On BioScience and Life and Such

Posts Tagged ‘science’

Meeting update, talks in the category: “Did he really say that …?”

In Uncategorized on September 3, 2008 at 5:26 pm

I am in Milan, a very Italian city with extraordinary shopping opportunities and quite a few cultural highlights (the last supper painting, the “duomo” and La Scala can be mentioned). I am attending the annual International Union against Sexually Transmitted Infections (IUSTI) meeting. Browsing through the programme I see that I have a lot to look forward to and a lot to learn this week. But, also looks like there will be room for some fun….

Although STI’s are a serious matter, a few of the talks have titles that sounds entertaining, which of course, makes them a must-hear, – which I am sure is (mostly) intentional. Some examples:

Best ones first:

How to catch the casanovas

Entertainment education for sexual and reproductive health

That last one I hope is not porn.

In the category “lost ?”


In the US !!??

Next category: still lost, but spatially defined:

Syphilis and Genito-Ulcer Diseases: Where are we now?

Well we’re clearly not in the upper part of the body are we….

And finally in the category, not lost, but still:

Chlamydia Screening in Europe: do we Know where we are going ?

And in the category of titles that just sound strange:

A quantified green tea extract in the treatment of external ano-genital warts

Vulvodynia: a brief overview

Putting sex back into STI prevention

“A brave new world?” – Experiences of STI testing, prescribing and
dispensing via the Internet

If this last title holds any truth, I am simply horrified by the prospects of STI dispensing via the internet…..

And finally, for the fashionable (very Milan’ish !!)

Designer genitals/genital adornments

Joking aside, this looks like it is going to be a very informative meeting. And, behind most of these titles are, even if they sound strange, serious issues like dealing with the continuing spread of sexually transmitted infections and how to eradicate the bugs causing them. The implications are no laughing matter as all HIV-patients and infertile couples (Chlamydia, Trichomonas, Mycoplasma ?) will tell you.

Toll as free marketing material

In Uncategorized on August 27, 2008 at 8:18 am

post to news.thinkgene.com

Usually, I do not read marketing literature very thoroughly. I tend to rely on peer reviewed reports for reliable background information. For science news and views, I use the journal news-sites and the blogosphere. I think I am mainstream this way.

But, there are other sources as well. I should know having done my share of marketing and sales. I found a shining example  while skimming through SABiosciences marketing newsletter, Pathways # 7

In this newsletter was a really nice review on Toll-like receptors and innate immunity. It was well written, to the point and informative. Just as a review in a journal would be. In addition the illustrations were excellent, – probably better than in your average science journal.

I consequently discovered that SABiosciences are good at this. There are lot’s of other examples of high quality marketing material that also serves a scientific information purpose, on their website. Just have a look at this one example, a poster on cAMP-signaling:

I love when commercial entities add to the knowledge and information base in an altruistic manner. It goes to show everyone that knowledge based industry is more than the money, – it’s also what the name says it is, – knowledge.

Sadly I tend to forget that marketing material is a decent and free (open access !!) source for scientific information. Come to think of it, I have learned a lot from knowledgeable sales reps as well. Let’s give these companies and their representatives some of the credit they deserve for this. Even if that means being a little more forgiving towards their unscientific bias. After all they need to sell to survive, and how do you sell without bias……?

Huge or tiny, either way I am being tricked

In Uncategorized on August 25, 2008 at 8:56 am

In my quest to discover why I am gaining weight, I have come across this article that says that we are being tricked into eating and drinking larger portions….

