On BioScience and Life and Such

Archive for October, 2009|Monthly archive page

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Nothing is ever absolutely negative

In Uncategorized on October 31, 2009 at 1:19 pm

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Homer Simpson exclaiming the famous quote
Image via Wikipedia

On a late Friday afternoon

Quality control department:  “You missed the last two samples in this dilutions series”.

Me:  “Yeah, that’s kind of why we use dilution series – to find our detection limit”.

Quality control department: “But, even though very diluted, those two samples were positives. That means this was an error and needs an error-report”.

Me: “Well no, we define a limit where we can be 99,99% certain that we can reproduce a positive result, these dilutions will be well below that limit”.

Quality control department: “But, that means that you can newer be 100% sure of a negative answer”.

Me: “That’s correct, although the concept you are touching upon (the lack of absolute negation/negativity) is valid for any test and consequently, of a philosophical nature”.

Quality control department: “Then we can never give out a negative answer, at least not without saying that there’s a chance it may be positive after all”.

Me: in silence “¤%%”&&¤…doh” and out loud “”Would that be wise ?”.

Quality control department: “We believe so !!”.

Please notice the use of the word “believe”.

So there you go, hit in the face by the same arguments that created the vaccine-autism wars, the ID vs. natural evolution discussion, the religion meets atheism quarrel……..you cannot prove the absence of something, ergo – it must be there. The mother of all fallacies, but impossible to scientifically refute.

I’ll keep trying though.

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The Scheveningen Meeting: a Thrilling and Uncensored Story of European Molecular Diagnostics

In Uncategorized on October 27, 2009 at 11:30 am

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Sunset @ Scheveningen (HDR)
Image by Harm Rhebergen via Flickr

Well, while the title alluringly suggests so, this was not a conference for reporting spicy hot ground-breaking news like twelfth generation ultra-high through(the roof)put sequencing, full biome DTC chiponomics or gene-enhanced elisaluminetics or what have you. I’m kind of glad it wasn’t.

Instead this was a down to earth meeting where labs presented their experiences with molecular methods that are used every day in labs. Tests actually ordered by physicians in real-life medical settings. Methods are still PCR and sequencing…..and they are still used in microbiology (including virology), oncology and genetics… but, that’s it basically.

Being a diagnostic lab-professional I had many valuable insights to help in my everyday routines, which is what was expected from the meeting. I’m not going to blog that since it has limited general interest.  I’d like to however, expand on three trends that made me especially happy to see:

1. Economy: Many of the speakers emphasized the skewed nature of health care funding. Diagnostics normally receive between 0,5 and 5 % of the total health care budget. Usually, diagnostics is also one of the first places were budget cuts are effectuated. This stands in a mind boggling contrast to the potential savings one could achieve by investing in more testing. A sobering example is the swine flu testing policy applied by my own country which is……..don’t test. In  fear of capacity problems and over-diagnosing, the recommendations have been to stay home for a week if you have flu like symptoms – in addition you are strongly advised not to go see your doctor and doctors are advised not to test those patients that violate these recommendations. Of course, this does not work very well, labs are still swamped by swine flu samples, but the net result, nevertheless is the huge cost of absence from work and an immense amount of people worried for no good reason. Testing everyone, I strongly believe, would have been a lot cheaper……and…..although I am admittedly not objective in the matter, I think extensive testing should be a general principle. Investment in diagnostics is a good investment…..over diagnosing I simply do not believe in. Feeding diagnostic knowledge down to the treating physicians on the other hand is a real problem. But, a solvable one.

2. Networks: Many speakers spoke of collaborations between labs. In the research field such collaborations are common and acknowledged by most as a necessity. Not so much in the diagnostic lab until know. It makes me very happy to see that this is changing.

3. Web-tools: The above collaborations are of course aided by interaction on internet. It would be strange if not at some point, the facebook spirit didn’t reach diagnostics too. Now it seems, it have or at least is starting too. In addition, web 2.0 diagnostic tools are becoming more and more accepted, and several talks mentioned such tools. This I found so exiting, I will cover them in a separate post.

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My tribute to open access week

In Uncategorized on October 20, 2009 at 8:25 pm

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Open Access (storefront)

Image by Gideon Burton via Flickr

I am all for open access, my own initiative being sciphu.com – still in early stages and with several unresolved issues. Issues that may prove to be altogether unresolvable, because of the extreme openness of the blog-publishing concept. Still, as  a tribute to the open access initiative and in the spirit of such extreme openness I am proposing another open access category: “open access job-applications”. Please find my first contribution below.

