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It’s not all about the genes, well it’s not all about the environment either

In Uncategorized on October 16, 2008 at 8:23 pm


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When having a good debate on a given topic, there will usually be arguments ranging from one extreme to the other (and anywhere in between). The true answer you will find, is never those extremes.

The middle ground is sometimes hard to maintain in discussions and debates because the extremes keep hitting each other in the head, making impenetrable noise as they do so. Examples I have been involved in lately are debates on race, IVF, abortion, junk-DNA and open access publishing. Arguably, this mechanism is present for almost any discussion.  So also for the the debate on how much of human nature is shaped by genes and how much by the surrounding environment, -the nature vs. nurture discussion.

Reassuringly though, as most debates mature, they do tend to move towards the golden mean. Most people are confident now that human biology (behavior) is a result of a combination of our genes and the environment in which we live and grow. I am confident about this too, but I see research giving support to this notion far to seldom. First example I remember, was this article on domestic violence and genetics:

A functional polymorphism in the gene encoding the neurotransmitter-metabolizing enzyme monoamine oxidase A (MAOA) was found to moderate the effect of maltreatment. Maltreated children with a genotype conferring high levels of MAOA expression were less likely to develop antisocial problems. These findings may partly explain why not all victims of maltreatment grow up to victimize others, and they provide epidemiological evidence that genotypes can moderate children’s sensitivity to environmental insults. – Caspi A et al. Role of genotype in the cycle of violence in maltreated children.Science. 2002 Aug 2;297(5582):851-4.

I remember reading it and thinking, – yes !! Finally some evidence proving what we all thought we already knew . And I’ve kept waiting for other reports to similarly illustrate this gene/environment interplay so clearly (for the record, I know that the MAOA-results have not been unequivocally reproduced). Now, I have seen sporadic reports on other gene/environment interactions, but the mountain of evidence I had been expecting since 2002 just has not appeared.

That’s why when I read this review on ADHD the other day, which was exemplary in referencing and discussing gene/environment interactions, I was pleased and reassured that this field is far from forgotten about. Here are some descriptive quotes:

The neurobiology of psychiatric disorders is not about inevitability but is instead about vulnerability and propensity; it is only in certain environments that the disease is likely to emerge.

and

One of the explanations why results of genetic studies of ADHD have been contradictory is that not all individuals carrying a vulnerable genotype develop the disorder as the genetic effect may only become apparent among the subgroup of individuals exposed to a certain environmental risk. Thus, the importance of studying gene–environment interactions in behavioral disorders lies in the hypothesis that some genes show effects only in groups of individuals subjected to specific environmental stressors. – Kieling C at al. Neurobiology of attention deficit hyperactivity disorder.Child Adolesc Psychiatr Clin N Am. 2008 Apr;17(2):285-307, viii.

There is the definite possibility that I may not have paid enough attention and contrary to what I believe, one can find a mountain of publications on gene/environment interactions. If not (and I’m right), the reason there aren’t that many publications on this topic may be that research into this field is really hard to do. And that of course, is a good excuse.

But, regardless of the presence of this mountain or not: in order to use genetic research with any confidence in medical practice (and future research), the exact contributions from genes and environment needs to be worked out for as many traits as possible. And that (I hope) is our inevitable future – knowing our genes and what they will do to/for you given your surroundings. Subsequently, being able to manipulate these two factors will transform both nature and nurture. Potentially, we’ll reach the golden mean.

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The Likes of Blog Publishing (Open Access Day 08 entry)

In Uncategorized on October 14, 2008 at 5:03 am


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This post is my entry for Open Access Day 2008. It is about blogging, peer-review publishing, open access, elitism, prejudice and exclusion.

I had this dream: publishing directly on the web mixed with interactive comments to individual publications was to replace traditional peer-reviewed publishing in scientific journals. I set up SciPhu.com to achieve this. The core idea was (and still is) that any publication would remain fluid in its format and content since communication with referees was continuous and interactive. By letting the publication evolve in this way it should asymptote towards perfect.

