Looks as though the practise of patenting genes may be at an end (at least in the USA) Judge Invalidates Human Gene Patent - NYTimes.com.  It's always seemed odd to me that patents of natural objects suc as genes were allowed in the first place - this case concerns patents held by Myriad Genetics on the use of BRCA1 and BRCA2.

A federal judge on Monday struck down patents on two genes linked to breast and ovarian cancer. The decision, if upheld, could throw into doubt the patents covering thousands of human genes and reshape the law of intellectual property.

The case was brought jointly by the American Civil Liberties Union and the Public Patent Foundation.  This case has been interesting - my memory of events is that Myriad knew where the genes were, but that it was the public human genome sequencing projects which provided the raw data that enabled Myriad to determine the gene sequences.The implication of this ruling, if it's upheld, may be interesting.  I suppose smaller biotech companies with principal IP assets in the form of gene patents might find themselves in trouble.  The NYT article continues:

Judge Sweet, however, ruled that the patents were “improperly granted” because they involved a “law of nature.” He said that many critics of gene patents considered the idea that isolating a gene made it patentable “a ‘lawyer’s trick’ that circumvents the prohibition on the direct patenting of the DNA in our bodies but which, in practice, reaches the same result.”The case could have far-reaching implications. About 20 percent of human genes have been patented, and multibillion-dollar industries have been built atop the intellectual property rights that the patents grant.

I notice from a quick Google search that John Sulston released a statement back in 2009 supporting the ACLU case (BRCA - Statement of Support: Sir John Sulston):

I applaud the efforts of the ACLU and the Public Patent Foundation in challenging the patenting of human genes, and in particular the patents on BRCA1 and BRCA2. A patent on a gene specifically bestows the right to prevent others from using that gene. Rather than fostering innovation – one of the primary goals of the patent system – gene patents can have a chilling impact on research, obstruct the development of new genetic tests, and interfere with medical care.Genes are naturally occurring things, not inventions, and the heritage of humanity. Like a mountain or a river, the human genome is a natural phenomenon that existed, if not before us, then at least before we became aware of it.

Sulston's statement also illustrates the chilling effect of gene patents on research and development, specifically citing the chain of events which led to Myriad's patent application. Of course there are differing views on this: the NYT report quotes various individuals from the patent/legal/business side of the affair who clearly believe that medical research progress will be dented if individuals or companies are prevented from profiting financially from gene discovery (rather than inventing some application based upon gene discovery).This decision is to be welcomed, although the NYT reports that the decision is likely to be appealed.

As can be read over at the  Team Grumpy blog, the Icknield 32k time trial today was a bit of a disaster.  Last year my team mate punctured en route to the start, so we rode separately (and therefore got no result), while this year I had a mechanical problem which prevented me from starting.  The problem stemmed indirectly from yesterday's puncture sustained while returning from the NBRC club time trial.My current time trial bike has these nice pedals - Speedplay X-1 titaniumpedals:[caption id="attachment_641" align="alignnone" width="355" caption="Speedplay X-1 pdeal and cleat"][/caption]You'll note that the cleat (or "shoeplate" in British) is rather different than in other pedal systems where the clipping action resides in the pedal itself.  Here the clip action is within the shoeplate, which is quite large and complex, containing a couple of heavy gauge wire springs.  It was this design feature which led to my downfall this morning.While trudging home yesterday, I walked for a time on the verge, which led to the accumulation of mud on  my shoes.  Upon getting home, I cleaned then washed off all the mud I could see, and checked that the springs in the shoeplate at least moved.  What I didn't do, of course was check that they would still engage the pedal.At the point Team Grumpy was about to ride off to the start, I realised I couldn't clip onto the pedals.  I was unable to clear up this problem in time to get the ride in, and my team mate ended up riding solo (but in the 2-up section, so received a 'DNF').  In the end I had to disassemble the shoeplates, and extract a tiny quantity of mud that was preventing each spring from moving the full amount.So, there's a lesson there - Speedplays, which are otherwise excellent pedals which offer unrivalled float and very smooth clipping action, have cleats which are really quite sensitive to the ingress of mud. In future I'll take better care of them!

