage of the computer more and more as a ‘substitute mind’ or ‘language’—to manipulate, redirect and organise the vast genetic information that makes up the physical substance of living nature.

Vast biological information
Today, molecular biologists around the world are busily engaged in the most extensive data collection project in history. The researchers are mapping and sequencing the entire genomes of creatures from the lowliest bacteria to humans, with the goal of finding new ways of harnessing and exploiting genetic information for economic purposes. By the end of the twenty-first century, molecular biologists should have deciphered and catalogued the genomes of tens of thousands of living organisms—a vast library containing the evolutionary blueprints of many of the microorganisms, plants and animals that populate the Earth. Mapping the genomes of so many species will yield quantities of information that will dwarf by orders of magnitude anything encountered before. The biological information being gathered is so great that it can only be managed by computers and stored electronically in thousands of databases around the world. For example, the complete human genome—only one of the species that will be sequenced and mapped—were it to be typed out in the form used in a telephone directory, would take up five hundred volumes of a thousand-page directory of a typical city. That’s a database containing more than three billion entries.

Taking the analogy a step further, if we were to print out the data on all human diversity, the database would be at least four orders of magnitude bigger—or ten thousand times the size of the first database. In future, scientists are likely to concentrate their efforts on micromanaging and updating databases for small regions of the genome of individual species, and coordinating their research with others by way of ‘genome work stations’—computer terminals that can provide researchers with access to the genomic databases of their colleagues around the world.

Multidisciplinary cooperation
Collecting, downloading, managing, and utilising genomic information will require closer cooperation of researchers in the related fields of physics, mathematics, engineering, computer science, chemistry and molecular biology. The Human Genome Project has hastened the coming together of the computer and genetic sciences. Sequencing and analysing the three billion base pairs would not be possible without the help of computer scientists and increasingly sophisticated computational techniques.

The Human Genome Project is turning biology into an information science. Mapping and sequencing the genomes is just the beginning. Reorganising the whole of the natural world at the genetic level, with an eye to converting it to an array of useful commodities in the marketplace is a challenge. Understanding and chronicling all of the webs of relationships between genes, tissues, organs, organisms and external environments and the perturbations that trigger genetic mutations and phenotypic responses, is so far beyond any kind of complex system ever modelled that only an interdisciplinary approach, leaning heavily on the computational skills of the information scientists, can hope to accomplish the task.

Virtual biology
Computers are also being used to create virtual biological environments from which to model complex biological organisms, networks and ecosystems. The virtual environments help researchers create new hypotheses and scenarios that will later be used in the laboratory to test new agricultural and pharmaceutical products and medical treatments on living organisms. Working in virtual worlds, biologists can create new synthetic molecules with a few keystrokes, bypassing the often-laborious processes, which can take years of attempting to synthesise a real molecule on the lab bench. With three dimensional computer models, researchers can play with various combinations, on the screen, connecting different molecules to see how they interact. Chemists are already talking about “compounds that could reproduce themselves, conduct electricity, detect pollution, stop tumours, counter the effects of cocaine, and block the progress of AIDS.

In 1996, first DNA chip was made. The DNA chip closely resembles computer chips; they are packed with DNA and are designed to read the reams of genetic information in the genomes of living organisms. The first DNA chip was designed to detect genetic abnormalities. Scientists say that the day is not far off when DNA chips will be able to scan an individual patient, read his or her genetic makeup in precise detail and even be able to detect abnormal or malfunctioning genes. DNA chips will eventually be able to determine which genes are flicking ‘on’ or ‘off’ at any given time. Other DNA chips might be used to scan a throat swab to identify a specific microbe that might be the cause of a patient’s sore throat, even identifying specific genes in the bacteria that are resistant to certain antibiotics.

DNA supercomputer
The final integration of the information and life sciences comes in the form of the ‘molecular computer’ a thinking machine made of DNA strands rather than silicon. Scientists have already constructed the first DNA computer and a growing number of both computer scientists and molecular biologists predict that at some time in the early years of the Biotech Century, much computing will take place along DNA pathways rather than on the integrated circuitry of a microchip. DNA’s ability to compute information greatly exceeds the most advanced supercomputers that exist today. Unlike most conventional computers, which are sequential and can only handle one thing at a time, DNA is a massive parallel computing machine and can theoretically compute a hundred million billion things at once. DNA is essentially digital, which means that it can count. A coding procedure was invented then for translating DNA base pairs into strings of ones and zeroes. Then poured together the contents of test tubes filled with genetically sequenced molecules, which allowed the DNA to simulate the electronic gates by which computers make their yes-no decisions. In short the DNA was made to think.

The DNA supercomputer will bring the information sciences and life sciences together into a single technology revolution with the power to remake the world.

To facilitate the research process, many Internet-based sites and ASPs are including e-commerce features such as links to suppliers of reagents, DNA sequences, or research clones. Whether it is with data visualisation programs or through integration efforts at large corporations and Internet-based ASPs, the goal increasingly is to put the tools in researchers’ hands. Bioinformatics offerings continue to evolve and target individual scientists, often through their desktop computers.

Bioinformatics companies say they will increase access to more data and tools as they are generated, moving beyond the most widely used gene-sequencing analysis to include areas such as gene expression, protein identification and structure, biochemical pathway data, pharmacogenomics, and chemical structure and activity. From a user perspective, scientists hope to get integrated packages of data, software, patent citations, literature, and supplier links to support their research. These combined elements are anticipated to decrease time spent in handling, manipulating, transmitting, and analysing data to ultimately speed up drug discovery and development.

Bioinformatics companies are moving beyond gene-sequencing analysis to areas such as gene expression, protein identification and structure, biochemical pathway data, pharmacogenomics, and chemical structure and activity.

Deepak Shikarpur is executive director of the Computer Society of India. Contact him at deepakshikarpur@yahoo.com