Inspiration of how a series of comments can serve to paint the whole picture, I took from posts (and their comment-threads) like Anna Koushnir’s post on female scientists (where the comments are sometimes borderline harassment, but the comments taken together as a whole, nails the relevant issues, I think) and Olivia Judson’s post “The monster is back” (I could have taken any post with more than say -10- comments)……

I realize now that I was a bit naive in believing this could completely replace a system that has worked so well for so long. The system has after all allowed the scientific community to retain an unsurpassed credibility, worldwide.

But……..I am not accepting defeat just yet, because traditional peer-review publishing has it’s problems.

Firstly, most articles published are not open access. That means that if you need a scientific article and you do not work in an institution that has paid a large amount of money for subscription to the given journal (or you have a private subscription) you will not be able to access it (you can pay for individual articles, but that will become very expensive over time). In contrast, blog publishing would be free and accessible to all. The cost of publishing on a blog is very low indeed. It does not need printing and it will not need conventional employees. Editors and peer-reviewers (those who comment) would all be doing work on a volunteer basis. Consequently, no need to charge the readers,…….- at least not for scientific use (commercial use could potentially have a different set of rules).

Secondly, traditional paper-publishing is painstakingly slow and, compared to web-publishing, extremely inefficient. Blogs and scientific news-sites can publish in a matter of minutes and provide continuous updates (and corrections) on almost any topic. Also, web-publishing allows you to track your readers in an unprecedented way, – and most importantly, it provides a feedback channel for them. This feedback I think is essential in the next era of publishing. It does however, need some structure. The commenting anarchy of today will not suffice.

Thirdly, – the complete lack of such anarchy, has been one the strengths of the traditional peer-review model. But, to such an extent has peer-review been controlled that it has become the opposite of anarchy, namely dictatorship. Reviewers are handpicked by the publishers, creating potential old boy networks, with the journal editors as presidents. To add to this, reviewers are usually anonymous, potentially masking any conflicts of interest, be it financial, work-related or personal. In addition editors and peer reviewers tend to have agenda’s different to those who submit their papers. Thus, the traditional system does not serve to get as much quality scientific information out as possible, – this is contrary to the intentions. Below, I’ll quote from a discussion I had with (editor) T Ryan Gregory, to illustrate elitism, prejudice and exclusion, as examples of editor-agendas (comments from this genomicron post):

1. Elitism

My concern is that publish first, comment second represents an easy way around the rigors of review by experts in which publication is dependent on positive reviews and revision. I am all for open discussion, but initiatives started by people who don’t publish much in the peer-reviewed literature or do not themselves review many manuscripts do not really appeal to me because it adds to my sense of concern that this is a backdoor. I am not trying to seem elitist, I am just saying that peer review, for all its problems, is there for a reason. Submitted by T Ryan Gregory on 22 May 2008 – 8:10am.

2. Prejudice

May I ask what your record is in terms of reviewing manuscripts and publishing peer reviewed articles?  Submitted by T Ryan Gregory on 22 May 2008 – 9:00am.

One might also be forgiven for thinking that someone with only a few publications might be looking to skip the hard (but necessary) stage of getting through reviewers. Isn’t it a bit odd to complain about the anonymous nature of peer review while moderating a “review” blog anonymously? Submitted by T Ryan Gregory on 22 May 2008 – 9:00am.

3. Exclusion

Peer review isn’t supposed to be democratic. It is supposed to be done by peers — a set of individuals with highly specific knowledge in a particular field. The democratic part comes only once the paper gets through that filter, when it is made accessible to the entire community. Peer review is a vetting process, not a rating process. Submitted by T Ryan Gregory on 22 May 2008 – 9:42am.

By now I have concluded that SciPhu or similar blog-publishing alternatives is not going to replace traditional publishing, and that other alternatives will have to. Blogs can/will however, still be a valuable addition to traditional publishing, perhaps serving to correct some of the flaws:

“….fact is, at least now, if you come up for review and your citations are all on SciPhu or PLoS, you are going to get clobbered.”

