On BioScience and Life and Such

Archive for November, 2008|Monthly archive page

What Ubuntu really means: a business model perhaps

In Uncategorized on November 27, 2008 at 12:23 pm

I know Ubuntu as a Linux distribution, but it is also an African expression. Until recently I only vaguely knew what it meant. Now I know more, it means:

kindness: humanity, compassion, and goodness, regarded as fundamental to the way Africans approach life (MSN Encarta dictionary)

The reason I found out was a commentary in a local news-paper which made a point that resounded well with me: in modern western society, a common belief is that you need to make yourself happy to be able to make others happy, – but in reality it is the other way around.

A traveller through a country would stop at a village and he didn’t have to ask for food or for water. Once he stops, the people give him food, entertain him. That is one aspect of Ubuntu but it will have various aspects. Ubuntu does not mean that people should not address themselves. The question therefore is: Are you going to do so in order to enable the community around you to be able to improve? (Nelson Mandela via Wikipedia)

A truth long known maybe, but forgotten in our self-indulging way of life.

Now, It occurred to me that if self-help coaches and therapists around the western world would use such an ubuntu approach, a lot could potentially change. Life-style advice would be to help others and through these actions achieve personal development.

Business idea then: Ubuntu self-help-others coaching. Get rich helping “lost their way” wealthy people and make the world a better place at the same time. Win-win-win.

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A follow up on DNA Dynasty and the logo

In Uncategorized on November 25, 2008 at 3:37 pm

post to news.thinkgene.com

If you go here you’ll find this statement:

To our friends from THE DNA NETWORK, we sincerely apologize for borrowing your logo without your prior permission.  We meant no offence nor do we have any intention to steal your assets.  We already have our official company logo (As seen on the top left corner).  During our initial design process, we needed some pictures to fill up the empty spaces to present the site to our management and design team for brain storming.  The beta site was meant for internal circulation only.  It was not meant for public viewing. Unfortunately, due to unforeseen circumstances, it became very popular in the search engine.  This was unintentional.

We have gone through some of the blogs written by THE DNA NETWORK community and understood that there are many strong opinions about our products, specifically Kids Innate Talent test.  DNA Dynasty Group is just a marketing company appointed by Shanghai Biochip Co., Ltd (SBC), a government funded National Engineering Centre of Biochip, to market their products.  If anyone would like to verify the validity of such test and the research thereof, you are most welcome to contact SBC directly for verification.

To be fair, I thought I’d mention this, especially to those of you that are network members since this is addressed to you.

For the record: I still think their products are misleading crap, government funding makes it worse if anything, and being “just a marketing company” is no excuse.

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Project: Distilling efficiency out of useless meetings

In Uncategorized on November 24, 2008 at 8:53 pm

Sick and tired of inefficient unnecessary meetings, I am trying to figure out how to (di)s(e)cretely minimize time-waste. This post is the beginning of a project which hopefully will result in less frustration. The final goal is that when a meeting turns boring, I’ll be happy.

Project aim

A comprehensive collection of discrete activities in meetings where:

a) Things you already know are being presented

b) Things that are irrelevant are being presented or discussed

c) Some idiot terrorizes the meeting with idiot-questions, and the speaker feels compelled to respond.

Inclusion criteria

Activities that the other meeting attendees (and the speaker) will not notice.

Exclusion criteria

1) Bringing a laptop could be the ideal solution, but not an option (in smaller meetings a handheld is a possible electronic substitute):


2) Activities solely for entertainment purposes.

Activities to be tested (first draft):

1. Lists, ideas

Method: Bring a blank piece of paper and a pencil/pen.

a) Make list of thoughts and ideas (work/career related).

b) Make to do lists for work projects or shopping (daily groceries, vacation trips, refurbishing project).

Comment: Approach been tested for a while, but not systematically. Risk of exposure seems to be low.  Systematic testing will have to include quality control of random thoughts and lists. Also need to design experiment to test the feasibility of working on the same lists in consecutive meetings.

2. Discrete physical exercise

Method: limb/whole body movement either unaided or with the help of various objects.

a) Muscle flexing and stretching. Possible muscle groups include upper and lower arms, legs, abs and pecs. Facial muscles not recommended until visibility measurements (see below) are concluded upon.

