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Generalized Dontreallyknow Amount (GDA)

In Uncategorized on June 20, 2010 at 7:51 pm

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For no particular reason, it’s been a while since I have been to a McDonalds. We did go today though and I noticed that McDonalds like many other fast- or processed-food suppliers have started putting %GDA (Guideline Daily Amount) tables on their products. This is the Quarter Pounder one for women (!?):

So….according to the nutrinionists making these tables, eating two Quarter pounders with cheese a day will give you all the protein you need, all the fat you need and a bit more salt than you actually need. Throw in fries, a coke and a multi-vitamin pill. Result: a bit to much salt, but in general – healthy eating.

Anyone but me spotting a problem with these %GDA tables ?

More crap from the junkies

In Uncategorized on May 22, 2010 at 12:09 am

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My three favourite junkies (junk-DNA supporters) out there are Professors Dr. Moran, Dr. Gregory and post doc. fellow Dr. White. This week they received a strong argument for their junk-DNA cause, which was this paper on how there appears to have been a lot of noise in some of the larger RNA-studies over recent years. This was covered elegantly in this Sandwalk post by professor Moran.

Now if only the Adaptive Complexity blog written by White would have just jumped on the same solid bandwagon all would have been fine, but no. Instead he attacks a lead author behind some of the above mentioned RNA-papers. Again, this would have been fine had it not been for the argument he uses, an argument which has the quality of third grade primary school science:

Second, John Mattick is clueless, and he should not be quoted. So junk DNA holds the secret to human complexity? Then I supposed it also holds the secret to the incredible complexity of an onion, which has five times more non-coding DNA than humans.

He goes on to give us professor Ryans definition of “The onion test”

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA1. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

This “test” I hope everyone sees is utter crap. If you don’t I’ll explain: the assumption is “more DNA = more biological complexity/functions” – which of course is wrong since organisms who apparently have very few functions can have more coding genetic material than more complex organisms (try google the number og genes corals have vs. humans). The assumption is wrong also because the onion may need to meet it’s changing environment with an entirely different genetic arsenal than primates, – the comparison is just way off unless you specify more.

I think the first comment to this Adaptive complexity post is brilliant:

Just out of curiosity tho, what’s the standard explanation for junk DNA? Is it just structural or something? – kerr jac

That question emphasizes what has been my main point all along: Dismissing something as junk is contrary to my idea of science being driven out of curiosity and the need to explore. If you label this DNA as “junk”, how do you answer this question with any confidence ?

The Intermittent Fasting Challenge

In Uncategorized on April 5, 2010 at 11:21 am

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Weight and height are used in computing body m...
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I have accepted a dieting challenge and will give intermittent fasting a try.

The challenge is a twitter-challenge and it’s initiated by @NerdyScienceMom. The challenge is to loose 10 lbs (4,5 kg) by 31. May.

Since I have concluded that the amount of exercise that I have time for is not sufficient as a dieting tool, my exercise regime will stay as it is (medium to high intensity 1 hour exercises two to three times a week). The only tool left in the toolbox is controlling my diet. I have been reading up on calorie restriction, but that seems way too complicated, and besides – calorie count based dieting has recently been put into serious question. I have long been skeptical to any claim that says that you can diet by eating the “right” sugars and fats, – I honestly doubt that you change things more than marginally by changing sugar and fat types. Just eating less of a balanced diet containing the proteins, carbohydrates, fats, salts and vitamins that you need on the other hand…..

Thus, I’ll be trying out intermittent fasting. The principle seems easy enough – do not eat every other day. I am going for two to three fasting days pr. week. The science on this method says promising, but mostly the data is somewhat preliminary. What seems clear though is that this method does not seem to pose any risk of malnutrition.

My starting weight is 79 kg, which is up one kg since the challenge actually started just before Easter. I blame too much spare time combined with moderately elevated physical activity (snowboarding), which as I have blogged before – makes me gain weight.

The target weight I have pledged to reach is still be 73,5 kg, which means I now need to loose 5,5 kg instead of the 4,5 I started out with. I’ll be posting updates (if I come across any testosterone on the way I’ll be updating vigorously). Please also follow the other participants in the challenge through the Nerdy Science Mommy blog.