This is very true. What I am saying is that I hope that it will be different in the future. Sciphu is probably not the final solution, but it is a starting point. And hopefully one of many similar initiatives to come. A site like this can be developed into a wiki or it can have staffed (unpaid) experts in given fields as reviewers or it can develop in any other direction. But, and this is important, it should never require fees of any sort from either referees, authors or readers. There are no fees attached to the sciphu site (it doesn’t even have google adds), it’s all non-profit scientific idealism. Submitted by Sciphu (not verified) on 22 May 2008 – 10:21am.

Money and open access, – this is the imperative issue that needs to be sorted out. Development of new publishing methods will most certainly follow. Peer-review publishing is dead, long live peer-review publishing.

Hence I pledge my complete and unrestricted support to any open-access initiative.

Some other views on peer review: nature debate on peer review, Certifying Online Research

Are you Suffering under the Creationist Terror Regime

In Uncategorized on October 8, 2008 at 9:23 pm


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Then free yourself……now !!

While reading “Postmodern evolution?” (a Nature News feature by John Whitfield) I found myself ripped out of the general feeling of bliss (caused by the fact that evo-devo is finally gaining some momentum). Because, first I read this:

Günter Wagner, an evolutionary theorist at Yale University in New Haven, Connecticut, puts up a slide bearing the words ‘Postmodern Synthesis’. Pigliucci is moved to make an editorial suggestion from the floor: “I’d really rather we didn’t use that term.” Wagner says the slide was intended to be tongue-in-cheek, but Pigliucci is worried about the impression the word creates: “If there’s one thing we don’t want, it’s for people to get the idea that there’s a bunch of evolutionary theories out there, and that they’re all equal.”

So, …. are we all forced into silence by the creationists ? The advice is not to use a term because it illuminates that there are new ways of thinking about an existing (and accepted) theory. We cannot speak in fear of being misinterpreted ? Such a coward attitude !

And then to make things worse, towards the end I read this:

…the dominant political concern was a fear of attack from fundamentalists. As Gould discovered, creationists seize on any hint of splits in evolutionary theory or dissatisfaction with Darwinism. In the past couple of decades, everyone has become keenly aware of this, regardless of their satisfaction or otherwise with the modern synthesis. “You always feel like you’re trying to cover your rear,” says Love. “If you criticize, it’s like handing ammunition to these folks.

Well, discussing in this cover-up manner will in my opinion, provide even stronger ammunition. Science is not about keeping your silence, quite the contrary.

Sometimes accusations of damaging the Darwinistic cause are used by scientists towards other scientist, – an indication of a societal reign of terror. To illustrate, here’s a comment to Oliwia Judsons blog post on Hopeful Monsters:

A “jumpy sort of evolutionary process” explains the complex organism’s sudden appearance, because there isn’t fossil evidence? Be careful or you’ll soon be agreeing with the Intelligent Design folk that there is such a thing as irreducible complexity. And “so far the data are suggestive rather than definitive”? Well, that opens a whole another box of problems, doesn’t it, Ms. Scientist Judson? Speculative articles such as these masquerade as science and do great harm to the whole field.— Posted by Charles M

Many are, of course aware of the situation, but nevertheless ends up bowing in fear of creationist attack (again from the Nature News feature):

” So don’t criticize in a grandstanding way, says Coyne: “People shouldn’t suppress their differences to placate creationists, but to suggest that neo-Darwinism has reached some kind of crisis point plays into creationists’ hands,” he says.

The glue holding a regime of terror together, are terrorized people. But, why be afraid, – facts are on our side. We are free to safely discuss the implications of these facts. There is no danger in this.

So please, please, stop holding your arguments back. It does not serve the cause of solidifying evolution as a fundamental force in biology. Speaking clearly on all scientific views of evolution theory on the other hand will, and holding back only makes things worse.

Quote of the month October 08

In Uncategorized on October 7, 2008 at 1:35 pm

I mostly disagree with Rebecca Taylor at Mary Meets Dolly, but this quote has a point, – several points actually, – and different ones I guess, depending on where you stand on religion….

Because science has no internal way to decide on ethical issues, it needs philosophy, history, theology and the law to be it’s moral compass. Nothing is quite as scary to me than the idea of science with no ethical constraints. Science without guidance from such scientifically distasteful things as “religion, politics, and personal ideolgies” is a horror I never want to witness.

