Future Ben

This week in lab I am STILL working on constructs. I managed to get my genes into expression vectors and get tags on them, mostly. I still want to put flourescent reporters on the same mRNA though.

I have added an IRES eGFP to nRamp2, my metal pumping protein. Now, whenever it is expressed you will also see GFP as an instant reporter on its activity. It is important to note that this tells you nothing about whether nRamp2 has been folded and sent to the membrane like it is supposed to. For that I need to use the tag I added.

That leaves Ferritin M. I can’t very well use the same color reporter, so I have to make something new. The Tsien lab at UCSD has come up with a few decent red fluorescent proteins. mCherry is the one I will be using.

In order to make an IRES mCherry I am using pBS, a vector meant just for cloning. First I am putting in the IRES through blunt end ligation then I’m adding mCherry by its BamH1 EcoR1 sticky ends. Once its assembled then I will put it into the expression vector pCDNA FerritinM-HA that I made last week.

Meanwhile my Manganese binding protein project is moving along swimmingly. I am expressing it in bacteria right now. The great thing about this protein I have discovered is that it sucks up trace amounts of Mn from the media and gives excellent contrast against a control.

Its funny how I spent all of last semester getting these tags and cloning out all of these iron proteins only to have this Mn binder to fall into my lap and work like a charm. I hate science!

MIT hosts a database of “Standard Biological Parts.” The idea is that a Synthetic Biologist can pick and choose these “biobricks,” and assemble a biological machine in the black box style of engineering. Now normally I just complain about the science or new technology featured. This is clearly a work in progress and I will do my best to suspend judgement. They readily admit that this system will be replaced with better paradigms. Here are my thoughts.

I’m doing my best to decipher this biobricks parts registry. I recognize a lot of the names, but their descriptions are are incomplete or less than accurate. Also, with extensive research done on every gene in here and a century of foundation science, why would they make up a whole new lexicon of descriptive terms? Perhaps they want to break from the old, but at the same time they separate the designer from the complexity of the components. An unfortunate side effect is that this obscures the nature of the components. Somtimes it is hard to figure out whether the componet is functioning on the DNA, RNA or protein level. They need to go a lttle deeper before I would use it.

In my own work I keep all of my components such as tags and reporters in a databse that includes their sequences and restriction sites. When I need something I have the all of the data right there. Yes it does get confusing sometimes. I have repeatedly introduced frame shifts or cut out an IRES between bicistronic genes. But the reason for that is my components are not refined yet either. (And I am dyslexic)

Granted, there are some interesting creations made using biobricks, I respect their efforts and hope to contribute to the Synthetic Bio community. However, biobricks seem on par with a scripting language. This is great for doing basic things and maybe that is all we can do with our current understanding. A more fundamental method of design will come however and with it we will accomplish so much more.

This article in the BBC online news is so depressing. How can I convince the children of the world that science is, “all that?” Perhaps when people stop being defensive by acting so proud of their own ignorance. That is the hardest part about science, and what people just do not understand. You have to get used to being wrong a whole lot. And get used to people PROVING you are wrong in front of all your friends. Or even proving yourself wrong. It can be really hard on your ego, and it is too much for a lot of people. Scientists who can’t take that kind of pressure wander the halls of science mere shadows of their former selves. They are called, “Product Reps.”

Rollover to turn the light off

The Nagy lab has been making very impressive GFP mice for years. They focus on using transgenic mice and embryonic stem cells to better understand development and genetic disease. Check out the massive library of flurorescent mice made by the Nagy Lab and their colleagues. Each one uses an inducible promoter to permanently activate the fluorescent marker. Very handy. If you have library access, pull Dr. Nagy’s latest review article in Development 2005 Dec;132(23):5130-2.

I don’t like Edwardo Kac’s work. I don’t even respect what he does. His art preys upon an audiences ignorance about biotechnology. I couldn’t stop laughing at one ASCI meeting when artist Joe Davis started shouting out “Alba was photoshopped! The emperor has no clothes!” I don’t know if that is really true, but it caused the speaker to retreat into stammering artistic doublespeak for the rest of the presentation. Alba, the GFP bunny is not really Edwardo Kac’s creation. He credits several scientists for providing “assistence.” Ha! Sure, it’s his rabbbit, but there is no mention of the process of creating the animal. Why is that? He doesn’t want you to know. Look up the process of making a transgenic it is dull and arduous and involves the sacrafice of dozens of animals. Most people today simply hand their gene over to a facility where a technitions do all of the work. “Genesis” is another great example. There are bacteria on a plate. There are all these G’s and C’s and A’s and T’s. There is even a bible quote. Whoopdie freakin doo! The weakness of Kac’s work, and what totally pisses me off, is that he could say just about anything and people would buy it. I understand the pop art aspect of it, but this isn’t a can of tomato soup. The science as mysticism mentality he inspires in an audience is the most dangerous form of sensationalism and is ultimately meaningless. Anyway, he wrote a book. Go thumb through it at the bookstore.

