Future Ben

I have been appointed the task of naming my first foray into synthetic biology/ protein engineering. I have never invented anything substatial enough to name before so I am having some trouble.

The protein is a new reporter for MRI. It binds paramagnetic Manganese and it creates a brighter signal than background tissues when imaged properly. What the hell do you call something like that?

My coleague and friend Yousef had this to say.

your construct could
termed as MP’s standing for either “magnetic protein”, “manganese protein”,
“metal protein”, “MRI protein” (a lot to stand for) to parallel the FP field
(fluorescent protein). Since there is no color such as in GFP and RFP
etc….Your enhanced MP (EMP) are reduced to 2 tone: darkening (DMP)and
brightening (BMP)proteins. In DMPs Ferritin would be one of them and in BMPs
yours would fall in this category…

BMP? I’m not sure it has pizzaz. Although I agree that an acronym would be appropriate. How about Manganese Enhaced Magnetic Resonance Imaging Protein? MEMRIP. Maybe MRI can be collapsed and I could just call it MEMP. If I did and Iron one it would be FEMP.

I have to figure this out before starting the patent.

Dude I don’t even know where to start. On the surface it’s not really that much of a crackpot site, it just has the all the standard layman’s freaky science highlights. Nothing about Atlantis, but what the Brazillian Stonehenge has to do with the future I don’t know. Maybe the dude is right and Light Transformation is going to be the single most important scientific theory of our time. Although its not so much of a theory as a series of wandering “what if” statements based entirely on handwaving and misderstood generalizations. ( I knew the spite would kick in)

So why on pick on somebody else’s vanity site which is also based loosely on science and the future. It’s a matter of priciple! There is a real danger in presenting your assumptions along with a little data. This website is the result. What kind of reference is the fucking Book of Knowledge: The Keys of Enoch? Who peer reviewed that? Actually, I am noticing most of the citations are largely self referencing. Of the few links that acutally work my personal favorite is this statement on the martian pyramids.

Pyramid structures which range in dimensions of 3.0-base to 6.0 km mean diameter have been identified in the Elysium Quadrangle of Mars. Geologic processes that could result in such features have not produced a satisfactory scientific explanation for some of the pyramids. Thus we must keep in mind that what may appear to be a natural hill from an aerial view may be a pyramidal artifact.

Perhaps, instead of preparing for the contemporary scans of the Martian micro-intelligence, we might prepare ourselves for a close examination of pyramidal structures as blueprints for bio-magnetic analogs? The Martian and Egyptian pyramidal grids may be models preparing us to meet the superior architects in our immediate universe? Perhaps, the pyramid is a future artifact?

And all this is based on what data?

OK…So based on this image alone, not only does Mars have pyramids from the future, any hill on Mars could be actually be a pyramid in disguise that might “hold the keys to man’s existence.” This dude comes right out and says that we should beleive that a bunch of piles of sand are magical because it would be awesome if they really were. Get over yourself!

Everybody wants to believe there is a pot of gold at the end of the rainbow and that all of our questions will be answered if we can just get over the horizon. And let us not forget that old chestnut. Everything you know is wrong, but I have got it all figured out, so come join my clique of people who know what’s really up. I would like to make through at least one Burning Man without having to hear a variation on that one.

But what if they really were pyramids? That would in fact be awesome.

What the hell am I supposed to do with that? I have spent a large chunk of my day trying to figure out another of these little puzzles and it has left me rather cross. In fact I have spent at least a dozen hours over the past few days trying to pick apart other people’s cryptic little maps. This is the promoter/enhancer of Flk1, some receptor that does I don’t know what. The point is that this sequence will cause expression in developing vascualture. The key word here is SEQUENCE. Why am I looking at a crude line drawing when they could just post a text file? No, instead I have to Genbank and BLAST my way through the mouse genome looking for the right piece of DNA then take my best guess at what they cut out. Did they not know the sequence? I guess this stuff came out in 1995 so it wouldn’t be surprizing.

I remember an a review paper about Genomics being, “too much information” to be useful. Give us our bright and shining gel bands of approximate size! Luddites! I dig through notebooks of paper notes, pictures, crude maps all for one text file worth of information. And the actual DNA is nowhere to be found. Its a wonder anything ever got done that way.

So here I am, doing reverse bioinformatics to digitize what has already been published. Compiling my sequences in VectorNTI and creating dynamic maps that have more information that I am going to use, which is just about enough.

