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Sunday, December 15, 2013

Essay for biology course

This essay was written for the MIT MOOC course, Introduction to Biology: The Meaning of Life.

About the course: The course is, in summary, fucking brilliant!

If you take it just to understand a little about genetics it’s worthwhile. They bring the whole of biology, genetics, biochemistry and genomics alive! It's 14 weeks of about 3-4 hours a week but it could change your view of the world.

Students are in for an incredible ride describing 150 years of science* which is explained in pretty simple terms. There are real world examples and the compelling stories that are really necessary for ordinary people like me to really grok the material.

The videos of classroom lectures are with real students (some of whom are real, shut up that girl!) and with Professor Stephen Lander who is my new science pin up! 

Not only a scientist with a brilliant career (Humane Genome Project) but a great lecturer. He’s right up there in the great tradition of fine American science communicators along with Richard Feynman and Carl Sagan, in my humble opinion.

The software modelling tools embedded in the webpages used for the courseworks are absolutely stunning. Looking into the heart of complex proteins, thinking about what all that wet stuff inside us is doing...realizing that there is order and simplicity underlying complexity...and that mutation and change is built right in as a mechanism that allows evolution and the adaptation of organisms. Looking at the science behind all this, I can see why scientists get so exasperated by creationists I mean, you can argue about the existence of invisible beings, but the biochemistry of life proves evolution by adaptation through constant mutation. This is probably the best course I have ever “attended” in my fairly long life...

So here's my essay after Landers discussed his role in advising the US Supreme Court in the case** where a company had patented the genes for breast cancer:

In my opinion, the US Patent Office has, for many years, awarded patents for things that they shouldn't have. This includes genes, which to me are obviously discoveries of existing natural features; ("Farewell dear, I'm off to patent the South Pole!")

Silly enough, if the BRCA patent were strictly applied, a person carrying these genes may not have sexual relations or have a child that carries the gene! That could be copying the DNA sequences at issue, surely?

I am very glad that someone as sensible and well-informed as Prof. Lander was able to contribute rational input to the legislative debate. If the Patent Office had been doing its job properly, it would have saved everyone a lot of time, trouble and expense! Basic research discoveries shouldn't be intellectual property.

The people who funded Myriad's work on finding those 15 base pairs for BRCA were part of a "gold rush" phenomenon. They knew they were were taking a gamble and that they could have their patent invalidated. This and other genes were known to exist - even if the exact sequences weren't. Someone else would have found them shortly thereafter.

This kind of work really belongs in the realm of publicly-funded research in universities, hospitals etc. It's expensive, difficult, and quite often goes nowhere. The incentives for cleverness in these fields are, publication, peer recognition, public recognition and gratitude, exciting moderately well-paying jobs with tenure, the satisfaction of contributing to human knowledge, cures for diseases, and, in extreme cases, awards like the Nobel Prize.

Using government funding for basic research and then allowing private companies to do the commercial development of technologies, devices, and drug therapies appears to be more rational. It's not a simple question as to where the line is drawn, though.

Prof. Lander's cited example, where a friend of his didn't start to start a commercial  company to build a test for inherited eye cancer because of the many patents surrounding these genes, is, to me, proof of the failure of the patenting system in the US.

The system as it stands has damaged commercial interests - that person could have build a for-profit business where none existed - and the interests of the public who perhaps didn't get a better or cheaper test for a genetic disorder. It could be argued that he should have bought or licensed all the applicable patents, but mostly these are not available. They are being used for obscure purposes of squatting on intellectual property and excessive rent-seeking.

If the decision is made to uphold gene patents, other countries' R&D will continue and US research institutions, arguably the finest in the world, could be subject to unfortunate restrictions.

The US government is presently attempting to coerce other countries to accept US rules on intellectual property through bi- and multi-lateral trade deals, but this is not necessarily going to be successful.
The US Patent Office has done a disservice to US industry, research, the public and intellectual property holders as a whole by lending a disreputable air to the whole business of patenting.

It's patently obvious what Einstein** would have made of this!

* Science!!

** Myriad lost their case to patent genes in a 9-0 decision in June 2013.

*** Einstein worked in a patent office when he was younger, I believe. Although Einstein is quoted as having said that "God doesn't play dice with the world" - this course has made me realize that indeed, He isn't playing dice, He's been playing a massively multi-player lottery!
Note: This is a feeble attempt at a joke; I don't believe in invisible deities; don't get me started...

Cheap mildew killer recipes

Mildew is a mold (mould for you Canadians and Brits). It has a distinctive black stain that grows on moist surfaces, especially in warm conditions, but it doesn't mind a bit of cold it just grows more slowly. It has a distinctive unpleasant smell which is very hard to get out of fabrics or paper products. There are other fungus types that will grow in slightly less moist conditions especially on household dust particles that have accumulated. I hate to say it, but our grandmothers were right. Dusting is a good thing...sigh. I think I have too much stuff ;-)

The best formula is the mildew killer “cleaning soda” so beloved of our foremothers.  (It is now marketed as Concrobium if you want to spend a lot of money on it. That product does come in a nice spray bottle, though.)

Practical Sailor magazine* recently did a test of anti-mildew sprays and this cleaning soda was the best formula that you can currently get. The cleaning borax solution came pretty close and was slightly cheaper ($0.39 as opposed to $0.49 per quart!) Bleach also works to kill mildew (and will help with stains) but it’s nasty and doesn’t last long to stop re-infestation.

Best solution is to get rid of the damp conditions that mould likes. If you can’t, use the cleaning soda solution to spray the area that is mildewed. Let it dry and leave it alone. Check every few months and reapply if the problem reoccurs. Apply at yearly intervals if you can remember. It does work even if the area is always wet.

Cleaning soda - best results, kills mildew and prevents re-infestation.
Alkaline. Use in spray or wipe on with a cloth. Safe in use, although I wouldn't drink it.
When dry this leaves a harmless, white, powdery residue especially on dark items. Later you may think this is mildew. Don’t worry, it probably isn’t. Brush or wipe it off if you need to.

in 1 quart (2 litres) hot water dissolve:
  • 1 tbsp (15 ml) baking soda (sodium bicarbonate)
  • 2 tbsp (30 ml) washing soda (sodium carbonate)
  • 2 tbsp (30 ml) TSP (trisodium phosphate)

These other recipes are given in case you don’t have the ingredients above:

Cleaning borax - pretty good, kills mildew and prevents re-infestation.
Somewhat toxic, if you breathe borax or spray.
Alkaline. Use in spray or cloth. I'd use rubber gloves. Avoid breathing spray.

in 1 quart (2 litres)  hot water dissolve:
  • 2 tbsp (30 ml) baking soda (sodium bicarbonate)
  • 2 tbsp (30 ml) Borax (sodium tetraborate)
  • 1 tbsp (15 ml) TSP (trisodium phosphate)

Bleach - removes mildew stains somewhat and kills mildew. Only short-lived protection (the chlorine evaporates), it's a bit unpleasant to use, toxic. However you can get it everywhere.
Alkaline. Use in spray or cloth. Use rubber gloves. Avoid breathing spray.
Can discolour fabrics and soft materials.

In one quart (2 litres) hot water mix in :
4 oz. (200 ml) of 3% bleach (sodium hypochlorite)

* Practical Sailor magazine November 2013. (They should know; boats always have damp and often have mildew problems).


St Lawrence Rowing

Test content from SLRC