Life Science Tools of the Trade

Just a quick shout-out to (other) Richard over at the Naturally Selected blog, who in turn points at a Faculty of 1000 review of a very interesting article by Michael Gilding, entitled “Rampant Misattributed Paternity:  The Creation of an Urban Myth”. You can download the article, for free, from the journal website, right here.

While the article starts off sounding like a defence of Gilding and colleagues’ involvement (and occasional lambasting by interested stakeholders) in a 2005 paternity story involving an Australian politician, it rapidly evolves into an interesting, if rather anecdotal, deconstruction of the myths surrounding the incidence of non-paternity, at least in some sectors of “Western” society. It seems, perhaps unsurprisingly, that even the best estimates in the scientific literature appear to be pretty soft, and that most of what is popularly “known” is blatantly wrong. Popular estimates of 10-30% are not supported by scientific evidence, which suggests a rate closer to 1-3%, at least in the most believable studies.

I can recall being told during my PhD that “about five percent of families” in some of our disease studies had a case of non-paternity; given an average family size of, say, 2.2 children, that’s about 2.5% overall. That was a totally empirical (and thus non-rigorous) estimate, but seems “about right”.

Why is this important? Well, imagine how confounding a non-paternity rate of ten, or twenty, or thirty percent would be in a genetic association or (shudder!) linkage study, looking for variants conferring risk to a particular phenotype (that’s “disease” or “disorder” to medically-inclined readers). Even rates on the order of one percent can make things tricky. But – in this age of genome-wide, microarray-based association studies – questions of paternity are now trivial to resolve, and individuals manifesting obvious non-inheritance (which we can easily find with just a handful of polymorphic markers on a typical microarray containing hundreds of thousands) can be filtered from the final data set.

So is the presence of occasional non-paternity in genetic studies a big deal, or not? Well, it’s easy to detect, to be sure, but can still be a real problem in very small studies (such as those using genetic data to assess drug response in an early-phase clinical trial, where subject numbers may be quite limited). Is knowing the “true” population rate important? I’d argue that it probably isn’t. But it seems to me to be a moot point, since the best way to discover it would be via a very large, familial study, using population-based subjects – in other words, not selected as being part of a particular disease cohort. And I don’t buy for a second that (a) any funding agency is likely to pay for such a study, and (b) any Research Ethics Board would ever be likely to approve it anyway.

Still, Gilding’s article is an interesting read, and it’s nice to see an article noticed, reviewed, and yes, even blogged (a couple of times) even though it’s published in a journal that isn’t indexed in PubMed.

Just a quick guerilla post to point anyone who might be reading at a worthy initiative – the Scientia Pro Publica blog carnival, which as I understand it is a regular initiative to bring interesting science to the attention of the general public.

I’ll let Stephen Curry, the host of this edition, fill you in on the details. More can be found at this post from his blog, Reciprocal Space, including a link to the submission form. Here’s Stephen…

“…if you’ve read or written a blogpost about science, nature or medicine in the last couple of weeks that you think might enchant or enthrall a public audience, please think about submitting it to the carnival.”

The submission form has more detail on the general idea behind Scientia:

The purpose of this blog carnival is simple: to provide a large public platform that celebrates the best science, nature and medical writing published within the previous month in the blogosphere. This means the host should be able to understand what you’ve written. If the host can’t understand it, neither will the public. Acceptable submissions include “translations” of scientific papers, original essays about a scientific topic or theme, and reviews of books about science. Other submissions may or may not be accepted at the current host’s discretion. Topics range from basic to applied sciences; from physics, chemistry and biology to pharmacology and medicine. Scientia is published on the first and third Monday of each month, and of course, because this is a traveling blog carnival, it is seeking hosts.

Submissions will be published on Monday, March 1, so you’ve got a little time to either write something, or snag a post from the last couple of weeks or so. Of course, since it’s ongoing, you can contribute as often, or as infrequently, as you like.

Go on, you know you want to.

If you’ve written anything excellent since December of 2008, you’ve got a few days left to submit it to OpenLab 2009, an initiative to curate and publish (on paper, no less!) the best of Science Blogging, including prose, poetry, comics and other artwork. You can learn more about this worthy initiative here, or click on the button below to nominate something – yours, or someone else’s.

Go on, you know you want to.