It’s the thinking that makes you fat stupid

In Uncategorized on October 3, 2008 at 2:19 pm


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Following the post “I get fat when I exercise is that normal” I have come across some interesting articles that introduce some rather unexpected scapegoats for my weight gain. The first two were the effect of pack size and the most recent one (found via friendfeed user laura) is mental activity, or Knowledge Based Work (KBW) as they call it in the article.

Health professionals and scientists generally consider that the increase in obesity prevalence in our community is attributable to changes in the way of living over the last decades. These changes pertain to the evolution of food habits and also to the progressive increase in sedentariness, which has been promoted by a modern lifestyle.

What I keep wondering is this: is more exercise the best approach to fight the obesity-epidemic, isn’t it eating habit’s we should focus on ? My personal experience is that increased exercise does not necessarily mean less body fat, (because exercise influences my eating habits negatively). In this paper the authors show results suggesting that KBW promotes excess energy intake and thus, another variable on eating habits is introduced.

This study showed that KBW acutely induces an increase in spontaneous energy intake, and promotes an increased fluctuation in plasma glucose and insulin levels. This study contributes to the documentation of a new risk factor for a positive energy balance, with the potential to lead to overweight in the long-term.

They note that an explanation for these effects of KBW is that the brain relies solely on sugar for energy, while exercise also can utilize fat.

This switch in the macronutrient oxidation profile can be realistically considered as a potential cause of the suspected effects of KBW on energy intake.

The authors also note however that eating more does not result from an increased sense of hunger. If I interpret them correctly, you are basically eating more without noticing:

Taken together, these observations suggest that activities requiring a significant cognitive demand favor an overconsumption of foods, without increased feelings of hunger, which could result in body weight gain as a possible long-term outcome.

The answer I guess is not to think less, but of course to eat less. The challenge you face is to eat less than your brain tells you to, and that challenge it seems, is a tougher one for those doing knowledge based work. In my experience this is also a challenge when you exercise. Exercise however, most certainly induces an increased feeling of hunger, – and if one can generalize based on my example, this lends support to the authors notion that exercise and KBW utilizes different energy depots.

Overall, I find the paper very interesting and there is no question that their results go to show that the overweight-epidemic we are seeing in the western world most probably is caused by a complex set of factors influencing eating habits. Exercise I believe, may turn out to be not that important after all.

And that, obviously, is food for thought.

ref: Glycemic Instability and Spontaneous Energy Intake: Association With Knowledge-Based…Chaput et al. Psychosom Med.2008; 70: 797-804

Hey junk people, I accept your challenge (part II)

In Uncategorized on September 25, 2008 at 2:19 pm

A follow up from this post and an ongoing discussion with Professor Larry Moran over at Sandwalk.

Let me start by saying that even though this has been a lengthy discussion, I do not think we’re disagreeing that much, – on the basic facts that is. And the comments following my first post, his second post, my third, his fourth and this (the fifth) post on the topic hopefully will illuminate this fact.

Secondly I will introduce this post as I did the last, with my c-gamma gene (PRKACG). This gene serves as an example of how introns, retroposons and even alu-elements can contain indicators of function.

The c-gamma gene is transcribed in a species specific manner, (primates only), it’s expression is also tissue specific (testis only). The gene is contained within an intron of another gene, it’s 3′ sequence constitutes an exon of this other gene and lastly, putative regulatory elements where found in and around alu-elements in it’s upstream 5′-region.

Now, you can argue that these are all coincidences, … and refuse to speculate on any function. You may even be right in doing so, which I elaborated upon in my previous post. But, this gene is one of the reasons I refuse to put the label “junk” on everything that has not been ascribed a function. In my opinion, the species and tissue specific transcription, the conserved reading frame and the peculiar positioning of this gene, are all indications that this sequence may hide a function. There are other examples too, especially when it comes to transcription of alleged “junk” which in my mind is enough to warrant further investigation and scientific speculation.

