On BioScience and Life and Such

Archive for the ‘Uncategorized’ Category

Ten things we didn’t communicate that well

In Uncategorized on May 5, 2009 at 5:34 pm

post to news.thinkgene.com

Title page of the first edition of On the Orig...

As life scientists, we failed in our communication with the rest of the world when our messages became:

1.Survival of the strongest (which was supposed to be survival of the fittest)
2. Abortion is ending human life (when what it really means is not starting one)
3. Our DNA-sequence determines our future (when all it does is give the starting point for our individual continuously changing phenotype).
4. Race is not determined by genes (when it fact it most certainly is).

Update – additions:

5. Science has all of the answers (from FredCoBio).

6. Genetic modification is something only done in the lab (from MrGunn).

7. Most published research findings turn out to be false, and this is the cost of innovation (from MrGunn).

8. “We will cure X in Y years.” Seems a lot of the public has become disillusioned because we still haven’t cured cancer or AIDS, or “made good” on stem cell research (from Shirley Wu, more here).

9. Any exercise will help you lose weight. When the truth is that the exercise needs to be extensive and the right type.

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

More comments and suggestions most welcome.

Enhanced by Zemanta

Quote of the month April 09

In Uncategorized on April 20, 2009 at 7:39 am
{{Potd/2006-08-30 (en)}}

Image via Wikipedia

From this friendfeed discussion:

is tea the old coffee?

Paulo Nuin, Brasilian (connaiseur of coffee ?) and author of The Blind Scientist.

This should make him happy.

Enhanced by Zemanta

Retraction. I have seen a nanobot, it’s a bacteria

In Uncategorized on April 17, 2009 at 8:51 am

post to news.thinkgene.com

I wrote this previous post complaining that I had not seen biomedical nanobots in spite of predictions from prominent futurists.

A retraction is in place since I just read that a research group had succeeded in remote controlling  bacteria  to go in any desired direction (via H+ magazine, p 12):

To do this, Martel used bacteria that naturally contain magnetic particles. In nature, these particles help the bacteria navigate toward deeper water, away from oxygen. “Those nanoparticles form a chain a bit like a magnetic compass needle,” says Martel. But by changing the surrounding magnetic field using an extended set-up coupled to an MRI machine, Martel and his colleagues were able to make the bacteria propel themselves in any direction they wanted. -from here

How you control a (magnetizised) bacteria with MRI, is beyond me, but I guess this can count as a proof of principle nevertheless.

The medical-nanobot scenario just became much more likely.

Enhanced by Zemanta

Quote-fest 0409

In Uncategorized on April 3, 2009 at 11:22 am

H+ magazine special edition. All quotes below taken from the spring issue of H+ magazine.

hmagazine

1. From Ru Sirius on p.9:

If you embrace these [bio-progressive] rights, expect heavy resistance, because you will find yourself in for a territorial pissing match with most of the leading religions. Religions have traditionally ruled over the “seed” issues – issues around conception, death, the body, self-definition, gender and sexuality. But given the intrusive potentials of advancing technologies, this is a discussion we need to start having now.

2. from Moira A. Gunn on p.27:

….we need to create all this data to figure out who we humans are and how we tick. But unfortunately, we don’t know what data we need for what, and what — in the end — will prove useful. We are still shooting in the dark.

3. From Vernor Vinge on p.31:

The fundamental change that may be taking place humans may not be best characterized as the tool-creating animal but as the only animal that has figured out how to outsource its cognition — how to spread its cognitive abilities into the outside world.

4 + 5. From Alex Lightman on p.33:

If companies are living people, the drop in life expectancy for companies is comparable only to the fastest dying country in the world that is not at war — zimbabwe, where life expectancy has fallen from 60 in 1990 to 34 today.

The moral of the story is that, for those of us in our forties and up, we need to redouble our efforts at birthing problem solving technologies, and we need to make the future happen now or never (at least within the lifetimes of adults in 2008). or we better hope that Vernor Vinge is right and that the Singularity doesn’t require anything close to a healthy economy, in which case those smarter than-us bots can take charge and knock off all of our problems like ducks in a row.

6. From Douglas Rushkoff on p.37:

The way out — as I see it — is to begin making our own money again. I’m not talking barter, but local currency. Money is just an agreement. And the more a community trusts one another, the more effi ciently the moneys they develop can function. We can create units of currency based on anything; if we don’t have grain, we can earn it into existence instead by babysitting, taking care of the elderly, or teaching in a charter school. every hour worked is an “hour” of currency credited to your account.

7. From Jason Stoddard on p. 38:

Let’s be clear on this. We’re not going to wake up in a magical world where iPods and McMansions grow on trees overnight. Before that can happen, every part of today’s value chain has to be overturned. Everything. Production of raw materials, transport and refining, design and engineering, manufacturing, distribution . . . even our own sense of worth.

And there are plenty more. The magazine is highly recommended reading.

Unloading: HPV-vaccination

In Uncategorized on March 25, 2009 at 9:02 am

post to news.thinkgene.com

Genome organization of human papillomavirus ty...

