On BioScience and Life and Such

Archive for February, 2009|Monthly archive page

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Flip a coin Diagnostics ? Worse ? Better ?

In Uncategorized on February 25, 2009 at 3:40 pm

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A good easy to do , quick test for colorectal cancer is something diagnostic labs have been wanting (and trying to make) for many years. Now, DNA-direct has introduced a new genetic test. The test is based on methylation of the vimentin gene.

As a learning excercise for myself (and my lab), I’m going to run through the numbers to try to assess whether this is a good test or not and consequently whether we should look into something similar (like this commercial test-kit).

The Bayesian method of assessment is very general and can be used for any diagnostic test where the following is known:

  1. Disease incidence – Colorectal cancer in US approx 50 / 100 000 = 0,05 % (numbers from National Cancer Institute).
  2. Test specificity (true negatives) – approx 86 % (from DNA-direct web site).
  3. Test sensitivity (true positives) – approx 75 % (from DNA-direct web site).

Now what we want to do is calculate the Bayesian probability of actually having cancer when you have a positive test result (procedure from here). Summary of calculations as follows: i) 75 % of 50 true cancer patients test positive = 37,5, ii) 100-86 = 14 % of 99950 true healthy patients test positive = 13993. Bayesian probability i/ii = 0,27 %.

The test may be cost-effective as a general population screening test since a positive test means your chances of having colon cancer at the time of testing has increased from 1/2000 to 6/2000. In addition, if you choose the right age group (aged over 50), screening using this test may be a good thing. Decisions on population screening however, are made  by health officials on a national level and not by individual labs.

Representing an individual lab and seeing that the chances of you having cancer when you receive a positive test result using this test is, – believe it or not -, o,3 %, which means that out of a thousand people tested only 3 of them will be diagnosed correctly, – the only possible conclusion must be:

Worse than a coin flip, – Not a test I would use in my laboratory.

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The need for restraint III

In Uncategorized on February 21, 2009 at 5:38 pm

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Missionary style sex position.

Just too much fun! via Wikipeda

I once thought overselling science was the biggest threat to scientific credibility. Credibility scientists need to achieve general acceptance in the public, and subsequently continued funding (progress).

Recent developments have made me think that rushing into commercializing new biomedical technology,  like embryo sorting and genetic testing may pose a larger threat. Examples are genetic tests for athletic ability and embryo sorting based on more or less uncertain predictions of phenotypes without medical significance.

Granted, athletic testing and embryo sorting will  not become a reality for most of us for a long long time. Athletic ability one can usually assess wit the naked eye, and having sex to create offspring is far too much fun for it to go away.

– Then all the more reason to pause and think twice before unleashing commercial products to the unsuspecting and unschooled (in genetics) lay man. Even more reason to pause, when those products have disputable accuracy and are of questionable value

These are the early days of the genomic era, there are many, many things we still do not know, especially when it comes to the nature vs. nurture relationships. Since the future keeps evading finite predictability,  absolute disease risks (or any other risks or absolute probabilities for that matter) within the full time span of a human life, remains utopic.

We are moving in the right direction, all-encompassing disease prevention and/or treatment is on the horizon together with increased longevity.

Let’s not screw it up for ourselves. Our credibility is all we have, – please people show some restraint…..

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Quote of the month February 09

In Uncategorized on February 11, 2009 at 2:15 pm
Frank Wilczek at Nobel press conference in Sto...
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Nobel prize winner Frank Wilczek (quote from here):

The most exciting thing that can happen is when theoretical dreams that started as fantasies, as desires, become projects that people work hard to build. There is nothing like it; it is the ultimate tribute. At one moment you have just a glimmer of a thought and at another moment squiggles on paper. Then one day you walk into a laboratory and there are all these pipes, and liquid helium is flowing, and currents are coming in and out with complicated wiring, and somehow all this activity is supposedly corresponds to those little thoughts that you had. When this happens, it’s magic.