If there’s one thing my PhD supervisor taught me (and I’m hoping she taught me more than just this, but this one is important):

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“Data” is a plural noun. Data are plural, they are analyzed (or analysed, if you prefer) and when you post them to that website, they HAVE been saved.

Thank you for your attention.

In this post-90’s biotech era which we all inhabit, I’m finding that brand recognition is becoming a confusing game indeed. Old favourite boutique vendors like Molecular Probes have been swallowed up by enormous, multi-tentacled distributors like Invitrogen, and keeping track of who’s distributing your favourite brand of pipettor, or water filter, or tissue culture media, can make for hours of fun and games. Even the big players keep getting bought and sold – just try to sort out the whole Merck/EMD fine chemical business, or the ownership structure of VWR, if you have some time to kill. And I’m still trying to get my head around Thermo Fisher. What does Thermo Electron have to do with distributing pipette tips and latex gloves? How, if at all, is this related to Thermo Finnigan? It makes my head hurt just thinking about it.

And then there’s my personal favourite suite of technologies du jour, loosely grouped into “next-generation” DNA sequencing, or NGS. Illumina buys Solexa, Applied Biosystems buys Agencourt Personal Genomics (but not Agenourt Bioscience, which is owned by Beckman Coulter – are you following this?), Roche gobbles up 454 Life Sciences. Pacific Biosciences is next, mark my words, with rumours of intense interest from Applied Biosystems, and probably many others. Helicos too, perhaps, so look for a merger or acquisition there, although with a market cap of $147 million and $50 million in the bank at the end of 2007, they could probably stay on their own for a while.

In the case of Illumina’s almost-works-most-of-the-time Genome Analyzer, most people still call it a “Solexa”. At the recent AGBT conference, which I’ve rattled on about in more detail elsewhere, practically the only people using the term “Illumina Genome Analyzer” were members of the large posse of Illumina employees in attendance. And most people don’t call the ex-454 machine a “Roche” GS-FLX; to most, it’s still a “454”, although this seems to me to be waning a bit under the crushing weight of Roche’s marketing machinery. Remarkably, the 454 Life Sciences website still exists, and is still a much, much better source of information on this NGS system than the Roche website, which is large, messy, and rather full of the 150,000 other things that Roche sells.

On the other hand, Applied Biosystems seems to have triumphed in branding their SOLiD system, and virtually nobody seems to remember that this was developed by Agencourt Personal Genomics and that the chemistry used was, for a time, referred to as the “APG process”, even by AB itself. Now it’s just SOLiD, small “i” and all, and the scientific community in general seems to have accepted that brand. Timing, I suppose, is everything.

Now, if someone could just explain to me why all these darn NGS boxes are blue…

Over the holidays, I spent some time perusing the internet looking at different science websites.  The number of websites pertaining to the biological sciences is amazing.  You’ll find websites from the serious to the comical.  Here are two that you may or may not have heard of.

http://www.protocol-online.org/

http://www.phdcomics.com/comics.php

Hope 2007 is off to a great start for everyone!

As I thumbed through the August issue of Biotechniques, one particular ad caught my eye. I know. You’re asking, “What’s the full page ad that caught my attention?” It was for none other than SAB!

The ad has a picture at the top of the page with some info about the site below. Simple, easy to read and easy to spot.

It only left me with one question…. does anybody know who the people in the picture are?

Tired of making your own slides?    Looking for the easy way out.  VisiScience has a database of over 3000 slides you can use for your Powerpoint presentation.  Anything from common shapes to molecular pathology, it looks like they have you covered. 

It sounds like a great idea and a time saver.   The only problem, this lab is way too cheap to fork out that amount of money.  Looks like we’ll still be making our own slides!

 www.visiscience.com

Because of the archaic way in which our institute does its external requisitioning (well, there’s a new system but please don’t get me started on that. Actually, it’s Part 2 of the ‘ordering’ rant , which yet bubbles in your correspondent’s cauldron) we have a level of self-authorization for orders. That is, anything less than a certain amount doesn’t need signing by the PI.

So there is a real incentive to find out the prices of reagents before writing an order. This is, I am forced to admit, not purely from the altruistic motive of not wanting to disturb the boss (or indeed from trying to save the taxpayer’s money); sometimes he’s difficult to find and at others I don’t want him to know what experiments I intend to perform. Such is the enigma that is British science in the 21st century. (more…)