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Finally some serious genetic testing (post I)

In Uncategorized on September 18, 2009 at 12:49 pm

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The structure of Cholesterol
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Despite some ridiculous legal obstacles in this country, we are finally able to set up some proper genetic tests. I need to update myself on these tests – and what better way than to do it while blogging about them at the same time.

We are setting up 8 tests in this first stage of expansion, which I plan to cover in 5-6 posts.

1. Familal Hypercholesterolemia. A disease leading to highly elevated levels of cholesterol and increased risk of heart disease (good review here). Rough numbers: heterozygosity 1:500, homozygosity 1:1000000. Multiple genetic variations (SNPs, insertions/deletions) in LDL-receptor gene. Preferred analytical method: sequencing or genotyping (real-time PCR) a selection of genetic variants.

Normal function of the hepatic low-density lipoprotein (LDL) receptor is obligate for normal levels of plasma LDL cholesterol. The LDL receptor regulates the concentration of plasma LDL cholesterol by internalizing apolipoprotein B-100- and apolipoprotein E-containing lipoproteins by receptor-mediated endocytosis. Mutations in the gene encoding the LDL receptor protein give rise to one of the most common classical autosomal dominant inherited disorders in man, familial hypercholesterolemia (FH). The estimated prevalence of heterozygous FH is 0.2% (1:500) in most populations of the world. – from here

In addition to LDL-receptor mutation analysis (which will take a little while to set up) we’ll be doing SNP-analysis for ApoB-100. One SNP-assay of R3500Q in the ApoB-100 gene.

Familial defective apolipoprotein B (FDB) caused by the R3500Q apolipoprotein B gene mutation may mimic FH but the clinical course, however, is often milder than that seen in patients with LDL receptor gene mutations. -from here

Tests to follow: Thrombophilia, Hemochromatosis, Lactose intolerance, Osteoporosis, Macular degeneration and Crohn’s Disease.

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End of summer quote

In Uncategorized on September 13, 2009 at 8:51 pm
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From Watchmen (introduction to chapter VII / ending of chapter VI):

Is it possible, I wonder, to study a bird so closely, to observe and catalogue its perculiarities in such minute detail, that it becomes invisible? Is it possible that while fastidiously calibrating the span of its wings or the length of its tarsus, we somehow lose sight of its poetry? That in our pedestrian descriptions of a marbled or vermiculated plummage we forfeit a glimpse of living canvases, cascades of carefully toned browns and golds that would shame Kandinsky, misty explosions of color to rival Monet? I believe that we do. I believe that in approaching our subject with the sensibilities of statisticians and dissectionists, we distance ourselves increasingly from the marvelous and spell-binding planet of imagination whose gravity drew us to our studies in the first place.

This is not to say that we should cease to establish facts and to verify our information, but merely to suggest that unless those facts can be imbued with the flash of poetic insight then they remain dull gems; semi-precious stones scarcely worth the collecting.”

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They say men haven’t evolved towards domestic use

In Uncategorized on September 10, 2009 at 2:11 pm

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Male symbol. Created by Gustavb.

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First off, I have to admit that my scientific knowledge is a bit sketchy on this one. Nevertheless – my impression is that there is a (scientific ?) consensus out there saying the following:

The nature of men is that of the restless promiscuous hunter. Evolution has provided pressure towards maximizing the spread of male genes through procreating with as many women as possible. This way the number of offspring one man can obtain is maximized. Apparently observations supporting this view are the vast amount of sperm cells produced in the male reproductive organs and the continuous (not cyclic) nature of this sperm-production. The logic is, I think, that the production of all these sperm cells would be futile if destined for only one woman with a cyclic reproduction cycle. So far so good.

Consequently, the masculine “nature” is continuously compromised in our modern monogamous lifestyle. Male infidelity is often excused using the arguments above. The same arguments also makes domestic life and caring for the family into a compromise with “natural” masculinity.

Still good ?

Even if making as many offspring as possible seems like a good strategy to pass on (male) genetic material, isn’t it possible that another strategy would work just as well.

You could argue that continuous sperm production is present to counter a single woman’s unpredictable cycle, – or compensate for miscarriages, – or compensate for children born by this woman dying young (not so rare in those older days). This make-one-woman-pregnant-many-times strategy could potentially lead to as many offspring, themselves reaching reproductive age, as the multiple partner strategy.

If you buy into that last argument, there is no reason why the selective pressure on men has been towards domestication and taking maximal care of his one-woman family. And, against inclination towards infidelity.

