Future Ben

I am back in construct design mode, and a deeper lesson just dawned on me. I have been playing with a human protein in a human cell. It’s the metal transporter DMT1 that I will be talking about in Kyoto next week. Not surprisingly, this protein is tightly regulated at every level. How do I get around that problem?

I could edit out parts of the sequence and figure out what parts are regulatory, but that could take a long time. It turns out that a long time ago E.coli picked up the gene for DMT1 through horizontal gene transfer. All the regulatory parts have long since mutated away. Thanks for the help. I am going to use the Bacterial protein as a starting point, but of course it’s not that simple. First off bacteria prefer to use different codons for proteins. you can still get bacterial genes to express, they just don’t do it very efficiently. i have to synthesize the gene for mammalian expression. That’s not so tough these days. A trickier problem is the membrane. E.coli have a different thickness of membrane than a mammalian cell. I will have to do some serious sequence gazing and mental modeling to fix this problem. Sadly there is no structure to work with. If there was somebody else would have done this already.

Damn I have to geek out here for a minute. I am listening to this dude give a tlk on the lambda repressor. It’s been 20 minutes of rambling about how life is just mass action and kinetics. He has the smug confidence of a man who doesn’t know how dated he is. Denying Systems Biology is the new Inteligent Design.

Seriously, just because you figured out that the Cancer field is mostly bullshit doesn’t make you Linus Pauling!

Now Len Girrenti is talking about Sirtuins. Makes sense that Sir2 in year and worms points to a working Sir2 in humans.
“I don’t know of caloric restriction will make you live longer, but it will sure feel like it did”. Ha!

I guess the whole point of taking resveratrol is to pretend like you are living like a yogi. Awesome!

Sirt1 stimulates BDNF production. Who is taking a systems approach? There must be a bunch of people.

It makes me think about going all out on aging. That field is never going away.

It’s a rainy day. When it’s like that outside I find little things to do around the lab.

I have a series of surgeries next week so I better get all my scissors sharp and organized!

I finished running all of the gas lines for a new oxygen enriched anesthetic system. Once the last part was in place I had to step back and get a picture.

Techically not steampunk, but all the gauges and pneumatic hoses next to the superconducting electromagnet reminded me of a panel from Girl Genious.

Next I will install a tesla coil and a giant knife switch.

I have made 9 lines of transgenic mice. The idea is these mice are expressing GFP and my synthetic MRI reporter gene. We are at line 3 with no sign of expression.

I know transgenic mouse technology is not very reliable, but I am braceing myself for the worst case. I added an extra feature above and beyond what a normal transgenic DNA construct warrants. I fear the cost of my futureization habit will be epic fail.

It is in my nature to meddle with elements beyond my understanding.

It is a little known fact the med center is kitty corner to the Chinese UN consolate. It’s also just down the street from the UN. Roll that up with an ER and a helipad and you have spectacular traffic. I like the night traffic more because at least you can watch the flashing lights of the emergency vehicles and think of the playa at night. If China the UN and the police have one thing in common it is that they take themseves to seriously.

Oh the irony of my moniker. (One I did not choose for myself I should add.) Anyway so very long after mobile blogging started, I have finally gotten to it. And what better first post than the place I spend most of my time. Ah sweet purgatory that is lab

When I was a little kid I remember wanting to be an inventor. Oh the things I would invent! I would put together tinker toys and imagine I was building a giant windmill or a shrink ray. Oh those halcyon days of youth.

Here I am actually inventing something and it is not at all as I expected. Sometimes it feels the way I imagined seeing something from my mind take shape in the real world, but most of the time it just sucks. Things fail all the time! If it isn’t some stupid mistake it is a fundamental flaw in my reasoning. Some creeping unknown that stabs me in the back when I least suspect it.

Yes I am just railing because experiments aren’t turning out the way I want them too. And yes I made my bed and now I have to lie in it. I could have taken baby steps forward and worked on something easy. Well… you have a point.

What is it within me that makes me take on a project that demands my ability to distill molecular biology, protein engineering, animal surgeries and MRI physics into one creation? Is it overconfidence or kid in a candy store naivety that makes me reach and reach until I am beyond my depth. Of course it’s both. And maybe that’s OK?

Sigh… back to it then.
Onward I press into the dark. Hopeful that dawn will soon light my way.

I presented a talk to the NYU Biotechnology club today, Metabiotechnology: or Why Biotech Sucks Right Now. Attendance was low but the crowd was more bemused than offended at the title. Often as you put a presentation together your thesis develops. And feedback from your audience is even better for that purpose. Drew and Dusan were particularly helpful but I was surprised at what did and did not resonate.

I will try to post the talk if I can figure out how to get powerpoint into wordpress. Basicly my thesis is that the current hegemony of Biotechnology is Biobusiness. While there is nothing inherently wrong with a free market the system is monolithic and there are huge needs that are very poorly served. The most prevalent being the needs of developing nations.

As I was preparing and during the presentation I realized that it was worse than that. The science supporting Biotechnology is often undermined by profit motivation. My case study on this was the “Green Revolution.” Initially plant breeding and ecological management through pesticides and herbicides seemed like a good idea. It has become pretty clear in the past 20 years that this is not the case and that there are much more sound and sustainable practices. Yet people with access to all of the data pointing to the failings of previous generation technology continue use ultimately damaging methods. In fact they have subjugated Biotechnology to continue even farther down this destructive path. (Hence the subtitle.)

So the evils of greedy corporations aren’t all that new, as several people pointed out. But what surprised me was the audience response to my proposal. If Biotechnology is currently monolithic and profit motivated then the weaknesses of that system opens up the possibility of Biotechnology that is dynamic and either need, OR profit motivated.

Maybe I didn’t express that clearly enough, but I got a lot of knee jerk capitalism. “Technology has to have a product,” or “that system works a lot better than government funding.” Both true statements, but not in anyway an argument against need motivated Biotech. And I acknowledge that there are government grants to encourage people to develop need based technologies, but there has to be something more, something new.

I am glad I used the agriculture case study because the great weakness of current agriculture is that it is monoculture based. And that is exactly the problem with Biotechnology and Big Pharma. Sure there are a lot of little Biotech companies, but they are all playing the same game. Especially since they all presumably follow the FDA rulebook. A true disruptive Biotechnology would bypass this whole system. Is paradigm shift old enough to be retro? It sounds stupid, but there were very intelligent people in the audience who couldn’t imagine that there could be an alternative to our current system.

If you equate it to other paradigms, Biotechnology is ready for it’s own version of the personal computer, model T, cotton gin. I think sequencing was the equivalent to the printing press or early computer. Biotech is fortunate in that it can take all of the lessons from the electronic and information technology fields. Open source, distributed systems and other meta-technologies. The question is, what will that technology be? If history is any teacher we won’t know until it becomes pervasive.

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.