Future Ben

“this exciting but somewhat risky project.” -futureBen’s committee

Saturday, September 11, 2010

I didn’t win the prize

First off I want to be clear that I didn’t expect to win the young investigator’s award. OK, I am still bitter about it, but I am bitter about lot’s of stuff. So while I am not particularly upset about not winning, it was the finalists who really irritated me.

All three featured commercial products some with affiliation to the “judges.” That really set the tone. Sure there is no point in reinventing the wheel, but using something you bought as directed by the manufacturer is not exactly ground breaking. To her credit the winner was actually collaborating with a chemist to improve the agent. La di frigging da.
None of the finalists used any methods other than imaging. Sure it’s an imaging conference, but if you are going to claim your labeled differentiated into a particular type of cell, you are obligated to back that up with some staining. “We injected some bone marrow, it did aomething, you can see it, isn’t that awesome?” Wow, mail that back to 1988 when it wasn’t taught in first year immunology!

So what was the judging criteria. judging from the abundant use of the RGD peptide for labeling avbeta3 integrin, it was mostly based on FDA approved nonthreatening tech. By nonthreatening I mean it doesn’t challenge anybody’s research. To set such a conservative standard for grad students and post docs is a travesty. This is the point in our careers where we should be challenging the status quo or at least looking at biology in a new way. Sadly, medicine is too parochial and corrupt to allow real creativity to flourish.

posted by Futureben at 8:34 pm  

Thursday, September 9, 2010

Thanks Marshall Plan

I am in Kyoto right now. Really I am! this is my second time in this city. It’s the 3rd if you count the time came through just to eat Anago at the Nishiki market.

I am here for an imaging conference, but I am taking the opportunity to stay at a ryokan and absorb the culture as best I can.

Japan is generally a pretty foreign place to the likes of people like me, but the extent the people here go to ameliorate the alienation. Here I am the only white person in this little okonomiyaki place but there is a helpful english menu all the same.

Of course this isn’t remarkable. I am attending an international conference conducted in English. The scandanavian girls who stopped and asked for directions, which I was patently unqualified to give, started in English. If the greatest generation fought and died for anything it was to establish English over German or French as the international language.

I am not entirely comfortable with that fact. I took Spanish and Mandarin and do my best to pick up what Japanese I can, but in the end the native speakers I interact with will be better at English than I will ever be at their languages because they have to be.

And for what honestly. True the US publishes more scientific papers than the rest of the world but we as a culture reach so much farther than we as a people.

Or so the complaint goes. But wait, isn’t that a inherently racist statement? Who are the American people? Certainly not all native English speakers and obviously not all white. It is this truth alone that helps me accept the decades of cultural imperialism. Our only claim to our global language is the sheer number of people who learn our language in order to live in America.

On the flight back I caught myself again. I was one of 10 white people on the plane, but not until I lined up for entry did I realize that 1/4 of the passengers were Asian Americans.

posted by Futureben at 2:43 am  

Wednesday, June 9, 2010

Sharing with E.coli

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.

posted by Futureben at 8:26 pm  

Friday, June 19, 2009

Should have stayed home

I am in a mood. It is unfair to completly blame my state upon the absence of my lover although that poor situation most certainly exacerbates this affliction. Everything around me is moving a little too fast and I feel uncomfortable in my skin. At once tired and restless I have been wandering Brooklyn for 3 hours one step behind synchronicity.

This began as a friendly offer to accompany TwinA to the Disorient fundraiser. As usual the lab kept me late. As I walked to the train I started to become aware of how off I felt. The notion of prolonged social interaction became increasingly axiety inducing. Almost to the train Twin A texted me asking to pick up batteries since Leo had already laid claim to the DIY blinky pendant I was supposed to be wearing.

My raison d’ĂȘtre foiled, it was pure stubbornness that pushed me on. I bought 2 9V batteries for 7 dollars and continued on my way. On the platform I recognized Orion and several other Disorient core. He and I have spoken on many occasions and greeted each other by name just one week prior, but the anxiety that he might not remember me became too much to hazard the interaction. I willed myself invisible which doesn’t really work on anybody but Orion for some reason and he walked right by me without so much as a glance.
I rode the train to Bedford standing next to a man in a pink sequened miniskirt whom I once loaded a cargo container with. He was wearing the same straw cowboy hat. Still I felt to out of place to share my reverie with him. I stepped out at Bedford though no one else who mattered followed suit. Still, I would never trust my portage to the G train so I contined on through the vapid wasteland that is the Bedford stop on the L.