A very similar morning to last week's time trial: however, the rain was confined to the ride up to and back home from the event rather than the event itself.  The time trial was the first counting event in the 2010 NBRC time trial league.  A dozen or so riders turned out for the event.I rode the new Cervelo again, and once again with the tubular-shod Corima wheels, of which more later.  As with last week's event, there was a stiff headwind down the opening stretch to Chicheley, but I found it a bit easier than last week.  The whole course was a bit nicer this week without the driving rain.  I rode all the climbs seated rather than out of the saddle.  Unfortunately I found the saddle slipping in the clamp, which meant sometimes I was comfortable, sometimes less so with the saddle nose pointing upwards!I crossed the line in 24:03, an improvement of 27 seconds from last week - this was enough for second place behind Tony, who finished in 23:15.  Back at Astwood village hall, we all regrouped to await the results from the timekeeper.  Unfortunately, upon departing, I discovered my front tyre was soft - clearly a slow puncture.  JayBee kindly lent his track pump and I topped it up before setting off for home.  Conveniently, Clive was behind me in his car when I stopped in Cranfield University to top it up again, and once more I had the use of a track pump.All was now going well until my back tyre popped with a loud hiss, at about two miles from home.  Since I was unable to budge the tub (it was pretty slippery and wet, and fixed with tub tape), it was an annoying trudge home, spoiling a rather good morning.  Ho hum, perhaps I need to keep a 2010 puncture log!  In the meantime I'm going to switch back to using Continental tubular glue, which in my experience is easier to deal with for replacing tubs at the roadside.Results

								Pos. on
Pos	No	Name	Club	Time	Cat	Vets Std	.+ / -	Vets Std
1	8	Tony Parks	NBRC	23.15	V45	26.30	.+ 3.15	3
2	10	Rob Saunders	NBRC	24.03	V50	27.33	.+ 3.30	2
3	12	Lindz Barral	i-team.CC	24.14	S
4	11	Ian Marshall	TeamMK	24.31	V41	25.42	.+ 1.11	5
5	5	Andy Sharman	TeamMK	24.35	S
6	3	Glenn McMenamin	NBRC	25.33	S
7	7	John Buchanan	TeamMK	26.32	V40	25.30	.- 1.02	6
8	9	Gilbert Wheelwright	NBRC	27.45	V67	31.30	.+ 3.45	1
9	4	Clive Faine	TeamMK	27.49	V64	30.45	.+ 2.56	4
10	2	David Skeggs	NBRC	28.05	V41	25.42	.- 2.23	7
11	1	Alan Lawson	NBRC	29.45	V41	25.42	.- 4.03	8
12	6	Tony Brunton	NBRC	30.48	V45	26.30	.- 4.18	9
Time Keepers :- Steph Cousins & Tony Farmborough NBRC
Pusher off :- Bryan Scarborough NBRC

Well, here we go!  Another website reorganisation - these re-jigs seem to happen every couple of years.  This time, I've taken the plunge and decided to switch from Azrul's MyBlog (and its counterpart commenting system jomComment) to corePHP's Wordpress Integration for Joomla! 1.5.This will no doubt be an ongoing overhaul, but first impressions are pretty favourable.  CorePHP have developed a set of Joomla! components and modules that integrate the very popular blogging software Wordpress into Joomla! 1.5.  Installation of the principal component was straightforward, as was the import of my existing blog entries from MyBlog.  The system seems pretty neat: there are some sidebar modules that can be set to hold the various Wordpress widgets.  I suppose there are some downsides to relying on developers keeping up with the latest Wordpress releases, but the version installed seemed not to be particularly old (though not the latest).Documentation appears to be a little light - sufficient for installation to be easy, but not so helpful on aspects of installing the Wordpress plugins that have been modified/developed for the integrated Wordpress.  However, corePHP's website has an active support forum, and it seems that support is good - which is as it should be given this is a paid subscription.So, why did I switch from MyBlog?  Mostly because I found the MyBlog interface (both front- and back-end) rather clunky, and the JomComment component seems to build up a very large file cache.  And I mean very large - if not manually cleared, the backup component I use cannot work, and I run out of server disk space. And, of course, my experiences with a standalone Wordpress installation (Wonderful Life) had exposed me to the inner workings of running a Wordpress blog.