Yeah, so apparently a huge problem in Africa is that women aren’t producing enough babies for their husbands. You see in many parts of Africa a woman’s entire worth is based on her ability to produce children for men. A woman who reproduce “is worse than a dog.” What could be the answer to this grave social ill? In Vitro Fertilization of course! God forbid we address the issue of the blatant sexism that lets men think its OK to throw their wives onto the street for not producing children. Or maybe the rampant venereal diseases that are left untreated and cause infertilty. Unfortunatel nobody ever made any money promoting social elightenment or public health so the answer is of course to provide affordable IVF for the third world.

How can a world be so ass backward? Where a woman is mutilated at birth, has no access to or knowledge of contraceptives, no treatment for subsequent diseases, and after all of that, despite being the infertile member of a couple only 60% of the time is driven into the street when no babies come from the indentured rape that so often is marriage.

When I grow up I’m moving to Africa to marry a bunch of beautiful but recently divorced ladies and open a university for women. It will be a school with only three majors. Public Health, In Vitro Fertilization and Lesbian Studies.

This is just ridiculous. This is an article about science education in Arkansas. I have been very slow to accept the idea that biblical history carries so much weight in the American educational system. Thinking back, I don’t remember being explicitly taught evolution, but all but one science teacher I ever had felt quite comfortable saying, “millions of years.” Apparently that is taboo in some parts of our country.

Its easy to write off anti-evolution as an outspoken, but backwater movement.(Fun too) But this article shows that this is not the case. Arkansas has been independently ranked 37th in the nation for education. OK so their kids aren’t all Ivy League bound, but they aren’t dead last. (Hey Arizona, I guess you guys are better off going to school on Martin Luther King Day. Maybe it might help you guys catch up.)

This passage is just shocking.

So basicly the Arkansas educational system has been bullied into mandating ignorance. Yikes! No wonder the Clintons abandoned that state for New York.

Maybe this awesome Doonesbury will cheer you up.

The J Craig Venter Institute is one of the most modern innovative research centers in the world today. Dr. Venter has stirred his share of controversy with his “shotgun” approach to sequencing. In the late 90’s there was a concern in the scientific community that there was too much data to be meaningful. This notion seems laughable today as Information Technology has caught up to the flood of data, yielding some incredible advances.

Already Dr. Venter has moved past Genomics into what is now called Metagenomics. His recent expedition on the Sorcerer II consisted of sampling seawater every 200 miles in an around the world sailing trip. A common reaction to this is rejection of the idea that anything meaningful could be gained from Venter’s around the world boondogle. But there is a genius behind the Sorcerer expedition. Venter’s thesis is that the ocean can be considered a single living organism with specialized genetics to handle environmental differences. In this view determining species is unimportant. What maters is the genome of the environment. The Metagenome.

What does this mean to the rest of the world? One of the major efforts of the Venter intitute is Synthetic Biology. Why? With a collection of environmental metagenomes a clever Biologist can determine just what genes are necesary to thrive and construct or modify organisms accordingly. Another application is biosynthesis or biogeneration. The Venter instute is working on generating Hydrogen as a fuel source.

This type of forward thinking will lead to biotech’s next great expansion. Data is the key. For this reason The Venter Institute has partnered with UCSD to start CAMMERA: Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis. Once completed this optical network will allow researcher from all over the world to datamine the ever growing sequence information being generated. What discoveries and innovations this will lead to is anyone’s guess.

I noticed a post on boingboing about computer designed antennas about to be used in a NASA experiment. It led me to The Evolvable Systems Group at NASA’s Ames research center. From their site:

“The Evolvable Systems Group investigates computer algorithms that automate the design and optimization of complex engineering systems for current and future NASA missions. Our overall goal is to dramatically increase mission reliability and science return through development and application of adaptive and evolutionary algorithms.”

This is the ultimate form of biomimicry. A human mind comes up with the specs and some seed designs for the algorithm and an evolutionary design and test series is played out virtually. To be clear about this, the algorithms can only optimize the parameters you have thought to model, so there are some limitations. This makes these methods immediately applicable to well worn models like molecular and electromagnetic force fields. I can think of dozens of engineering and systems biology problems that are still having their parameters worked out and would be great applications for these methods.

I have been getting buried under my project lately, but I wanted to quickly present Caltec’s Biological Imaging Center. The center, headed by Scott Fraser. The imaging part is interesting enough, but what fascinates me is how this group pioneers new ways of seeing.

I first learned of the center at a ASCII meeting here in New York. David Kremers is (or was) an artist in residence there. He presented several projects the center was working on. Namely showing more than 3 dimensions of data in a single image. At the time it made less sense to me, but now that I am working with MRI I understand much better the need to present a huge amount of information in a single image. Take the time to check out the center website, and Scott Fraser’s labpage.

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.”