Content-type: text/html ~ Stephen's Web ~ The Human Genome

Stephen Downes

Knowledge, Learning, Community

Oct 27, 2000

The decoding of the human genome is one of humanity's greatest achievements, a crown jewel in the history of knowledge, an accomplishment so full of promise and potential it is impossible at this time even to grasp all of the implications.

In a riveting lecture, Dr. Lap-Chee Tsui of the Hospital for Sick Children described the research process and unraveled for the audience the many layers of the human genome.

He had two major messages:

1.      The human genome is complex and unbelievably difficult to decode, and

2.      The human genome project was - and could only have been - an international effort requiring the cooperation of teams of scientists around the world

He didn't say it, but I will: such an accomplishment is only possible in an environment of global communication and information sharing. Such an accomplishment can only be accomplished by a society as a whole. It must be one of those "social visions" described by d'Aquino and Stanley.

And he didn't say this, but I will: who owns the human genome?

This is not an idle question; large segments of the human genome project were accomplished by private companies who feel they have a proprietary interest in the outcome of the research. But what government will stand and say that the secrets of life itself belong to a particular individual or business?

On the other hand, Harvard was allowed to patent a mouse.

This question becomes more difficult when we look at actually implementing the knowledge from the human genome project. Consider, for example, the Physiome Project, the objectives of which are to add physical functionality to the genome by modeling and adding logic to observed physiological processes.

For example, Oxford professor Dennis Noble described how he modeled a human heart from the cellular level. When looked at from the genome level, the biological system is like a self-assembling computer. Understand how the computer works and you can understand - at any level of understanding - how different drugs interact with the body, how different character traits develop, and more.

This produces enormous savings in health care and physiological research - if the results are shared.

It is one thing to say blithely that we must foster a gift culture when it comes to giving dollars to the homeless; it is quite another to say the same thing when it comes to giving the secrets of human physiology to society at large.

ButÂ… what's good for the gooseÂ…

And remember: the people who benefit from information sharing will control the political processes that could bring it about. Though the transition will probably not proceed smoothly; we could easily envision a 'Seattle' over the issue of a genome monopoly. Or - more likely - long legal battles over a DNA-Napster in which the secrets of genetic manipulation are shared world-wide like a piece of music or the latest shareware software.

And once people are able to manipulate genetic material with their home PCs (and have no doubt about it, they will have this capacity), the issues of genetic copyright take on a whole new meaning.

The lesson here is that information comes in many forms, and if the mantra that information will be shared is true in one place, it is true everywhere.

Moreover, not only do we know that this is the case, we know how is is going to be accomplished.

Tsui, Noble and other eminent academics in the field are working against what is often called the "Tower of Babel" problem: many different vocabularies are being used to express the same concepts. The University of Alberta might have one set of terminology, Oxford another and Stanford yet another.

But because of the need for global collaboration and data sharing, they are working toward a common terminology. And because large projects - like the human genome project - require work from people in many disciplines, it is important that the terminologies be machine readable.

Noble's simulations, for example, require thousands of differential equations to be solved every second. In order to implement this in a computer, he would have to become an expert computer programmer. But instead, using a machine-readible language, he works in an environment which simulates these mathematical computations. What this means is that he and a computer programmer share the same language for expressing mathematical caculations. The programmer worries about how the computer will actually compute the value, and Noble worries about which calculations he wants to use at a certain time.

Thus, the Human Genome project and the Physiome project are moving toward a series of machine readable languages: MathML, CellML, AnatML, BSML, GEML, SBML and more (see ). These markup languages are all flavours of XML and all interact with each other.

A similar development is occurring in other fields. Online learning, for example, has the Dublin Core, IMS and SCORM, all vocabularies and protocols expressed in XML. Newspaper publishers have NewsML and RSS. The same process will in time spread to all areas of endeavour, including government. We can envision, for example, By-LawML, electionML, or PRML for press releases.

Citizens, using software which understands these languages, will be able to know exactly what information a government should have, how it should be expressed, and where to find it. It will be a hard-pressed government which does not share.

Stephen Downes Stephen Downes, Casselman, Canada

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