This article illustrates how the compromise effect alters consumers’ selection of soft drinks. Using three within-subject studies, we show that extremeness aversion and price insensitivity cause consumers to increase their consumption when the smallest drink size is dropped or when a larger drink size is added to a set. – Kathryn M. Sharpe,Richard Staelin and Joel Huber, “Using Extremeness Aversion to Fight Obesity: Policy Implications of Context Dependent Demand”, DOI: 10.1086/587631

But in the same journal I found this article describing how mini-packs also tricks you into eating more calories

Tempting treats are being offered in small package sizes these days, presumably to help consumers reduce portion sizes. Yet new research in the Journal of Consumer Research found that people actually consume more high-calorie snacks when they are in small packages than large ones. And smaller packages make people more likely to give in to temptation in the first place. – Rita Coelho do Vale, Rik Pieters, Marcel Zeelenberg “Flying under the Radar: Perverse Package Size Effects on Consumption Self-Regulation”, DOI: 10.1086/589564

I am still no further in understanding how to restrict my calorie intake after exercise. And now, to add to the misery, I am completely confused on which package size is better.

Note: These papers were not open access (shame on you Chicago Journals) and reading the full version may provide more answers.

What is an embryo if not cells with potential

In Uncategorized on August 22, 2008 at 10:05 am

post to news.thinkgene.com

Watch me dive head first into a can of worms

Embryonic stem cells are just that, – cells. They are life of course, but my belief is that the ethical discussion surrounding the use of them stems (sic) from……a potential for life. Specifically, a potential to lead to the live birth of a human being.

So what happens if we try and put numbers on that potential.

For fertilization and pregnancy the statistics are:

  • 33-43 % if the fertilization was a result of ART/IVF- wikipedia
  • 10-33 % after a single sexual intercourse – ref
  • ~90 % over a year for young women in a general population when having unprotected intercourse

    ..A sexually active teenager who does not use contraception has a 90% chance of becoming pregnant within a year… – Medline Plus

After fertilization, the chance (potential) for an embryo that has reached the blastocyst stage, of developing further is largely dependent on implantation:

A related issue that comes up in this debate is how often fertilization leads to an established, viable pregnancy. Current research suggests that fertilized embryos naturally fail to implant some 30% to 60% of the time. Of those that do implant, about 25% are miscarried by the sixth week LMP (after the woman’s Last Menstrual Period). As a result, even without the use of birth control, between 48% and 70% of zygotes never result in established pregnancies, much less birth. – from wikipedia

And finally, for giving birth to a child when pregnant (regardless of the health of the baby) the statistics are:

  • 85-90 % when pregnancy is clinically recognized – ref
  • 100 % 35-36 weeks post fertilization (premature birth) –wikipedia

From these numbers, would anyone suggest to ban contraception or advocate giving everyone access to free ART/IVF ? …. – No ?

But, if the potential for life is your dominant guiding light, you should. And also if you are arguing against the use of embryonic stem cells, be aware that you are arguing in favor of a chance potential of as low as 30 %.

To change the world I need to program

In Uncategorized on August 7, 2008 at 9:34 am

Quotes from The Next Renaissance, A talk by Douglas Rushkoff

I am not a programmer. I thought maybe blogging would suffice in doing my part to change the world, – that has been, and still is, the distant goal of my blogging endeavor.

Computers and networks finally offer us the ability to write. And we do write with them. Everyone is a blogger, now. Citizen bloggers and YouTubers who believe we have now embraced a new “personal” democracy. Personal, because we can sit safely at home with our laptops and type our way to freedom.

But reading further in this piece in a recent Edge edition made me realize that to truly make an impact, knowing some molecular biology and writing about it, will not cut it.

But writing is not the capability being offered us by these tools at all. The capability is programming—which almost none of us really know how to do. We simply use the programs that have been made for us, and enter our blog text in the appropriate box on the screen. Nothing against the strides made by citizen bloggers and journalists, but big deal. Let them eat blog.

At the very least on a metaphorical level, the opportunity here is not to write about politics or—more likely—comment on what someone else has said about politics. The opportunity, however, is to rewrite the very rules by which democracy is implemented. The opportunity of a renaissance in programming is to reconfigure the process through which democracy occurs.

Since for the time being I do not have the time or the money to educate myself a second time around, blogging will have to do. And I still believe there’s some impact in that (maybe not in my blogging, but there’s without a doubt power in the blogosphere as a whole).

At some point however, since true future power apparently lies in programming, – off to school again, in a mission to rule the world.

