On BioScience and Life and Such

Archive for August, 2008|Monthly archive page

Trading places II

In Uncategorized on August 28, 2008 at 10:59 am

Another quote with a religious scent where words happily can be swapped around.

Live your life in such a way that when your feet hit the
floor in the morning, Satan shudders & says…
‘Oh sh**…she’s awake!!

And swapping…:

Live your life in such a way that when satans feet hit the
floor in the morning, you shudder & say…
‘Oh sh**…she’s awake!!

You are free to choose who you depict as “satan”. The saying is now usable for non-religious people too, – and in my opinion, it has become a better one.

Previous posts in this series: Trading places


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 %.

I get fat when I exercise, is that normal ?

In Uncategorized on August 19, 2008 at 6:22 pm

In the Dr. Phil category of posts

A problem I have is:

I exercise, I get hungry, I eat. Which means I eat more when I exercise. Which again means that overall I have been (slowly) gaining weight over the years. I am constantly struggling to reverse the process, but the funny thing is that when I take exercise breaks, like vacations and such, I tend to loose some weight.

I know the solution to this is straightforward: EAT LESS, idiot !!

….But still, it has left me wondering whether putting an emphasis on exercise is correct when advising people on how to loose weight. Eating habits seems to me to be the key element rather than exercise,  – exercise may even slow down the weight loss process.

I would be happy If I am corrected on this, since I would like to carry on exercising. And while you are at it, I would love to be directed towards some convincing data that tells me whether:

The overall physical activity level has gone down in recent years ?

And if so: have the number of calories consumed gone up proportionally more than activity has gone down ?, – enough so to explain the epidemic nature of overweight in the western world ?

Final words on “The Elsevier Grand Challenge: Entry # 2”

In Uncategorized on August 16, 2008 at 6:07 pm

A follow up to this post on my submission to the above mentioned competition.

In the spirit of full disclosure and complete open access, here are the reviewers comments to the SciPhu entry:

Review 1
This is an interesting idea, very nice prototype.  But will people actually take the time do put up their papers and manage discussions?  And how does it relate to current publishing practice — augment it, replace, it, or in some other way change it?

Review 2
It seems to me that it would increase the amount of literature available by letting anyone publish, and would force the ultimate decision as to whether the paper is any good to the end scientist, who is already too busy.

I have serious issues with the notion that individual Scientists lack the ability to decide whether a paper is good, nevertheless and admittedly, the points are certainly valid (I have asked myself some of these questions many times myself).

Unfortunately these are also arguments against open access, unrestricted publishing as a whole. The reviews demonstrate a lack of understanding for the web 2.0 environment that all future publishing will have to relate to. In particular it is sad that that lack of time to “manage discussion” can be an argument. It is even more sad that “an increase in the amount of literature” is an argument.

It is ironic therefore that the winning project may have exactly these effects. In fact, looking at the project descriptions that went on to the second round, I am sure they will.

The Elsevier Grand Challenge: Entry # 2

In Uncategorized on August 13, 2008 at 1:03 pm
Please find below, my rejected submission to “The Elsevier Grand Challenge“. I humbly admit defeat to some terrific-looking projects, – best of luck to:
Sean O’Donoghue and Lars Jensen
Reflect: Automated Annotation of Scientific Terms
Timothy Baldwin, Lawrence Cavedon, Sarvnaz Karimi, David Martinez, David Newman, Falk Scholer and Justin Zobel
Effective Search, Classification, and Visualisation of Information from Large Collections of Biomedical Literature
Vit Novacek, Siegfried Handschuh and Tudor Groza
Teaching Machines to Teach Us: A Truly Knowledge-Based Publication Management
Amr Ahmed, Andrew Arnold, Luis Pedro Coelho, Saboor Sheikh, Eric Xing, William Cohen and Robert F. Murphy
Information Retrieval and Topic Discovery using both Figures and Captions in Biological Literature
Stephen Wan, Robert Dale and Cecile Paris
In-Context Summaries of Cited Documents: A Research Prototype for Academic and Scholarly Literature
Roderic Page
Towards realising Darwin’s dream: setting the trees free
Jose Gonzalez-Brenes, Aabid Shariff, Sourish Chaudhuri and Carolyn Rose
Automating the Generation of Life Science Protocols
Glenn Ford, Sameer Antani, Dina Demner Fushman and George Thoma
Tools to build and use Interactive Publications
Michael Greenacre and Trevor Hastie
Guided Tours in N-Dimensional Space:  Dynamic Visualization of Multivariate Data
Alexander Garcia and Alberto Labarga
A tale of two cities in the land of serendipity: The semantic web and the social web heading towards a living document in life sciences.
Whoever wins it is my hope that Elsevier publication turns open access, and to survive I think they will have to, in one way or another.