There is, as has become very evident from this discussion, evidence pointing towards much of the genome being “junk”, but there are certainly scientifically viable indications to the contrary too.  Listening to the counter-arguments and following links in this two-post series will tell you this.

Then… moving on to answers to Professor Moran’s last 4 points:

5. Why is the Fugu genome so much smaller than that of other fish?

and

6. When two similar species differ in genome size by a factor of two—probably due to an ancient polyploidization—is the majority of DNA in both species functional?

His argument is that since the genome size differs between species, much of it must be junk. But, you could easily use the same argument towards a function, by saying that the difference in genome size is a defining (functional) difference between species. We just do not know do we ! And, why does the difference in size not give you reason to speculate on function at least in parts of these regions ? Others have however, speculated far better than me on this topic, and a thorough introduction to such research can be found at junkdna.com and following this link to “The Principle of Recursive Genome Function“.

7. In the human lineage there are over one million Alu sequences. They all look like degenerate versions of 7SL RNA. Are all of these sequences functional? If so, what function could they be doing? And why do the human Alus look so different from the mouse ones?

I am not saying all Alu-elements are functional. On the “what is junk” scale, one extreme is that everything that hasn’t been ascribed a function is junk (Larry Moran’s position !?) and on the other end is “nothing is junk”. My position is somewhere in the middle: Some of the DNA in our genome is possibly junk. A number of individual Alu-elements will undoubtedly end up in the “junk”-category when more is known about our genome. That said, it has been shown that Alu-elements can constitute (parts of) regulatory and functional elements. It’s rather hard to tell which ones are functional by just looking at them. I therefore refuse to call them “junk” by default, – I strongly feel that the “junk”-label is a dismissal of any possible function(s) and should be used with caution if at all, – even for Alu-elements.

8. Most intron sequences do not seem to have a function. Why does the size of introns in the same gene vary so much in related species and why isn’t the sequence conserved in most cases?

This argument is similar to the genome size argument above, and the answers for bullet 5 and 6 are equally valid here. Thus, there may be many reasons for a variation in intron size and this variation is not a very good argument to support the “junk” hypothesis. Also, the intron can contain regulatory elements and the c-gamma example above goes to show that introns can even contain functional (as in transcribed) genetic elements.

…..

My final note is this: A lot of this alleged “junk”-DNA is being transcribed into RNA. If it was just “junk” then why has selection preserved the transcription from these regions when transcription is an energy consuming process ? I think the position of “junk”-DNA may have some persuasive arguments, but it’s exceedingly harder to argue that the transcripts from these regions are also “junk”.

No matter what constitutes junk, and how much of it there is, this discussion has been extremely rewarding for me personally. I need to admit that the “junk”-position is more understandable to me now. I even find myself agreeing with many of the arguments, like the importance of drift over selection.

Conversely, even though I think he will never admit to it, Professor Moran indicates in one of his questions during the discussion, that he too is not completely locked into the “everything is junk” position:

How many of those transcripts are functional, according to your speculation, and what the heck are they doing?

Which I think is a perfect ending quote because it goes to show that we are all wondering about this……and that our disagreement is not as fundamental as some have suggested.

Hey junk people, I accept your challenge (part I)

In Uncategorized on September 23, 2008 at 1:42 pm

Some say that almost a half of the human DNA is “junk”, I say that the evidence indicating otherwise is strong enough to allow for speculation on (and research into) possible functions. In a recent discussion with Professor Larry Moran over at Sandwalk, on this topic, I received this challenge:

If you enjoy speculation so much then speculate on this [list of 8 questions]…

And I’ll answer each question as thoroughly as I can (please, find the first 4 below) but first, as an introduction, I would like to explain one of the reasons I take interest in the subject of “junk”-DNA. Bear with me, it’s an interesting story….