I’m so sorry for ruining our excuses here my fellow men, but the whole man-as-a-hunter-excuse has been bugging me for a long time. I find it hard to understand why such an idea has been elevated to universal truth. I believe a need for behavioral excuses has overridden scientific rigor on this one. Anyone who can convince me otherwise is more than welcome.

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A couple of more things we didn’t communicate that well

In Uncategorized on August 28, 2009 at 2:50 pm

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I am putting together a list of things lost in translation between science and the public. The full list is compiled here.

Following a couple of discussions on friendfeed on exercise and dieting, I’ve come across two more items, they are:

9. Any kind of exercise will help you lose weight (When the truth is that the exercise needs to be extensive and the right type, if weight loss is to be expected).

10. Carbohydrates and fat are bad for you (When the truth is that we need a balanced diet containing both fat and carbohydrates).

yingyang

yingyang

Too much of anything – even a good thing – is bad. So is too little. – That goes for lack of exercise, but it also goes for too much/wrong exercise. Too much carbohydrates- bad, too little – also bad. Too little vitamins – bad, too much vitamins – also bad.

Balance on the other hand is what results in healthy living. Balance: – in exercise and rest – and in nutrients.

This has been known for centuries. And, it’s proven by science. Contrary to what many may think, life science is seldom about labeling something “good” or “bad”. Rather, it’s about trying to find what makes the right balance.

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Here’s why I get fat when I exercise (part II)

In Uncategorized on August 13, 2009 at 1:01 pm

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WEIFANG, CHINA - JULY 24: An overweight stude...
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The last couple of months I have lost about 8 kg

🙂

Previously, I had unsuccessfully been trying to lose weight by exercising more (Previous posts on this subject: “I get fat when I exercise, is that normal ?“, “Huge or tiny, either way I am being tricked“, “It’s the thinking that makes you fat stupid” and “Here’s why I get fat when I exercise“).

So this time I decided just to eat less. Not a different diet, just less of the same, and every other day I would skip a meal (lunch or dinner).

The new strategy worked like a charm, and I was planning on blogging my dieting results when I reached the 10 kg mark. But, then I read a veritable bashing of this TIME Magazine piece on how exercise does not necessarily help you lose fat. The criticism of this article I found very unfair. After all TIME was only telling us to put less faith in exercise as a dieting tool, – that’s fair enough isn’t it ? Besides, the points made in the article fit very well with my own experiences. Then a discussion on friendfeed followed, which I found very useful.

The TIME piece probably jumps to conclusions. The study he comments on does not support the conclusion that exercise makes you put on weight. Also the extrapolation of conclusions on adults based on data from studies on children may not hold water. However, the message that the TIME article conveys: the amount of exercise most people regard as sufficient to lose weight may act to the contrary, still hold true.

Looks like the consenus from the discussion is that exercise can help you lose weight, but it needs to be extensive (more than one hour more than 5 days a week) and it needs to be the right excersise (altough I believe the jury is still out on the effect of low-intensity exercise).

So, I’ll keep on skipping lunch and generally eat less, until I for some strange reason, should get enough time on my hands to prioritize 1-2 hours of exercise every day.

Downside is that I feel hungry a lot. Upside is that this may just possibly help me live longer.

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Tweeting and blogging from conferences – get real

In Uncategorized on June 18, 2009 at 1:19 pm

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Why does everyone completely miss the point on blogging/tweeting/friendfeeding from conferences.

Is it intentional because they feel unease in the face of our science 2.0 future ? I think so.

This is not about invading private scientific discussions between peers. Anyone arguing this must be having a separate agenda of some sort.

I’ve attended “advanced courses”, “subject gatherings” and “internal seminars”, – naturally, reporters were never invited….. and I wouldn’t tweet from those – who would ?

It is about drawing a clear line between such private discussions and appearances in public meetings. A public meeting is where invitations goes out without particular restrictions on who can attend (for much more thoughtful categorization, go here). In such venues no one has the right to censor what is reported. We (the free world !?) have gone to wars to defend similar rights. Pre-approval is what the CSHL meeting demanded of the journalists there, and the basis of the original post from Daniel. Such demands are unacceptable. You either invite reporters and define your meeting as public or you don’t, – restrictions on what is published from a public meeting is censorship – period. A thousand blog-posts, news-pieces , tweets and comments arguing otherwise is not going to change that.

If all this openness scares you so much, please feel free to follow the example of Dr Isis and

“start clamming up”

Good riddance.

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Afterthoughts in H+

In Uncategorized on June 14, 2009 at 9:15 pm

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A large glass of red wine contains about three...
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Exam done, and I finally have some time to read something of my own choice entirely – H+magazine.