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Find me a new term for “race”, please

In Uncategorized on February 5, 2009 at 9:02 am

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A single amino acid change causes hemoglobin t...
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Races doesn’t exist – well fine, but how do you want to label our genetic differences then. Stop using the “term” race because it leads to racism would be like treating a symptom while disregarding the disease.

Reading this post on Greg Laden’s blog we learn that using the term “race” in derogatory ways lead to racism. Well, duh, thank you captain obvious.

The discussion following the post adds some nuance to the subject, but still fails to adress the real problem: if you do not want to use “race”, which term would you want to use to describe groups who share a set of genetic traits ? Ethnicity maybe, a label of geographical location maybe, – what about “of Caucasian ancestry albeit with significant genetic differences to other Caucasians”.

Genetic traits can be grouped. In my work I need to do this when I do pharmacogenetics. Some of the genetic markers I need to test for are very common in Caucasians, some are very common in people of Asian ancestry and yet others are very common in people of African ancestry. Testing for all of them would be overwhelmingly many (and too expensive) so we need to make a selection of the ones that are most likely to be present in our patient population. And, we have to make this selection based on ethnicity, geographical loation of ancestry, or “race” if you will. I do this selection without any thought of other aspects of the word “race” . I do this to provide the best care I can to our patients.

One of the arguments in the above mentioned debate (and in the respective friendfeed entry) is that we do not need a label for these groups, – but I do ! To do my work in a proper manner I really do !

If anyone labels me a racist over having to do this, they are creating the problem rather than helping to solve it.

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BIOpinionated monthly quote-fest 0209

In Uncategorized on February 4, 2009 at 12:23 pm

1. A tweet from Mr. Gunn:

@MaverickNY For someone who toils daily to uncover the real truth of something, to be told that belief = truth is insulting to my efforts

2. From this post at Best Before Yesterday:

…….did I think desire and motivation was all about chemistry. I said there was no question about it. She talked about a “part of us that doesn’t want it to be like that”. I wonder. What is lost when we think of the mind as a machine? Magic? The ghost or soul? For some, a sense of wonder and mystery. Control. Because, remember, most people are not neuroscientists.

3. From this post at Ouroboros:

The structural similarities between the opposition to these two classes of “meddling” are pronounced enough that I think those of us in the pro-lifespan extension camp would do well to carefully observe how the debate proceeds on the question of cognitive enhancement — and take notes — because, someday, we’re going to be having the same debate about lifespan.

4. From this post at Genetic Future:

….call me idealistic, but I suspect that parents will love their IVF-conceived children just as much regardless of whether they were randomly plucked from a Petri dish or selected on the basis of genetic information.

5. From this post at business|bytes|genes|molecules:

With all due apologies, science != academic science. Join a startup, or start one.

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A train (wreck) of (religious) thoughts

In Uncategorized on February 1, 2009 at 11:50 am

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Early science, particularly geometry and astro...
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I made this argument in the last post that being “natural” (or biologically unaltered, which is more accurate in this setting) means keeping our self-reliance. And, loosing that self-reliance may be one of the main reasons people fear biomedical technology.

Then it occurred to me, what about religion ? After all mankind at all times have used religion in one form or another to justify/explain our existence, – and usually there is one or more almighty deities that are in control. Pledging allegiance to a god must certainly be to give away self-reliance ?

I’d like to argue the opposite. Religion is our way of pretending we control things that are clearly outside of our control. Thus, with a deity on our side we are self reliant even though it’s quite obvious in our daily lives that we are not. The central underlying assumption is that this God is on our side, – on our team.

Technology on the other hand does not take sides. Statistics, mathematics, physics, chemistry and biology are (in theory) completely objective – sometimes cruelly so.

The real delusion then is not the one that Dawkins points out – that God is a delusion (and I have commented on this before,  his arguments really doesn’t make a difference because beliefs or faith can easily be called delusional, but still serve the same purpose). Rather the real delusion is that God is on our side, – that god makes our team self reliant.

And consequently that science does not. But the naked truth is that the concept of self reliance is what is delusional – making scientific development go in the direction we want is  the least delusional and by far the safest way to make sure our reliance will be upon something benign.

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