True Greenpoint is by no means a short walk from Bedford and it was several hours and text exchanges with Twin A before I caught sight of the telltale pink afro wigs which are the hallmark of the Disorient subcultural niche.

This particular confectory halo was enveloping Jewels. Which presented a gamut of complex social issues. Jewels is dear to my heart and yet to see her outside of the context of our conclave would force a necessary reevaluation of our working relationship. It could be weeks before I would be comfortable working with her once the formalities I usually hide behind were washed away. Again, obfuscated my ego and added another person to the short list of people that actually worked on.

Dawn however is not on that list. Her training and former career addressed the wretched individuals who suffer from legitamate mental afflictions rather than my own self indulgent melancholic bouts. She caught me hiding behind a lightpost waiting for TwinA to come get me. Forced before an audience I searched for the appropriate poise but could find nothing within me.

At the door I was somewhat relieved to discover that I had no ID or valid proof of age. In self directed obstinance I made sure I wasn’t hiding my liscence from myself to cop out on the evening. It has been months since I went to a legitamate establishment via the front door, perhaps over a year. I made my apologies to all concerned and made a mental note to put the search for or perhaps the replacement of my liscence on my “to do” list after collecting my tax returns and buying Shinkansen tickets from Tokyo to Kobe.

I won’t recount the rest of my evening but succinctly, I learned about Grand st vs Grand ave and forgot to remember to check the cab meter, especially in Brooklyn where they can plausibly deny you ever existed. On the way home my old friend Deb texted me inviting me to her wrap party for her recent sculpture. In that instant an evening in the company of old friends seemed like the bromide I needed so badly. Those people were well aware of the trainwreck that becomes of my social grace. And for a moment I was cured.

This moment quickly passed as the batteries in my pocket bridged and began to overheat. The silicone skin of my phone had sheilded me long enough for the batteries to reach a critical temperature and just as my old compatriots communication was lifting my spirits scalding alkalai gel filled my pocket and burned my skin.

As I briskly removed my pants and let the cold shower washed over me a few minutes and a short cab ride later. I thought a out the evening and came to a realization. I should have stayed home.

posted by Futureben at 9:19 pm  

Tuesday, June 2, 2009

A systems approach to cancer

First off I hate cancer. I hate the disease almost as much as the vulturous profiteers who are assosciated with this ubiquitous disease.
That being said I am at the NYAS meeting, “A systems approach to the study of cancer.”
Andrea Califano: Interactome Analysis Reveals Master Regulators of Human Malignancies. ARACNe reverse engineering regulatory networks. Hmm if you apply information theory to regulatory networks you can predict edges to look for. ChIP on chip data has been show to have a false negative rate an order of magnatude below the predicted and later proven interactions.
The. Ext genome scale project should be devoted to assembly and validation of whole regulatory networks.
You definitely have to be a beleiver in Sys Bio to buy into this.

Galit Lahav: Dynamics of the p53 signaling pathway
P53 and Mdm2 regulate each other via transcription and through direct interaction so it works in a slow grade way and through damped oscillations. Sweet they made fusions that report relative levels oscillating and do a 30 hour time lapse movie. There we see they aren’t damped oscillations it’s just that more cells oscillate more under stress. You can show whole mouse p53 oscillations. Perfect for in vivo imaging. So the pulsitile dynamics allow for a wider range of regulation depending on the frequency of oscillation vs the stability of the regulated protein.
In order to look at a sychronized population they image individual cells and retrospectively synch their cycles with image processing. Another common in vivo method repeated.

Chris Sander: Network Pharmacology of Cancer
Anyone who starts off telling you how they failed to solve the protein folding problem is OK by me. Structure is function, but so is function. This is another repeating motif. He takes pairs of drugs to cause network perturbations. Hey this is the first time I recognized a differential equation! Go Hopfield network model!
Oh man I just realized why network modeling actually works. Even if you are missing nodes the model is still somewhat accurate. In a structural model you have to have every atom as a vector even if it’s a chaperone or membrane or whatever random thing the folding protein bumps into. The former bravado of a structural modeler is actually realistic in a network milieu.