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A Scientific Communications Manifesto

In Uncategorized on March 29, 2010 at 10:58 am

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We need to improve the trust in science and scientists. Steven Hill has a recipe for how.

A series of posts on Testing hypotheses…. lists 7 things that would improve trust in science and scientists. This list strikes me as containing all the essentials, and if I may, I’d like to propose that this list becomes the Scientific Communications Manifesto. Below you’ll find the list and links to all 7 posts. Please, go read, it’s probably some of the best few minutes ever spent (if you are a scientist, that is).

We need to get this message out and work for acceptance for taking these measures in the scientific community. If successful, public perception of the importance of science and what science is about may get a long needed overhaul.

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The slope is only slippery when dictated to be so

In Uncategorized on March 22, 2010 at 9:33 am

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Frankenstein's monster
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In a democracy, are there any reasons to fear the horror-scenarios of our biotech-future ?

I am listening three audiobooks by Dean Koontz. The books are called Frankenstein (apparently there’s no copyright on that name), and I bought them based on a recommendation from Mary Meets Dolly. In her blogpost she makes the point that the books are about transhumanism. Of this I am not so sure. The story is about how Frankenstein, still alive and going strong, is making enhanced humans to replace the existing, and in his eyes flawed, human race. Consequently, the story distinguishes itself from transhumanist thinking. Transhumanism is not about replacing anything and it is certainly not about diminishing the value of life. On the contrary, transhumanism is about valuing all life equally, even to the extent that entities harboring artificial intelligence is considered to have equal value to any biological life form. My self-declared transhumanist values gives anyone (and hopefully everyone) the right to enhance their own life as they wish. It is essential that a choice to do such enhancement is a free one. If these choices are forced, we are not talking about transhumanism anymore, we are talking about tyranny.

It struck me that all these scenarios of a future dominated by improved humans are all based on some crazy person dictating their view of “the correct human nature”. I wish someone would write a book on how genetic sorting and human improvements would play out in a modern democratic society with respect for individual rights and freedom of choice. Now that would be interesting to read. It would also give us a literary reference a lot more useful than the horror-scenarios everyone is using today, when discussing genetic engineering and human enhancement.

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Errors in ethics of genetic sorting

In Uncategorized on January 21, 2010 at 12:32 pm

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Six day old human embryo implanting
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The traditional ethical reasoning when it comes to embryo-sorting, is that sorting out embryos with a certain condition diminishes the value of those already born with this condition. Consequently, by this way of thinking, a selected embryo must have an increased value. The selection itself (the absence of a given condition) increases it’s value over any other embryo in the pool of embryo-candidates.

Using the following arguments one can see how this is a logical error.

All human life is valued equally, must have equal rights and must be paid equal respect. This is regardless of how it was made (sons of bitches are as valuable as sons of kings) – these concepts are straightforward, uncontroversial and commonly held by enlightened people.

It follows that the process of sorting is irrelevant to the value of the selected embryo. The human that is born has equal value to any other human, not more – not less.

How then, can this human born out of selection in any way influence the value of anyone else ?

Answer is: he cannot and he does not.

Sorting is not a process that creates or changes value. Not for humans, not for animals, not for any object. The value is assigned later and is usually set by arbitrary or fixed rules. Gold is worth more than silver due to scarcity, a race horse is worth more than a donkey due to the size of potential revenues. Nature does the sorting of humans (decides which individuals who will mate and when they mate, decides whether the fertilized egg will implant and so on..). We have striven to assign equal value to any and all life that is born, even if it is sorted by nature’s sometimes chaotic set of rules. We have reached the point where all civilized people agree upon equal value for all.

Us taking charge in the sorting process does not change that. Sorting is consequently not unethical in terms of human value. Sorting only becomes unethical if it becomes mandatory by rules set by others than the parent(s). The right to say no to sorting is vital. If the right to say no is respected, then embryo sorting is ethically uncomplicated.

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New years resolution: Respect anti-vaccers, believe it or not

In Uncategorized on December 29, 2009 at 10:08 pm

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I get mad at anti-vaccers. I get frustrated with extreme conservatives and overly religious people. Not necessarily because of their beliefs, but because of what their beliefs lead them to – like anti-abortion, anti-stem cell research and, in general, anti-technology and anti-science.