Back when I did my PhD, most of us PhD-students would get at least two projects to work on. One would be a “safe” project that would be reasonably easy to publish and the other one would be a high risk project where the outcome was more uncertain, but could potentially be published in ha higher impact journal (this is an approach I think all labs should follow !!). My “safe” project was to clone and characterize a gene for an isoform (of cAMP-dependent protein kinase) where the mRNA (cDNA) was already published (yes,believe it or not, this was actually publishable back in the days 10 years ago).  So, I cloned and I started sequencing looking out for exon/intron boundaries and intron sequences as was standard procedure. Problem was that I didn’t find any intron sequences. The genomic sequence was identical to the mRNA (cDNA) sequence.  At the ends where the cDNA and genomic sequences stopped being homologous, I found  direct repeats. These are the hallmarks of a retroposon. A retroposon is an mRNA that has been reverse transcribed and inserted into the genome. To add to this peculiar finding, my gene, the PKA C-gamma gene, it turned out, was a retroposon inserted into the intron of another gene (see illustration).

From my C-gamma paper: “genomic mapping of the STM7 gene demonstrated that the C-gamma open reading frame was situated within the intron separating exon 16 and 17 in the STM7 gene. In addition, part of the 3’-untranslated region of C-gamma (nucleotide 1478 to 1538 in fig. 2) constitutes an alternately spliced exon (exon 17) in the STM7 gene. The two genes are transcribed in opposite directions in the human genome, ……”

The common perception is that a retroposon is not functional. But, the circumstances in this case, I believe points towards some kind of function. C-gamma translates into mRNA in vivo (as is the case with a handful of other retroposon’s), and since it has an intact reading frame this mRNA can be translated into protein in vitro and in cell lysates. So is this protein detected in vivo ? ….and what if anything, does the protein do………?

This I’ll answer after returning to speculations on Larry Moran’s list of questions:

1. Why do pseudogenes and most of the transposon-related sequences look so much like broken genes?

By a broken gene I guess he means a broken reading frame that seems not to code for a protein product. The genetic sequence may still constitute a regulatory element influencing other genes (as was the case with the finding that led to the original discussion, see here for reference). Also, any trancribed RNA from parts of this DNA may have function either as long RNA molecules, miRNA’s or siRNA’s.

2. Why is the DNA sequence in most of our DNA not conserved?

Shorter segments may be conserved interspersed with unconserved regions. Also there has to be a great deal of non-conserved sequence to allow for evolution. This DNA serves a buffering capacity in that it is a reservoir for evolution (that does not make it “junk” !!, see below). Another point on conservation comes from the fact that miRNA’s function on the basis of their structure rather than a conserved sequence (many different sequences can give rise to similar two/three dimensional RNA structures). Thus conserved DNA sequences may not give any information on the function of such sequences and new approaches are needed to study their function.

3. Why can we delete large segments of mammalian DNA with no observable effect?

If you were an alien scientist examining a modern car you would find essential stuff like wheels, steering and breaks. You would also observe parts that seemed not to have any apparent function like the seat-belts, car-radio, air-conditioning, anti-spin system, ashtray, maybe a fire extinguisher and so on. These parts have a distinct function only under certain conditions and unless you are observing the car the instant these items are used, you might, -if you are of the “junk”-people, think that these parts are “junk”. Your conclusion would be strengthened by the fact that you could remove most of these items and the car would still be performing it’s basic functions (start, forward, reverse, turn, stop). Same could be true for the possible functions of large parts of our DNA.

4. Why is there so much variations in repetitive DNA within a species? Some people have segments that are ten times longer than segments found in other people. Are all of the nucleotides in the longer segments functional?

Repeat variation like STR’s are common variations that sometimes leads to functional differences between people, thus they are not “junk”. Similarly, Copynumber variation is a relatively newly discovered phenomenon that may have profound effects. That there is copynumber variation also in DNA yet to be ascribed a function, comes as no surprise and is not an argument for “junk”.

Then again, professor Moran might be right, it may all be junk. This may also be true for my C-gamma gene. because, the protein has never been found in vivo and consequently no function is known to date. Many have tried to find the protein (and/or a function) and some have suffered under the lack of results.

And I should mention in all fairness, that for me personally, it was wise to stop working on this and move on to other research projects and ventures.

Thus, I do understand the position of the “junk” people……..but, and here’s where my disagreement with them starts…..