Comment: Flexing while involved in other activities was as far as I can remember first proposed by the great Jean-Claude van Damme on the Tonight show some 15 years back. Need to validate physical benefit. Also, need to measure visibility of activity, -specific parameters: “over the table” and “under the table”.

b) Balance training. Sitting down – mostly arms and hands. Standing up – in theory any limb.

Comment: Sitting down – i) no object: place both hands palm down between upper part of thighs and chair. Extend arms until thighs are suspended and balance for as long as possible. Repeat and record suspension period. ii) With object: balance any object at hand – pencil, coffee cup, biscuits, cake, pastry – start with palm of hand (palm up, down, sideways – combinations) , then all fingers, then 4 fingers, then three and so on. Time your balancing skills and record them. Note: payoff unknown, exposure risk – high.

c) Visual training. Detail perception exercises ? To be updated.

d) Meditation. Eyes open, mantra, silent, To be updated.

Further reading and resources on the topic:

Bullshit Bingo, Solutions similar to mine, A top 20 list, ….

Project description to be continuously updated. External input most welcome.

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Warfarin Pharmacogenetics: The Biochemistry

In Uncategorized on November 21, 2008 at 12:19 pm

post to news.thinkgene.com

More in-depth version of the coagulation cascade

Image via Wikipedia

Warfarin (marketed under brand names like Coumadin, Jantoven, Marevan, and Waran) is a drug that inhibits blood clotting – the formation of insoluble fibrin clots which stops bleeding. The drug is used to prevent/treat thrombosis – the formation of blood clots that can cause life threatening damage (through clogging of blood vessels).

Since the natural clotting ability is inhibited with this drug, serum concentrations elevated above the intended level can lead to severe side effects – life-threatening bleeding complications. Consequently, monitoring of patients using Warfarin is critical.

Some patients are at higher risk than others, and pharmacogenetic analysis can identify individuals that are either overly sensitive to the drug or metabolize the drug inefficiently. Both these conditions leaves the patient in risk of complications. Such patients should be monitored carefully and a reduced Warfarin dose is usually strongly recommended.

Metabolism through Cytochrome P450 (Cyp450) enzymes displays individual variation for many classes of drugs, so also for Warfarin. Cyp 450 pharmacogenetics will be covered in a separate post. This post will focus on the biochemistry of oversensitivity to Warfarin which can be described as follows:

Blood clotting is a multistep process involving a number of proteins and co-factors (see image above). Warfarin inhibits the maturation (post translational modification) of some of these proteins, clotting factors II, VII, IX and X. Unmodified, these factors will not function properly and the formation of the insoluble fibrin clot is inhibited.

The post translational modification in question is carboxylation, and it uses Vitamin K as a co-factor

carboxylationimage from: Vita Kbv

Vitamin K is decarboxylated in the process and needs to be recycled. The enzyme Vitamin K-epoxide reductase (VKORC) is essential in this cycle. It is this re-carboxylation by VKORC that is inhibited by Warfarin.

vitamin-k-cycleimage from: Linus Pauling Institute, Oregon State University

Warfarin mode of action summary: more Warfarin leads to less Carboxylated Vit K. Consequently less Factor II, VII, IX and X is carboxylated and inhibition of clotting occurs.

VKORC’s susceptibility for binding Warfarin varies between individuals, and this is the basis for the pharmacogenetic assays. From Wikipedia:

Polymorphisms in the vitamin K epoxide reductase complex 1 (VKORC1) gene explain 30% of the dose variation between patients: particular mutations make VKORC1 less susceptible to suppression by warfarin. There are two main haplotypes that explain 25% of variation: low-dose haplotype group (A) and a high-dose haplotype group (B). For the three combinations of the haplotypes, the mean daily maintenance dose of warfarin was:

  • A/A: 2.7±0.2 mg
  • A/B: 4.9±0.2 mg
  • B/B: 6.2±0.3 mg

VKORC1 polymorphisms also explain why African Americans are relatively resistant to warfarin (higher proportion of group B haplotypes), while Asian Americans are more sensitive (higher proportion of group A haplotypes).VKORC1 polymorphisms lead to a more rapid achievement of a therapeutic INR, but also a shorter time to reach an INR over 4, which is associated with bleeding.

Contributing to haplotype group A is a polymorphism in the regulatory region of the VKORC-gene. The A-allele of this SNP decreases the activity of the VKORC-promoter (less mRNA – less protein – higher proportion of total VKORC protein affected) and subsequently increases Warfarin sensitivity (see OMIM for more). This polymorphism (or ones in linkage with it) is normally among the SNPs that are tested for in the lab.