Even the brain’s a mess, but we’re ok

In Uncategorized on July 9, 2008 at 11:04 am

post to news.thinkgene.com

As a perfect follow up on the previous post “How everything is a mess and still ok” where the subject was noise in gene expression, comes the following piece of news from e! Science news (research published in the July 4, 2008 issue of the Public Library of Science – Computational Biology):

“What we discovered is that brain maturation not only leads to more stable and accurate behaviour in the performance of a memory task, but correlates with increased brain signal variability,” said lead author, Dr. Randy McIntosh, a senior scientist with the Rotman Research Institute at Baycrest. “This doesn’t mean the brain is working less efficiently. It’s showing greater functional variability, which is indicative of enhanced neural complexity.”

and when comparing children to young adults

Researchers found that not only did the young adults score better on the face recognition tasks (i.e. they showed more stable and accurate cognitive behaviour) compared to the children, but the young adults’ brain signal variability actually increased – got noisier.

“These findings suggest that the random activity that we think of as noise may actually be a central component of normal brain function,” said Dr. McIntosh.

There’s this emerging understanding that noise is good. Noise is the diversity/plasticity that ensures proper performance and evolution of specific traits. Noise is the stuff from where melodies emerge.

This is a new way of looking at things. Our world-view used to be that melodies were created from nowhere in brilliant musical minds and noise (presumably as found in the minds of the rest of us) was a barrier that functioned only to obscure and hide the tunes. We are discovering that the opposite is true: chaos is the stuff from where good things emerge. And the brilliant minds (or biological processes if you will) are the ones able to pick the melodies from the chaos.

I too want to have the guts to be this honest

In Uncategorized on July 4, 2008 at 8:57 am

From this bayblab post on sleep by Rob:

The article also contains many other interesting aspects of sleep research including some conjecture on why evolution favoured sleep as such a prevalent behavior,

And then he admirably ends with……

but I didn’t understand much of it.

Thank you for leading the way Rob. I hereby promise to admit more often that I don’t understand things.

The universal PEG

In Uncategorized on July 1, 2008 at 12:00 pm

The most popular publication on SciPhu.com is on gel drying of SDS-PAGE using Poly-Ethylene-Glycol (PEG). PEG is used in many industrial applications as well as in research-experiments in the lab. Now Nature news reports that PEG may have a (distant) future in Medical applications as well. The nature News piece quotes Richard Borgens of Purdue University saying PEG acts by:

absorbing water, promoting the healing of cell membranes and preventing “the exchange of things that cause decay and degeneration of the cell”. Once it reaches human trials, PEG could be carried by trauma units and administered as soon as emergency crews reach victims of blunt-force trauma.

Especially the phrase

…..preventing “the exchange of things that cause decay and degeneration…..

,..appeals to me.

Hurray for PEG, – and may I remind you that using monodisperse PEGs (PEGs with a defined mass) increases the accuracy and reproducibility of anything you would want to use it for.

Genetic counseling as a patient right, not as a progress killer

In Uncategorized on June 20, 2008 at 12:57 pm

Genetic future had a thorough and balanced post on Direct To Consumer genetic testing. The following discussion between Daniel, Deepak and Dr. Murphy shed further light on the issues surrounding this topic.

Seeing this discussion from the outside I have the following thoughts to share (the text underneath is also a comment on the above mentioned blog post):

I can tell you that I live in a country where genetic testing is regulated extensively: any pre-diagnostic or pre-symptomatic test can only be done by a few authorized (public) medical genetics centers, and must be followed by genetic counseling both before and after testing. These strict test-definitions actually include “innocent” tests like cyp-testing for pharmacogenetics. I can promise you that you do not want a situation like this. Over-regulation hinders progress and takes away personal freedom. While I am sure that some regulation should be in place (like lab-analyzes quality control and restrictions to avoid overselling of tests and/or test-results), medical counsel is not really that essential. This point is underscored by the fact that patients seems to largely ignore the potential impact of even the most damning of genetic test-results (Huntington’s, see my previous posts (1, 2, 3) on genetic counseling). That said, patients that feel insecure when faced with their own genetics (which is probably a lot of them) should most certainly have the opportunity to consult a physician knowledgeable in genetics. This however, should be implemented as a patient-right rather than industry-prohibition.