I am heavy on animal themes lately so here is the ultimate future animal page. The Future is Wild is an animated Animal Planet show. The show creators got Stephan Palumbi from Stanford and a number of other scientists and illustrators to come up with animals that might exist 5 100 and 200 million years in the future. I love this kind of speculative stuff. But one must remember that it is hard enough to figure out what the climate will be like in 5 years, let alone 5 million. Still it revives my childlike wonder at the mutability of nature.

The Integral Trees This is the first Larry Niven book I ever read, and I have to say it was the best. Imagine 2001 meets Lord of the Flies. The decendents of castaways make their way through a world without gravity, the Smoke Ring. In just a few generations humans have already adapted. Without the compression of gravity, their toes stretch out like fingers, and their entire bodies are wispy and elfin. Damn I loved this book. Its sequal, The Smoke Ring is equally rocking. I remember wishing so fervently that I would wake up in the Smoke Ring and my own body would grow out to match that of the locals. Of course now we know that bones need to be compressed in order to stimulate growth, but who knows what happens in microgracity. Perhaps everyone who grows up in space will strectch out and grip with their feet as we once did. One day Ben. One day.

I’m probably just in a bad mood today, but this report from The Interdisciplinary Canter for Technology Analysis & Forecasting at Tel-Aviv University really annoys me. I’m not entirely sure why though. It may be somewhat accurate for all I know, the annoying part is the commoditization of things that haven’t happened yet. Every investor wants little chips that do things better and cheaper so that they can reduce overhead and raise profit. If a nano/biotech revolution did sweep the world, they don’t understand that it could also destroy commerce. Imagine self replicating and self repairing medical diagnostic equiptment. How do you sell it when anybody can just make a copy? The ultimate technologies will be not only accesible but manufacturable by the smallest mountain village. And the only comodities will be innovation and raw materials. The true revolution will be a reconciliation between industrial and agrarian. And that will be all kinds of bad for multinational corporations and globalization. It is my fervent hope that every single widget they are hoping for is rendered obsolete by something they couldn’t possibly imagine. And all of their planing and panel discussion will have wrought nothing but their doom! As long as I’m dreaming, I would be the creator of that technology. And I would laugh…into the night. I am also bothered by all of those little technologesque illustrations so liberally applied. Those are way tacky.

Genetic Savings and Clone offers to clone your prized cats for $32,000. Instead of transfering the nucleus from the donor to an egg this company tranfers over the packaged DNA. The idea behind Chromatin Transfer, I presume, is that the epigenetic milleu of the egg nucleus properly regulates the donor DNA to develop properly.

What is interesting about this company isn’t so much the technology, or even if its a good idea to clone a cat when there are so many up for adoption. What interests me is that its a biotech company that deals in a luxury item. At what point will geneticly modified animals become affordable?(If you call $32,000 affordable.) The initial overhead would be much higher, but once a new line was developed it could be bred normaly. Yeah, right. The company that did that would be legislated right out of existence.

This if from the associated press: “Cy, short for Cyclopes, a kitten born with only one eye and no nose, is shown in this photo provided by its owner in Redmond, Oregon, on Wednesday, Dec. 28, 2005. The kitten, a ragdoll breed, which died after living for one day, was one of two in the litter. Its sibling was born normal and healthy.” It looks too strange to be real right? For all I know it’s photoshopped, but the mutation is possible. The oddly named gene Sonic hedgehog or Shh is resposible for a crest of cells to come down, separate your eyes and form your nose. Mutations in the gene cause these sorts of birth defects all the time, just not so drastic. They manifest as cleft lips. In animals these mutations are fatal because the babies can’t nurse.

It’s likely that this kitten was a sport who happened to have non functioning Shh, but the most common occurence of cyclopism comes from Jevine poisoning. This chemical comes a plant veratrum californicum. It affects mainly sheep who might eat the plant, but the plant is also used as an herb to treat vomiting and cramps under the name Hellebore. Best to just ride out that morning sickness lest your child end up like this.