To conclude, identifying individual genetic variations allow us to predict protein variations that in turn predict sensitivity to certain drugs. In the case of Warfarin such pharmacogenetic analysis can be life saving.

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This pisses me off a little

In Uncategorized on November 19, 2008 at 9:47 pm

post to news.thinkgene.com

From this Nature News piece on preimplantation SNP scans of embryos (my highlighting).

[Jacques] Cohen [research director at Reprogenetics, a genetic-testing company in West Orange, New Jersey] says that as the understanding of disease genetics progresses, use of tests that seem controversial now may become more acceptable in the future: “If you had the chance to decrease your child’s risk of a disease like diabetes and you didn’t, society would blame you.

So much is wrong with this statement.

First he is taking the focus away from the very real and disturbing issue of embryo-sorting based on uncertain risk estimation of predisposition to complex disease.

Secondly his statement underscores the importance of the environmental factor in such complex diseases, but it completely misses the point. If you want your children to avoid diabetes, then make them eat right and exercise. You can do that today without any knowledge of their genetics.

Thirdly, currently, society doesn’t seem to blame parents that neglect their children’s health by feeding them unhealthy food or fail to encourage (enforce) physical activity, – why would a genetic test change that.

Lastly, putting such blame on parents has some very problematic socio-ethical issues attached to it.

I hope this is an example of misquoting, I really do….

Update – more on the company Reprogenetics in this post on Sandwalk.

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Me: Visible, Traceable, …. Miserable ?

In Uncategorized on November 18, 2008 at 3:07 pm

post to news.thinkgene.com

allelic length variation among 6 individuals

Image via Wikipedia

I am more and more visible. I blog, tweet and use services like friendfeed and LinkedIN. I started out with an alias, but now have my name out there. My picture I anticipate will follow soon. There are services I do not use, – like facebook, – it’s still to “unprofessional” for me (I like my web-presence to be mostly work-related).

As a consequence of this visibility, or more specifically, the subsequent information sharing, I am wiser now as a person than when I started my extended web presence about a year ago. Much wiser in fact. The personal gain has been tremendous.

Work-wise (sic !), we have been planning to set up human ID testing services which would imply creating  DNA-profiles for human identification. Such identification can be used in criminal cases, immigration cases, genealogy research, paternity testing and more.

I realize from learning the nitty gritty of DNA-profiling, and seeing how the technology develops (and becomes cheaper),  that I am (we all are) more and more traceable.

Thus, my body (DNA) as well as my soul (web-presence), is now out there for everyone to see

The big question then becomes: Is this virtual hereditary omnipresence dangerous to me ? Are we approaching George Orwells Big Brother scenario ?

I (maybe naively) say no, it is not dangerous. Because, to some extent I still choose when to be present on the web and to which groups I am visible. And, If I choose not to do illegal acts, – and If the system works the way it is supposed to, I would be kept out of any DNA-profile registry (if my profile is not registered, then my identity is not revealed by my DNA, and I can retain my anonymity).

If I end up in such a registry because I am falsely accused of something, or framed……or if someone decides to do a SNP scan of me without my knowledge……..or if my web-identity is misused……now that’s a different ballpark altogether, and I’ll try and explore the danger that lies in such abuse in future posts. Fact is though, in these cases we are talking about abuse and abuse is “dangerous” in any setting.

For now I’d like to make a point to the contrary: At least when it comes to sharing personal info on the web: It could in fact turn out to be damaging to my future career and reputation not to do it. Damaging, because web-sharing is rapidly becoming the norm (pointed out by Bora Zivkovic on friendfeed):

Exactly! 20 years from now a person who does NOT have drunk Facebook pictures online will be suspicious – what was there to be whitewashed? or is this person too timid or antisocial?

Nevertheless, I still choose not to sign up on Facebook since anyone valuing my personal life higher than my professional one when hiring is not worth working for.

And that’s just it, even if I’m being naive about this, I still have a choice not to share, – and as long as that choice is a free one, then there should be no reason to sound the big brother alarm.