flies&bikes is an evolving website covering my interests which vary from biology through technology to cycle sport.  It has evolved from plain and simple html through several versions of the Joomla! CMS.  The present incarnation now uses the well-known blogging software Wordpress.I maintain several other related websites:Wonderful Life is a blog covering my interests in atheism, particularly as they relate to biology and creationism.North Bucks Road Club is the website of my cycling club.Northwood Wheelers is a website dedicated to the eponymous (but now defunct) cycling club, of which my father was a member.Team Grumpy features stories concerning cycle timetrialling, particularly as they relate to 2-up team time trials.The Team Grumpy blog is Team Grumpy's blog, and most definitely tongue in cheek. 

Cyclingnews.com reports that Alejandro Valverde has been accused (by the Spanish media) of implicating a team-mate as the owner of the Operacion Puerto blood bag  during his failed defence against the recent CAS blood doping case emanating from Operacion Puerto (Valverde Denies Naming Teammate In CAS Appeal | Cyclingnews.com).  Interesting, since according to the report, the blood bag was labelled "18 Valve. Piti".  Now, who among the 2002 Kelme-Costa Blanca team could that label possibly correspond to?  Well, Cyclingnews.com has a nice archive that generously lists the members of the 2002 squad:

Santiago Botero Echeverry
Francisco Cabello Luque
Juan Miguel Cuenca Martinez
Juan José De Los Angeles Segui
Isaac Galvez Lopez
Carlos Garcia Quesada
José Javier Gomez Gonzalo
Aitor Gonzalez Jimenez
Ignacio Gutierrez Cataluna
José Enrique Gutierrez Cataluna
Jose Cayetano Julia Cegarra
Francisco Leon Mane
Joaquin Lopez Torrella
Roberto Lozano Montero
Jesus Maria Manzano Ruano
David Munoz Bañóz
Leandro Navarrette
Gustavo Miguel Otero Gomez
Javier Pascual Llorente
Santiago Perez Fernandez
Jordi Riera Valls
Alexis Rodriguez Hernandez
Oscar Sevilla Ribera
Antonio Tauler Llull
Julian Usano Martinez
Alejandro Valverde Belmonte
Angel Vicioso Arcos
José Angel Vidal Martinez
Constantino Zaballa Gutierrez

Now, just who in that gang would have their blood labelled "18 Valve. Piti"?  I mean, apart from the obvious.  Valverde's legal team have denied that anything other than a general comment that the blood could have come from a team mate was made:

"Alejandro Valverde has never accused any rider forming part of the peloton and, as a consequence, what [has been] written in relation to that point is totally wrong," read a statement released by representatives of Valverde on Sunday.

"Mr. Valverde’s lawyers limited themselves exclusively to defend the rider’s interests and they never made such accusations against the cyclist mentioned in the [Spanish] newspapers."

I haven't read the said Spanish newspapers, so I am not sure which of the riders listed above might be a likely target for the accusation, and Cyclingnews.com aren't saying - other than to say that the rider is still in the pro peloton.  If Valverde's bizarre claim is true, and Dr Fuentes was liberally spreading false ID around the blood bags in his tender care, that represents another layer of dubious and dangerous practice in the doping scene.

Powered by ScribeFire.

