Lady Gaga spoof is catharsis for Biologists

Title says it all….

Dieting for Biotechnologists (Part I)

I am at that point in life when you are too old to keep eating as if you were 18 and too young to just give up and let the pounds pile up. That’s why I’ve decided to fight back and loose those ‘love handles’.

So, who cares? and why are you talking about that in this blog? you might ask. Well, because I’m gonna approach the problem the only way I know, i.e. research, play around with all sorts of gadgets and getting data until matlab says no more. And that means I’ll learn (hopefully) and share with you a bunch of stuff about the physiology of dieting, exercising, energy consumption, metabolism and all the technology out there to help anyone on a similar quest.

Let’s get to it. First things first, an inventory of resources available include:

• Google Scholar
• University of California Libraries
• All peer reviewed publications known to human kind: e.g. Web of Science, ieee Xplore…
• Computer with Matlab and iWorks
• iPhone (iFitness, Lose it!)
• Gym membership
• Asics running shoes (though I’m thinking about getting Vibram five fingers because of this)
• Garmin Edge 705 (with cadence meter and heart rate monitor)
• Trek Pilot 1.2
• Trader Joe’s and Wholefoods (as organic food supplies)

Today I’ve started with a little bit of research, which is the least physically demanding thing I’ll have to do if I’m to shed those extra pounds.

Most of you probably have heard that ‘a calorie is a calorie’ which implies that basic thermodynamics apply to our body too and that energy in minus energy out equals energy stored. While thermodynamics obviously DO apply to our body, the whole system is a tad more complicated. That’s why that has always struck me as a rather simplistic model.

Indeed, I read this interesting paper about metabolism, energy balance and body weight and their model is definitely more complicated. They start by asking a good question, if lowering your energy intake generates an energy imbalance, how does that translate into a change in body mass? The problem is knowing where the energy that we spend comes from. If all the extra energy were to come from fat everything would be really easy, but alas it is not. The energy content of fat is 9400 kcal/kg while lean tissue contains only 1800 kcal/kg. That means that for the same level of starvation (=diet) you’ll get different weight loss rates depending on your body weight composition. Turns out that the amount of fat vs lean muscle I am losing follows what’s called the ‘classic theory of Forbes’. It says that the percentage of fat loss vs initial fat mass follows a logarithmic curve proportional to the overall weight loss.

Bottom line. If I loose 10 lbs and I had 30 lbs of fat on me the relative fat loss is greater than if I loose 10 lbs and I had only 20 lbs of fat on me. That means the more fit I am… the harder it is to loose those last pounds of fat. That makes sense and you probably have some experience that validates this model.

to be continued…

Lab Automation 2011

As I said before I was in Lab Automation (Palm Springs, CA) this year presenting a poster. Although I only went on Sunday night and Monday I got to see enough interesting stuff. About Sunday night I’ll only say that the ‘Opening Night Celebration’ was fun, the River Dogs Band played (I think they did last year too). The music was good, I only have a complain/suggestion… if the whole event is supposed to be a networking event turn down the volume or leave 30-45 min before the band starts playing so that people can talk and meet. It was almost impossible to hear anything in the tables other than the person right next to you.

Monday I went to the opening keynote speaker which was fantastic, Chad A. Markin gave an excellent talk. He started off introducing a few of the things that made him well known such as Dip-Pen nanolithography. For those of you not familiar with the concept I’ll just say it basically consists on taking an AFM (Atomic Force Microscopy) tip, coat it with anything you want to pattern and start patterning, you will get a monolayer of whatever you’re depositing. They do all sorts of fancy stuff sprouting from that concept. Take an array of tips for instance and tilt it, that’ll create a differential force when you touch your surface having some tips barely touching and some forcefully pressed. What you get is a patterned gradient, cool stuff.

He followed by the main topic of the talk which was ‘Oligonucleotide Nanoparticle Conjugate’. These nanoparticles are made of a gold core to which they attach a bunch of oligonucleotide strands that will assemble hanging radially from the core, like a hairy ball. The bottom line is that they can form these structures and use them as transfection agents. Their numbers in terms of uptake percentage (99.9%) and the range of different cell lines they’ve used make this potentially very useful. If you want to read more I found this which goes a little deeper.

The rest of the morning I went to a bunch of talks that… let’s say, were not the best. Right after lunch we had the poster session were alas I could not see much since I had to be in front of mine. After the poster session I went to a couple of talks worth mentioning. The first given by Thomas Laurell about acoustophoresis. He concentrated on the use of acoustophoresis in microfluidic systems as a substitute to centrifugation. The other talk worth mentioning was the one given by Elliot Hui. He talked about microfluidic pneumatic logic as a tool to generate integrated computers in microfluidics. I think it has a lot of potential as it is and the clocking mechanisms and peristaltic pump that he showed were impressive. My only concern is that in these types of computers information is coded as pressure, which in a microfluidic system is not the only type of information you have, so how do you translate concentrations, colorimetry, etc into a pressure? If anyone can figure that one out then the sky’s the limit for this technique.

After that I walked around checking out some exhibitors. There was a lot of fluid handeling, which for a microfluidic guy like me… well it wasn’t too interesting. Don’t get me wrong, robots and all that stuff are A LOT of fun, but they’re too big for a guy used to microliters worth of sample. Anyway you had some of the usual suspects in lab equipment; Agilent, Douglas Scientific, Beckman Coulter, Corning… etc. Then you had a few microfluidic ones, but I’ll only mention ChipShop from Holger Becker whom I’ve talked about before.

Bottom line, it was fun. I got to see some people I had met in other conferences, I got to present a poster, learn some new stuff and meet new people… I think I might go again next year.

HIV life cycle video

The other day a member of my lab gave a presentation about HIV and it reminded me of this video. It is from 2002 and although it is not as cool looking as the more recent BioVision videos it gives you a pretty good idea of what the life cycle of the HIV virus is.

More videos for the geek: LabTube.tv

This week I was in LabAutomation2011. In the lobby they had a bunch of bags with the LabTube.tv logo on them. I did not know what it was so I checked it out.

Turns out it’s a website that has been around since late 2009 and where anyone can post videos about anything biotech/research/laboratory related. You can find videos ranging from tutorials to company and product advertising. The website was quite buggy when I checked it out but it was tolerable.

In terms of its contents, it is an interesting site worth browsing to discover new companies and products and maybe checkout some tutorials. Keep in mind however that unlike JoVE there is no peer-review process so the content may or may not be reliable.

I think the more videos out there about these things the better. And it is even better if they are easy to upload, share and find and all in one place. So a site like this has potential but labtube.tv has a business feel to it that I don’t like. It is more a marketing tool than a social experience for science geeks where the main goal is to share information about science, techniques, and why not also products/companies. It’s 2011 and there’s a lot of good social network products out there. I guess my expectations are higher on that regard. Anyways, all in all a good site but it needs improvement.

I’ll write a few more things about LabAutomation2011 later this week.