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I’m not sure why I blog

In Uncategorized on November 17, 2008 at 10:19 am

But I suspect maybe:


(Which, I figured, is also the politically correct and trendy answer……..and……….there is poetry in it’s simplicity)

Syncroblogging link

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A Three Stage Program to Become an Open Access Fundamentalist

In Uncategorized on November 13, 2008 at 2:51 pm

post to news.thinkgene.com

I must admit that I am not a fundamentalist myself, nor am I sure I will ever become one. But I try to advocate open access, and as much as possible I follow the first two steps below. In addition, I have set up a free site for anyone to publish according to step 3 which is sciphu.com (but any site will do…..ideally one using widely accepted publication identifiers – sciphu.com isn’t…yet).

Following the recommendations in step 1 and 2 makes you a supporter and Open Access activist. Following recommendations in step 3 will make you a full-fledged Open Access Fundamentalist…….

1. Supporter stage. Openly support initiatives like PloS and contribute to activities like Open Access day.

2. Activist stage.

a) Publish in Open Access journals as much as possible.

b) Mail authors for reprints. Whenever you need an article published in a pay-for-access journal, write to the corresponding author asking for a reprint. Even if you have access through your institutional subscription (or get it through friends and colleagues), write the author to notify him/her that the paper is not open access. This increases awareness….

3. Fundamentalist stage. Send in your paper to be peer reviewed like you normally would (preferably to a pay-for-access journal). Receive your reviewer comments, edit according to those comments, but do not send your manuscript back to the journal. Rather, publish on freely accessible web page. Include the peer-reviews if you want, but clear this with the reviewers first.

Image by asher taken from Elephantitis of the mind

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Uses of DNA nr. 22-26

In Uncategorized on November 11, 2008 at 11:47 am

post to news.thinkgene.com

Animation of the structure of a section of DNA...

Image via Wikipedia

This post follows previous posts 10 ways to use your DNA, 9 more ways to use DNA and Add this to the “uses of DNA” collection.

22. Find invading species in your garden pond. You may need some help to design the assay (species specific primers and probes). But from there it’s a straightforward road to eradicating unwanted organisms that you were unable to see.

23. DNA art made from genes possibly contributing to athletic skills, intelligence and love (??!). See Eye on DNA’s blog posting about the offer from DNA 11 (coincidentally, this is also a follow up to use of DNA nr. 11).

24. Clone your dog – two companies can offer cloning of your dog: BioArts and RNL Bio. The two companies have been arguing (like cats and dogs !) however, over who owns the rights to such cloning.

25. Make a quilt using DNA sequence. Artist Beverly St. Clair makes quilts where each patch corresponds to one of the four bases in DNA. Beautiful and intelligent at the same time …..

Picture from genomequilts.com by Beverly St. Clair. It depicts the DNA sequence GATCGCCCTT

26. Poo-ID. The Israeli city of Petah Tikva has decided to do something about their dog poo problem. The solution: create a DNA profile from the poo and then, find the owner in a registry of dog-DNA. See here for more info.

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Tests that make me cry, and stealing too !!

In Uncategorized on November 7, 2008 at 4:45 pm

post to news.thinkgene.com

This company (DNA Dynasty) must burn. First for stealing the logo from The DNA network:


But, more importantly they must burn for doing what they do – from their blog (my highlights):

Dr Y.M Wong, who runs an anti-ageing management practice at Paragon Medical Centre, is a doctor who recommends his patients to DNA Dynasty to complement his treatment. “My patients are put on a stricter programme for disease-prevention if they are discovered to be susceptible to a certain gene,” he said. According to the firm’s flyer, the Genetic Discovery Test can identify up to 33 genetic traits, such as intelligence, emotional quotient (EQ) and entrepreneurship. Some, like businessman Lau, 44, have sent his kids for the Genetic Discovery test to “save money”. He said: “Now I know my one-year-old will be good at business. He has high EQ and leadership skills. “My older child, who’s three, will be good in science and can perform well as an engineer. With this knowledge, I know how to develop their talents without wasting time sending them for different enrichment programmes.

And burn to the ground….since, in response to this:

Dr Andy Miah, a bioethics lecturer at the University of Paisley in Scotland and the author of Genetically Modified Athletes, told The Times: “By using gene tests for sporting aptitude, children might be dissuaded from sports they enjoy, simply because somebody has decided that they will never be a great performer.”

They answer:

Yet Ms Sally Soo, managing director of DNA Dynasty, remains unfazed. She said: “It’s been proven that Jamaican runners are faster than their counterparts of different nationalities because of their genes. “I believe that a 1-per-cent variation makes a world of difference between two people.”

In lack of words, I’m weeping for the future of responsible medical genetics.

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