Heavy overnight rain had passed over, leaving just a dreary cloudy sky when I set off to ride up to Astwood for the second event of the North Bucks Road Club time trial series.  Upon reaching the Astwood village hall, it was clear there was an excellent turnout.  Unfortunately, I didn't manage to sort out a 2-up partner, and chose to ride solo.  Ian Stokes was there with his exclusive hand-painted NBRC aero helmet, which I wasn't permitted to avoid complimenting - actually it's rather well executed.

After a bit of pootling about (and a little saddle tightening), I lined up at the start.  By this time the drizzle had started, and with a minute to go, the wind whipped up a bit and the rain turned rather heavy.  By then I was rather glad I wasn't paired up with a new TT partner, since the wheels I was using had carbon "no friction" rims!

I missed this story on Cyclingnews.com the other day (CAS Confirms Valverde's Italian Ban | Cyclingnews.com), but it would seem that CONI's ban on Alejandro Valverde's in Italy (which includes races passing through Italy) has been upheld by CAS.  Valverde was banned in May 2009 after it was found the blood stored as part of the "Fuentes affair" contained his DNA. The Cyclingnews.com report goes a little further, saying:

According to analysis performed in a Barcelona laboratory as part ofthe initial Spanish investigation, the bag of blood contained EPO andso the CONI banned Valverde for two years.

It's also reported that the UCI plans to take action aimed at extending Valverde's ban worldwide.  In my view there's a wider issue - how can one of the biggest doping scandals have failed to result in more action being taken against offending riders?  Is it fair on the few riders who have been penalised that others involved have not been challenged? 

[The cyclingnews.com page linked above has a useful timeline of the Operacion Puerto case as it relates to Alejandro Valverde]

Powered by ScribeFire.

Back in the 1970s, when I nearly took up competitive cycling as a teenager, I was a failrly regular reader of Cycling, then the weekly cycle sport magazine in the UK (known colloquially as The Comic).  Of course, I went off to University and discovered a variety of youthful interests that put paid to any serious involvement in cycling as a sport.  My memory of Cycling at that time was of a black and white newspaper like magazine, printed on pulpy paper, but full of stories about the great time triallists of the era.

Fast forward about 15 years.  I had just spent the last four years of the 1980s working in a lab in London, when the whole lab moved to Scotland, lock stock and barrel.  I decided to get a bit more exercise as a largely sedentary lifestyle had filled me out somewhat, and what better way than to take up cycling again, and explore the Scottish countryside.  I bought a bike, and started buying Cycling Weekly (as it was known by then) again.  Having plucked up the courage to join a local cycling club, I finally started racing club then open time trials.

A bright but very cold and frosty morning greeted us as we loaded up the car to drive over to Resolven to ride in the 2010 Port Talbot Wheelers 2-up '25'. In fact we were both apprehensive - about the weather, yes, but also the uncertainty of what form our winter training had led to. In my case, I was reasonably confident, but I was aware of being rather overweight and lacking in mileage - most of my winter training had been in the form of relatively brief turbo sessions in the garage. On the other hand, my team mate Gerry had left resumption of training until late December, and had then been afflicted with a lengthy cold (possibly the same thing that got me during most of December). So he was pretty sure he was going to be riding sub-par.

We got to Resolven and signed on. The race HQ seemed to be colder than the car park, which by the time we arrived was nicely bathed in sunshine, raising the temperature to slightly above freezing. After setting the bikes up and getting sorted, we briefly warmed up. I tweaked the Polar computer so that it would work from the GPS sensor, and we rolled up to take out place behind the fourth team (we were fifth off in a nearly full field). Our time came, and off we went, out on to the DC and done the valley, with a glorious tail wind. We were riding pretty smoothly together, and we took care that any speed discrepancy didn't pull us apart. I don't think it would be indiscreet to observe that Gerry was indeed below par, but still, we gradually reeled in the teams that has started before us.