Norwegian Biotechnology Advisory Board
PO Box 522 Sentrum
0105 Oslo
Norway

Oslo 14/10-09

Nils Reinton

Open * application for your position as senior advisor for the Biotechnology Advisory Board
I hereby apply for the above position. My background is biochemistry / molecular biology. I earned my Ph.D. in 2000. I’m now working in diagnostics research and development, mainly using gene technology methods.
I write two blogs commenting on the use of biotechnology: one in Norwegian (genom.no) and one in English (BIOpinionated.com). I participate in forums that discuss biotechnology and biomedicine on a daily basis. I have previously written contributions to the debate in Norwegian newspapers (see attached CV for references). I am passionate about my discipline and nurture a strong desire for an advisory board with a proactive commitment.

I have the following two reasons for applying for the position:

1. Correcting past sins. Including i) the biotechnology advisory board’s predominantly negative attitude to GMOs and Biomedicine with populist statements about HPV vaccination as the most glaring example, ii) the boards warm support to the world’s strictest regulation of genetic tests and other medical applications of biotechnology wherein the definition of pharmacogenetics as  “presymptomatic testing” is the grossest example, and the mandatory stamp of  approval given to only very few selected  laboratories is a generally descriptive example of contributions to over-regulation, iii) the board’s support for a biobank law that has nearly eradicated clinical trials in a country that could have contributed enormously.

If hired, I will attempt correct this by involving qualified persons that can inform about the harmful effects to research and development, of such over-regulation.

2. Change the current technology-hostile attitude of the board. Our country is in a unique position to develop technologies for the future, we have money and we have human resources. We should also be very well positioned to address ethical issues related to biotechnology since we are a law-abiding people living in a well-functioning (and thoroughly regulated) democracy. Norway’s prerequisites should ignite a wholehearted investment in biotechnology to help solve medical, environmental and economic problems to the best of both Norwegians and the rest of the world. Instead, fear of technology has won out among politicians and bureaucrats, including the biotechnology advisory board. Combined with a precautionary approach that is more pronounced with us than any other country natural to compare to, we have been left behind in what could have been thriving industry oriented biological technology development.

One suggestion for improvement is tolisten to resourceful people with constructive ideas for the ethical use of biotechnology. Furthermore, I propose to include a technology-friendly mission statement that ensures that the biotechnology advisory board always keeps technology’s potential as a starting point rather than focusing on (real or non real) damaging  effects of biotechnology.

There are tremendous opportunities in biotechnology, and in recent years advances in the field have shown us that much of the fear of this technology have been exaggerated. A natural skepticism should be maintained, but a shift towards a basic positive attitude is needed.

I have professional skills, I am flexible, outgoing and self-sustained. I can contribute in a positive and challenging manner if I was offered this job.

Regardless of the application outcome I request that my appeal for a more technology friendly attitude be considered carefully.

Sincerely,

Nils Reinton

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I wish I wrote this

In Uncategorized on October 8, 2009 at 7:42 am

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An excellent excellent opinion piece in Nature by Bruce T. Lahn & Lanny Ebenstein. Since I cannot write as elegantly as they have, I’ll just urge anyone reading this to go and read the whole thing because it contains grains of gold like this on “biological egalitarianism”:

We believe that this position, although well-intentioned, is illogical and even dangerous, as it implies that if significant group diversity were established, discrimination might thereby be justified. We reject this position. Equality of opportunity and respect for human dignity should be humankind’s common aspirations, notwithstanding human differences no matter how big or small.

and this:

For now, to intentionally overlook the influence of group diversity on disease susceptibilities and treatment outcomes is to practise poor medicine.

followed by this:

….there is a much larger reason to embrace human diversity in all its forms, in our view. Humanity’s genetic diversity — small or large, within or among groups — is a resource for, rather than a detriment to, creating a more fulfilling and prosperous society. Just as people have come over time to cherish cultural diversity, so we hope that attitudes will warm towards genetic diversity.

topped off by this:

For example, although IQ is a useful metric of some aspects of intelligence and it is partly heritable, it is far from a complete measure of total mental capacity. Therefore, acceptance of human genetic diversity in its totality necessarily leads to the rejection of unidimensional rankings of the capacity of human individuals or groups. If anything, the study of genetics is taking us towards an ever greater appreciation of the multidimensional nature of human potential.

And summarized like this:

  • Promoting biological sameness in humans is illogical, even dangerous
  • To ignore the possibility of group diversity is to do poor science and poor medicine
  • A robust moral position is one that embraces this diversity as among humanity’s great assets

Beautiful reasoning. I hope it impacts like a large meteor.

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