After reading through about half, – skipping over some over-the-top adds (Neurvana p.6), realizing that  futurists talk has become = = Kurzweil talk, and deciding to opt out of some speculative diet recommendations (deuterium food p. 13) –

I read about breeding drosophila selecting for late-in-life first offspring. Granted, to see effects in humans will take some time, but still a brilliant idea, – and so simple:

Rose’s years of painstaking Methuselah fly stud-servicing produced a fracking miracle: flies that live 4.5 times longer than ordinary flies. Do that with humans for 10,000 years – 500 generations – and you’ll start approaching rose’s results. But to get the advantages today you’d have to start back before there were cities.- from p.18-19

Before there were cities -2 I believe, because …. – it’s already happening. At least in my part of the world. I personally know very few people who’ve had children before the age of 30, – many of my friends will be approaching 40 before family-life starts. Taking my circle of family and friends as a case report, the previous generation was 5-10 years younger when they had their first child. Keeping this up, we soon will be 50-60 before having children. That means evolutionary selection criteria will have to change dramatically to keep up.

So let sirtuins be sirtuins and calorie-restriction pass you by – life extension is coming our way…. – in 498 generations or so….

Keep drinking red wine though –  it’s good for so many things.

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Toll as free marketing material II

In Uncategorized on June 5, 2009 at 1:38 pm

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A follow up to this post where marketing material from SABiosciences was presented. It turns out they now have PowerPoint slides for free download too (sign-in needed). A great example of how industry (including their sales/marketing departments) can participate in spreading knowledge. And great as a resource for those of us who need a cascade-slide for explanation every now and then. You can use these slides in academic non-commercial settings as long as you mention (acknowledge) the company.

Pathway example

Go here for downloading.


Quote-fest 0509

In Uncategorized on May 17, 2009 at 7:54 pm
Dumbledore as portrayed by the late Richard Ha...
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1. From this post on Gene Expression (found via this excellent post):

the study of human genetic variation is in its infancy, and once it hits adolescence it’s going to start becoming a real pain in the ass.

2. From a comment on this post on Anna’s Bones:

My argument, however, was very simple: If you don’t believe in evolution, don’t get the flu shot. It’s hypocritical.

3. From this post on Blind Scientist on scientists as communicators:

We are horrible communicators, most of our websites are dreadful and do no contain any useful information and when we are confronted with a dumb Playboy bombshell we lose the argument. We lose because usually the argument is so ludicrous that we have no patience to explain. We lose because we are unable to communicate in lay terms. We lose because we’re not entertainers or crowd manipulators. We lose because we make our arguments difficult to understand. We lose because we get angry.

4. From “Harry Potter and the Philosopher’s Stone” by J.K. Rowling:

After all, to the well organized mind, death is but the next great adventure. – Professor Dumbledore on p. 215, line 31

5. …………and…..:

…the trouble is, humans do have a knack of choosing precisely those things which are worst for them. – Professor Dumbledore on wanting Money and life extension, p. 215, line 35.

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The slippery slope, maybe not so slippery after all

In Uncategorized on May 9, 2009 at 6:47 pm

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Newlywed male same-sex couple at Gaypride 2006...
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I read this (via AnnaBones):

Yesterday, when Gov. John Baldacci (D) signed a marriage equality law, Maine became the fifth state to allow legal same-sex marriage. On the Christian Broadcasting Network today, Pat Robertson responded by claiming that the “ultimate conclusion” of legalizing same-sex marriage would be the legalization of polygamy, bestiality, child molestation and pedophilia. “You mark my words, this is just the beginning in a long downward slide in relation to all the things that we consider to be abhorrent,” said Robertson.

And it occurred to me that the “Slippery slope” argument used when discussing genetic testing (I have used this argument myself) may have this same hysteric dimension…………based on unfounded anxiety (and prejudice ?).

No doubt, there is a definite possibility that our anticipation of discriminative genetic sorting and the incoherent slippery slope argument above share some of the same f(e)ar-fetched elements………..at least as long as democracy and free will/expression prevails.

Could it be the genetic testing slope isn’t slippery at all ? Just a plain good old slope. And maybe it’s not ending in the “brave new world pits of hell”, but rather, going upwards ending in this  city of happy people. Then again maybe neither. What we should expect post the genetic revolution is most probably today’s world with a little less suffering (from disease that is).

Either way, when I see reflections (however twisted) of my own anxiety in crazy, homophobic, christian conservative, right wing nut-heads, it is time to do some serious reconsiderations.

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