Image via Wikipedia

The national biotechnology-board in my home-country has decided to announce that mandatory HPV-vaccination needs to be postponed. Why ? because “the long term effects are uncertain”.

&%¤#&%%%##** idiots.

This vaccine is probably the most tested vaccine ever. The issues surrounding its use concerns sexuality and young women. These issues are controversial by nature.

There is however, nothing controversial about the proven safety of the vaccine.

The job of an advisory-board of scientifically literate people, is to see beyond the politicized aspects of the matter, not to politicize them more.

The long term effects of a lot of what we do in our everyday lives are uncertain. If you demand 100 % certainty progress stops.

…….and in the meanwhile, many women will develop cervical cancer, some of them will die. Now that is 100 % certain.

Enhanced by Zemanta

One more thing on abortion

In Uncategorized on March 19, 2009 at 2:59 pm

post to news.thinkgene.com

A bar chart depicting selected data from the 1...

Image via Wikipedia

The other day I overheard a conversation. A man says he is proud of staying together with his wife for many, many years. They have four kids, three boys and a girl. He goes on to say that in the early days of their relationship, his wife got pregnant. Since they were both young and had dreams and aspirations for the future, this caused some fierce arguing and they almost broke it off. The abortion (which they disagreed strongly upon, but finally agreed to go through with), the man said had saved their relationship and ……(the use of the following word caught my attention)……enabled them to go on to have 4 kids and a happy marriage.

Nobody can predict the future. Every single little thing we do, every tiny choice we make, shapes our future in unpredictable ways. While abortion can be viewed as taking a life by some, others may view it as choosing not to start one. In this world of uncertain outcomes, choosing not to start a life may enable you to start many others in the future.

Life does not have simple answers. It’s shades of gray. Gray matter.

Enhanced by Zemanta

BIOpinionated monthly quote-fest 0309

In Uncategorized on March 16, 2009 at 9:14 pm

1. From this post at cotch dot net:

For eight years, the United States was the brawling village idiot of the developed world, so far as Europe seemed to be concerned.

2. Daniel MacArthur of Genetic Future comments on the claim that scientist shouldn’t study race and intelligence:

Poisoning the well in this fashion is a highly effective strategy for shutting down debate on a particular topic – but this is a terrible strategy for a scientist to adopt.

3. From this post at The Bird’s Brain:

I don’t think science is about skepticism. It is about critical thinking, which is necessary for proper support of skepticism. Yes, be a skeptic, but look at as many sides of an issue as you can, and remember that there are probably others that you have not considered. An opinion is just that, an opinion, not a statement of fact. We all have them, but that doesn’t make us experts.

4. On studying religious faith from this post on Cotch dot net:

What a fascinating way to approach the issue. Not whether an idea is right or wrong; what it has to offer.

5. From this post on Sandwalk:

There are so many crazy people out there that the average skeptic simply doesn’t have time to fight them all.

6. From this news piece on how working women are to blame for the global financial crisis:

Women are twice as likely as men to work in the public sector. They account for two-thirds of the Civil Service and three- quarters of all public employees.

Yet they are barely represented in the useful public services of firefighting and arresting people. Encouraging women to leave the workforce would go a long way towards addressing the budget deficit without any downside whatsoever.

7. From this post on Sandwalk:

We had a really fun time discussing the topic, aided, perhaps, by the excellent wine list at the restaurant. I wish I could remember all the points I made. I think some of them were brilliant.

Quote of the month March 09

In Uncategorized on March 8, 2009 at 10:05 am
Gioachino Antonio Rossini (1792-1868), composer
Image via Wikipedia

Gioachino Antonio Rossini, the famous opera-composer who created The Barber of Seville (the most famous of  his 39 operas):

How wonderful opera would be if there were no singers.

And I add: Politics without politicians, news without journalists, stock-exchange without brokers………

Reblog this post [with Zemanta]

On testing for Downs syndrome

In Uncategorized on March 4, 2009 at 12:42 pm

post to news.thinkgene.com

Photograph of child with Down's syndrome showi...
Image via Wikipedia

The following is my response to this Mary Meets Dolly post on prediagnostic genetic testing for Downs Syndrome.

To add some facts arguing against your view on genetic testing for Downs syndrome:

In my home country, where the right to abortion has been established many, many years and where every women (public healthcare) over the age of 38 is offered genetic testing for trisomy 21, the number of children born with Downs has remained unchanged also after the introduction of genetic testing. Thus, your assumption that this testing leads to less children born with this syndrome may not hold true. Also, I do not think that most people believe that the world would be a better place without Downs. I think however, that most people understand that this is a severe disease and that life with Downs is a challenge for the family as a whole. As for the lessons of life, it is truly sad when someone says that we need the sick and disabled to learn these lessons. Such a statement demeans these patients by saying they function as tools for us to understand the less fortunate.

Enhanced by Zemanta

Flip a coin Diagnostics ? Worse ? Better ?

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

post to news.thinkgene.com

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.

Enhanced by Zemanta