That we haven’t found a function so far, does not mean that there isn’t any. Reports on new functions of DNA sequences are frequent and one of them was the ….. “opposing thumb” regulatory element….

This belief that there’s hidden function to be found, treasures to unearth if you will, is the difference between those advocating these parts of DNA as “junk” and me. In my opinion, It’s not the details of what is junk and what isn’t, ..- and how much, that bothers me…..

It’s the attitude. To dismiss something as junk is contrary to my idea of science being driven out of curiosity and the need to explore. Curiosity may kill a cat every now and then, but I’ll take that risk and continue to praise the scientist who recognize possibilities in the junk rather than dismissing it.

Answers to the last 4 points made by professor Moran to follow….

What you know is based on luck in this day and age

In Uncategorized on September 16, 2008 at 11:46 am

The other day I was listening to a talk on evidence-based medicine and how to navigate the literature without getting lost in too much information. The speaker went through some of the guidelines to effectively use scientific evidence in the clinical practice and medical research. These guidelines alone constitute information overload it seems, but if you want to try yourself, a starting point can be found at Cambridge university Library.

One of his conclusions that I found particularly interesting, was that to penetrate this massive amount of information, you need to use Sturgeon’s law. This law states that: to avoid information overload, you have to assume that

“Ninety percent of everything is crap”.

I immediately thought of friendfeed, not because there’s a lot of crap there, which there isn’t, not in my crowd anyway, ….not yet… But, because friendfeed is the current spearhead aggregator of information, – information from channels that were already overloaded, like twitter, the blogosphere and web-news.

Here’s a descriptive tweet (on friendfeed) from Berci Mesko some time ago:

“I’m absolutely not worried when I see I have 1500 feed items to read. Am I totally mad?”

A possible solution (using something similar to Sturgeons law) comes from the blog post Why I Stopped Reading Blogs (for a while):

1000+ items.  That’s what Google Reader told me I need to read to catch up with my RSS subscriptions.  It’s intimidating.  My RSS feeds were mocking me. I could see them with sneaky voices “hee hee, you’ll never read me, you don’t have the time. ha ha.”  The sad part is, they were right………..

….took a nice long look at the list and asked myself – does this matter to me?  Do I even know this person?  Will I be worse off without this content in my life?  No. No. No.

And doing something like this may help you avoid some dire consequences (from Slaw.ca):

They are numerous studies to suggest that information overload makes us dumber: Persons exposed to excessive amounts of information are less productive, prone to make bad decisions, and risk suffering serious stress-related diseases.

Me on the other hand, I never got to the point where I had 1000+ entries in my reader, I only have three or so blogs there. But, I also follow twitter and friendfeed. And then I’ve got a couple of (three ?, – maybe four ?) science news sites I go through on a semi-daily basis, and in addition I am following feed-networks like The DNA Network, and there’s mail correspondence and of course journals to skim through (and consequently, articles to examine) as well as a couple of books I’d like to read…..

What I do to keep from overloading is simply to click and read only when I have some time to spare. I also very rarely go beyond that first page of friendfeed and seldom look at historic postings on blogs or news sites. I just do not have the time. I have this life I need to live and it keeps getting in the way of the internet and reading in general.

This does however, mean that I am missing out on a hell of a lot and that the timing is essential to the information I get. Thus, although I have tried to optimize the information channels I take in, I am basing my information (knowledge ?) on luck of timing.

I will continue to do so I guess beacuse you just can’t have all the cakes and eat them too. Which basically is Sturgeon’s law, only reformulated, and a comfort to my ignorance.

Junk, DNA, RNA, Brain, Biology and Possible Solutions

In Uncategorized on September 11, 2008 at 10:10 am

We and all other organisms are complicated biological structures made from very simple building blocks on an information template of DNA. Individual variations in DNA are rather easy to work out although you do need lots and lots of DNA sequencers, data-storage facilities and data comparison programs. Fact remains, – you basically only need time and money to do this.