And the discussion goes on

Publication phusis, Call for help

In Uncategorized on June 16, 2008 at 11:10 am

I have had many thoughts on how to present scientific data, and will have many more. SciPhu is, so far, the compilation of some of those, and blogging is the adverse event from trying to realize them. I have however come as far as I can on my own and need help to carry this project through.

This is what I have been planning: SciPhu is supposed to develop into a certification site for scientific thoughts, ideas and data. It is supposed to gather a large community of competent reviewers from virtually any scientific field. These reviewers are supposed to provide thorough peer-reviews of any scientific presentation as requested for evaluation on SciPhu.com. A successful review is supposed to give the author(s) a stamp to put on their presentation as a guarantee for scientific quality and credibility.

Through a FriendFeed discussion (original post by Bill Hooker) I came across this commentary on the problems of evaluating online publications. The author, Gary A. Olson, presents some solutions that are very similar to the principles I’ve worked out for Sciphu.

Clearly, the scholarly community needs to devise a way to introduce dependability into the world of electronic scholarship. We need a process to certify sites so that we all can distinguish between one that contains reliable material and one that may have been slapped together by a dilettante. We need to be able to ascertain if we can rely on a site for our own scholarship and whether we should give credit toward a colleague’s tenure and promotion for a given site.

And he proposes to establish certification bodies to achieve these goals.

The major professional and scholarly organizations in each discipline should (devise a certification process in which a site owner can apply to have a site reviewed and recognized, perhaps for a nominal processing fee. The site would be subjected to a formal and rigorous review by peers in the disciplinary area covered by the site.

Which is a very good description of what I wanted SciPhu to be like (except for maybe the fee, which should be for commercial users only). I have taken the liberty to replace with SciPhu in relevant places in the rest of these bullet points (the original text in brackets):

  • Only those sites meeting the highest standards should be awarded certification.
  • Once a site wins certification from SciPhu (the national scholarly society), it should be permitted to display that stamp of approval prominently.
  • The certification should remain in effect for a specific and limited amount of time (since a site can change rapidly and without notice). The site should regularly seek renewal of its certification.
  • SciPhu (Each disciplinary organization) should issue a resolution recommending that departments construe certification of a site as indicating that it has met the highest standards of scholarship.
  • SciPhu (Each organization) should maintain an online registry of certified sites.

A central site accessible to all is much more efficient than local evaluation bodies. Also the potential to gather a large collection of qualified referees is present only on a truly international site. Such a broad site would also be able to satisfy the open-access requirements in our Web/Science 2.0 future.

The SciPhu blog was set up as a starting point to gather a community of peer-reviewers. Making the blog successful is going to take a long time however, and given this commentary as well as the current interest in different publishing models, it seems wise to try and speed up.

To do this I need help. I need help setting up a good site, – a wiki perhaps. I also need help advertising this to the broader Scientific community and recruit referees. Even with help, achieving success is not going to be a stroll in the park. But without help it is going to be near impossible.

The end result may not end up as originally planned: names, concepts and strategies may/will change on the way, but I strongly believe that this is a path worth traveling.

I also think that Gary A. Olson is to narrowminded when it comes to requirements and scope of such a certification. Doing this online with a large community of referees makes it possible to get peer-review very quickly because reviewers would be accessible around the world 24-7. And there is no reason to limit such reviews to scientific publications. Any news-piece, advertisement or company information with scientific content could get reviewing through a SciPhu-like site. Extending reviewing to non-scientific publication forums is also the commercial opportunity, or business model if you will.

If you are interested in starting a broad and open-minded collaboration on this (and I really hope you are), please leave a comment, send me a mail or even better, join and use The Life Scientists room on FriendFeed for further discussions.