But, from now on, I’ll stop getting mad, and I’ll welcome my frustrations. I just realized that I need to take the consequences from advocating the right to say “no” to technology. I believe the right to say “no” or more importantly, accept this “no” as just as fair and worthy a choice as “yes”, is the only way to protect ourselves from the perils of technology, be they merely ethical or plain deadly. My motto has long been, and still is: Equal rights for tech-denialists.

Why I realized ? I read two H+ magazine columns, one on correcting color blindness and one in athletic enhancement, both predicting the imminent arrival of the slippery slope genetic sorting future. A slippery slope I have done much thinking on myself, and now some re-thinking.

I very strongly believe that the only way to avoid the pitfalls at the end of the slippery slope is by giving everyone the irrefutable right to refuse to use all or any technological (including biomedical) advancement. And then to respect their choice. Only by giving equal rights to naysayers and tech-proponents will you avoid that any potentially society-threatening technology becomes pervasive and/or all-dominant. There will always be “anti-vaccers” to any new technology, and if the technology proves dangerous, they will, like it or not, become humanity’s saviors.

The consequence is that I need to accept the existence of anti-vaccers, I even need to respect their personal choice.

This does not mean that I will stop arguing my own beliefs, nor should anyone else. I still think the anti-vaccers are crazy, no offense !, and achieves only evil by allowing all but eradicated diseases to re-emerge. But, it means that I need to argue from a respectful perspective. Respectful because the principle of “the right to say no” is more important than any single cause, regardless how worthy.

Let this be my new-years resolution.

2 year anniversary :-)

In Uncategorized on December 7, 2009 at 2:29 pm
Happy Birthday album cover
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BIOpinionated is two years old today (7/12 2009). Will keep going !

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Calculating your health predictions

In Uncategorized on December 2, 2009 at 3:01 pm

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Casio COLLEGE FX-100 Pocket Calculator
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In our lab we’re setting up the PCA3-test designed to aid prostate cancer diagnostics. The test is representative of many emerging diagnostic tests in that it is a) a supplement to existing testing and b) useful only in a subset of conditions.

The PCA3-test complements results from digital rectal examination, PSA tests,  and prostate biopsies. Three tests that until recently have constituted the cornerstones of prostate cancer screening and diagnostics. The relationship between the results from these tests is dynamic and interpretation of test results is often complicated, sometimes very confusing and can, in the worst case, be very uncertain. Add the gene expression results from the PCA3-test and you have  a lot of valuable information, but a tough time filtering it into useful clinical information.

Physicians will learn how to combine the information either in med-school or in update learning courses later in their career. A slow and sometimes insufficient way to convey diagnostic information to the clinic, treating physician and ultimately, the patient.

Thankfully, we live in the information age and medicine 2.0 is well underway. Now the doctor or the patient can separately or together get online assistance in interpreting prostate cancer test-results. Well designed and user-friendly calculators like the “Risk of Biopsy Detectable Prostate Cancer” calculator or prostatecancer-riskcalculator.com (professional use) will help anyone undertand and begin to interpret lab-results. A big step forward in my opinion since information flow becomes quick and targeted.

Such calculators have also been made available for cancer risk prediction:  nomograms.org, for Marevan/Warfarin dosing: Warfarindosing.org, and as demonstrated in a previous post, for Testosterone: Testosterone.

There are probably a lot of calculators out there that I haven’t found yet and it’s highly likely that many more will be developed.

It seems clear to me that interpretation of clinical lab-results may not remain entirely in the physician domain much longer. Hopefully such automated interpretation will lead to patient empowerment and make  deciding on clinical action an easier task.

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Quote of the month November 09

In Uncategorized on November 26, 2009 at 9:32 am

It is a sad truth, but we have lost the faculty of giving lovely names to things. Names are everything. I never quarrel with actions. My one quarrel is with words….The man who could call a spade a spade should be compelled to use one. It is the only thing he is fit for.

Oscar Wilde, Irish playwright, poet, and novelist, The Picture of Dorian Gray, 1890