We know that the DNA sequence itself is diverse enough to make every individual exclusive while retaining enough common features for speciation. So, DNA explains a lot, but the final functionality including the ability to adopt to changing environments, depends on the next levels of variation…

Take the Necker Cube below. As described by  Edge writer Nathan Myhrvold:

This is a perfectly good 2D picture, but we cannot help trying to force into being a 3D object. The 3D reconstruction problem is ill posed—there are two very different solutions, each of which is feasible. So, when you look at it you alternately see one then the other—you can feel it pop in, or pop out. Without a unique solution your brain flips between the possible solutions.

The analogy to biology is as follows:

Strictly speaking, the cube is two-dimensional. But, for all practical purposes it is a three-dimensional object. At the same time it’s three dimensional form shifts from one confirmation to the other.

The analogy to DNA is that while the written DNA-sequence is linear (two-dimensional) the resulting molecular three dimensional structure allows for transcription into RNA and interactions with proteins both at the DNA and RNA level. These interactions in turn can lead to effects that vary depending on the surrounding environment. The Necker cube is made out of 12 identical lines giving rise to two different three dimensional conformations. DNA is made out of four versions of millions of basepairs. Resulting in a vast number of possible final variations of effects.

Biology handles a chaotic and changing environment using simple building blocks to make flexible, hyper variable, intricate and complicated possible solutions. Knowing the DNA-sequence, the transcriptome and the proteome is basically just discovering the two first dimensions in a many-dimensional organism.

New ideas, approaches and tools are needed to explain how this seemingly chaotic system works. Dismissing reasons for the obvious complexity using terms like “junk-DNA” is not going to get us anywhere.

Instead, let’s start by acknowledging that we know very little. All we know is that function comes out of an apparent chaotic mixture of DNA protein and RNA. Let’s speculate that everything is there for a reason. Without reason you loose hope and visions and those are qualities that science is vitally dependent upon.

Illustration taken from http://wisebytes.net/illusions/

Down Low Women, Milan Meeting Update II

In Uncategorized on September 5, 2008 at 2:12 pm


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A follw up on this post.

Being a molecular biologist lab rat, I do not have much experience with clinical work. I have been perfectly happy to miss out on the ickier parts of human pathology, and this weeks meeting on sexually transmitted infections (STI’s) seem to have strengthened my conviction. Some of the images I have seen has made me think I will never have voluntary sex again, – man have they been gross…

However, well into the second day, I have been immunized and finally find myself able to take in some of what the speakers say. And just to modify the somewhat comic impression from the last post, I will present a couple of talks that touch upon serious issues. At the same time it’s all about sex which makes them interesting (even though I’ll never have it again).

A talk that should have been on the list in the last post was

The Prepuce: Fact and Fiction

Which concluded that the prepuce (aka foreskin) is considered beneficial by some and without importance by others. The speaker Derek Freedman (Ireland) posed the entertaining question: “Do we have sex with our penises or with our brains” when commenting on the possible loss of sensitivity when circumcised. Now, the serious part was when he asked another and much more important question:

“Why has it taken so long to discuss circumcision to prevent HIV-transmission, and why is it not implemented in prevention programmes when circumcision confers 60% protection rates…?”.

A thought provoking question I think, considering that such a (relatively) simple procedure could potentially save millions of lives.

Another talk that I learned a lot from, and that touched upon some very different, but equally important issues, was

Down Low Women – by J.Risser University of Texas

Did you know that in poor areas of Houston US there’s a 2,5 % incidence rate of HIV. Did you know that women in these areas expose themselves to extremely high risk because having multiple boyfriends provides them, not with necessities like food and clothes, but with cell phones or money for a professional hair-do.

I ask them to help me with my wants; my needs I can take care of myself.

They are consequently not prostitutes as such, but still behave like them to posess (in my opinion) meaningless status-items. In doing so they are putting themselves at very high risk of HIV and other STI’s, – since they’re not using condoms in fear of exposing the boyfriends to each other, and since they apparently need several boyfriends to satisfy these needs. Appaling facts, – absolutely appaling.  If I get the chance I am going to come back and blog more on Dr. Rissers research. Because, even though the facts are sad, the issues are fascinating.

No wonder sexually transmitted disease is hard to fight.