SciPhu Project Description:

SciPhu.com (http://sciphu.com/) is a blog where anyone is invited to publish scientific content, and anyone is likewise, invited to review (comment on) these publications (blog posts). All posts and all comments are freely and publicly available to everyone. SciPhu= Science + Phusis (Phusis – An Ancient Greek word often translated as birth or nature – Wikipedia).

  1. Project Goals, Purpose, and Outcomes.
    SciPhu.com is a blog based, open access and unrestricted publishing model. A hybrid in the spirit of Wikipedia and JustScience.The idea behind SciPhu-publishing is to be able to publish and peer-review scientific information more efficiently than standard peer-reviewing.The SciPhu vision of the future of science publishing:

    a) Improve the process/methods/results of creating, reviewing and editing scientific content: We wanted the reviewing process while retaining its scientific credibility, to be faster and less rigid. One answer, we found, was blogger-reviewing (which in this setting is just a fancy name for commenting on blog posts).

    b) Interpret, visualize or connect the knowledge more effectively:
    Blogging is a good starting point since there are so many knowledgeable scientific bloggers on the internet scene.

    c) Provide tools/ideas for measuring the impact of these improvements. SciPhu.com is already launched and statistics on visitors, rating of posts (scientific articles), and comments are and will be, continously available for evaluation.

  2. Detailed Project Description: Content and Functionalities
    The end goal of SciPhu is to be able to quality control scientific information from any source, so that the twisted scientific reality that sometimes ends up in the popular press (and ultimately in public opinion) can be promptly countered with proper scientific information. To achieve this goal, a solid referee-base with scientific authority and credibility needs to be affiliated with the site. Building such a referee community is a major milestone and challenge. As a starting point towards this goal, the SciPhu.com blog provides a novel/preliminary blog/internet-publishing channel for the scientific community. Sciphu.com is already a way of publishing that is completely free of (any kind of) charge, less rigid, more efficient and more interactive than many existing publishing models. SciPhu publishing is unlimited open-access and has the potential to reach a broad audience and aims be a pivotal tool to keep scientific authority intact, free and unpolitical.
  3. Project Background
    Sciphu.com is run by molecular biologists currently working in diagnostics. Our professional and educational backgrounds are university PhD degrees and small business life-sciences research activities within, biochemistry, genetics, cancer (and cell) biology and molecular biology. We are enthusiasts of web development and experienced users of many computer applications, but have little formal training in programming and web-design/develoment. Running a blog and possibly a future wiki however, requires only minimum skills to achieve adequate functionality.
  4. Methods
    While SciPhu today is a blog, future plans involve developing the site into a proper web-portal of some sort within the next 4-7 years. A wiki-based model is planned as the next developing step within the next 2 years. Such a wiki would have enhanced interaction with publishers and revieweres and the posssibilities for building a referee-community will improve over the blog-model. The blog model requires very little programming as most of the necessary tools are already provided gratis by hosting companies (Blogger/google, WordPress etc.) or by blogging community members. A wiki-based web-site requires more programming and web-design, but still at a level manageable by enthusisasts rather than requiring professionals. However, the goal is to involve web-developers to reach the maximum potential of this publishing model. A requirement will always be free of charge, open access, without restrictions, both for reading and publishing. A possible future business model is to offer peer-review expertise to commercial publishers or other commercial entities in need of scientific content quality control.

This publishing solution is not very high tech (but, it may evolve to be), it does not enjoy the recognition that many of the high ranked science journals do (but with active commenting, it can).

As with so many other things in professional life, the potential lies in the numbers. Only if many scientists are willing to use publishing channels like these, will it become a success.

Also at minimum two other issues need to be resolved to make the model into a proper publishing channel: 1) DOI numbers and 2) Proper backup and safe long term data storage. To solve the DOI-number issue, the use of the researchblogging (http://researchblogging.org/) icon and tracking is used, but this solution must be improved upon, presumably in cooperation with an exisiting publishing entity.

This is the age of the web and no-limit communication accessible to all. Our recommendation is: Say goodbye to the stale publishing standards of yesterday and come participate in the interactive self-justice of web-publishing.

More on the SciPhu model:

1. http://sciphu.com/

2. https://sciphu.wordpress.com/2008/04/07/launching-sciphucom/

3. https://sciphu.wordpress.com/2008/05/19/new-post-on-sciphucom-the-advantages-of-blog-publishing/

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.

Quote of the month August 08

In Uncategorized on August 4, 2008 at 12:14 pm

Charles Darwin in response to a critique he received that The Origin of Species was too theoretical and that he should have just let the facts speak for themselves:

“About thirty years ago there was much talk that geologists ought only to observe and not theorize; and I well remember someone saying that at this rate a man might as well go into a gravel-pit and count the pebbles and describe the colours. How odd it is that anyone should not see that all observation must be for or against some view if it is to be of any service!”

As quoted in F. Darwin, The Life and Letters of Charles Darwin, vol. II (John Murray, London, 1887), p. 121:

This goes out to anyone who thinks the scientific method is dead just because we can database a lot of stuff.