Arnold Levine: single nucleotide polymorphisms in the p53 pathway
There are roughly 5 snps per gene in people. Not counting the untranslated regions. 18million total. SNPs and populations getting cancer. It reminds me that we would help more people if we spent our research budgets on public health. The other nice thing about SNPs is you can look at phylogenies over the last 30,000 years. I really appreciate that he presents all sorts of hypotheses about why these SNPs are more or less prevalent.
It turns out p53 upregulates LIF needed for implantation of embryos. So low levels of p53 can prevent pregnancy in women. It also can sense aneuploidy and reject implantation. So p53 can control germline cells. P53 is more of a germline preservation mechanism. The stem cell functions only came later in mammals. There is a p53 in very primitive animals.

This symposium shows a real turning point for me and cancer. We are finally realizing the deeper implications of cancer and stem cells and of course systems modeling as an informant for benchwork. Plus it gave me some solid ideas on dynamic imaging.

posted by Futureben at 1:05 pm  

Tuesday, April 28, 2009


Welcome to the new home of Imagenode and NYCSparkworks! TwinS and Ray needed professional workspace and I needed art and storage. Admittedly I am the financial junior partner on this, but I won’t need the same kind of floorspace those two use. Plus U will contribute to infrastructure as much as I can.

It’s weird that I started in living in that area so many years ago to have a live/work space. In those days all I did was build out my loft. Now when I actually need workspace I live in a little studio in Manhattan

posted by Futureben at 7:27 pm  

Tuesday, April 21, 2009

EEG to twitter. So what else is new?


So interfaces with EEG have been around for a while. But since the technology to make and analyze EEGs are getting it was time somebody did something inane with it.
From ReadWriteWeb

Technically, what Wilson did was come up with an interface combining an Electroencephalogram, or brain wave monitor, with an on screen keyboard for selecting letters. The system lights up each key on the keyboard but is able to notice a difference in brain activity when the desired letter for input is lit. Wilson compares it to clicking through multiple letters when texting on a mobile phone.

Once you’ve found a new way to input text – what are you going to do with it? Use it to Twitter, of course!

Clearly hooking stuff up to your brain is awesome and using it for some Web2.0 action is hip. But a lot of other fine work has been done.
Eva Lee Creates literal emotional landscapes in video using EEGs of volunteers. Not a direct harnessing of the EEG, but with a deeper meaning perhaps.

Also EEG has been explored as an interface for music

EEG is not the most elegant method our there, but it is less bulky than fMRI or EMG. Until we have cheap room temperature micro SQUIDs Expect to see continued experimentation for low bandwidth applications.

posted by futureBen at 11:15 am  

Monday, April 20, 2009

Barry the Worm. Coolest segmented worm ever?


Its good to know that no matter where you go or what you do, you will never be as badass as a 4ft long polychaete worm coated with nematocyst stingers. Barry, you are the, “Shaft” of the animal kingdom. Thank you for putting things in perspective.

From the Daily Mail

Aquarium staff have unearthed a ‘giant sea’ worm that was attacking coral reef and prize fish.

The 4ft long monster, named Barry, had launched a sustained attack on the reef in a display tank at Newquay’s Blue Reef Aquarium over recent months.

Workers at the Cornwall-based attraction had been left scratching their heads as to why the coral had been left devastated and – in some cases – cut in half.

After staking out the display for several weeks, the last resort was to completely dismantle it, rock by rock.

Halfway through the process the predator was revealed as a four-foot polychaete worm.

Staff eventually lured it out with fish scraps, but not before it bit through 20lb fishing line.

The tropical worm is capable of inflicting permanent numbness on humans with its sting.

Matt Slater, the aquarium’s curator, said: ‘Something was guzzling our reef but we had no idea what, we also found an injured Tang Fish so we laid traps but they got ripped apart in the night.

‘That worm must have obliterated the traps. The bait was full of hooks which he must have just digested.’

He added: ‘It really does look like something out of a horror movie. It’s over four feet long with these bizarre-looking jaws.

‘We also discovered that he is covered with thousands of bristles which are capable of inflicting a sting resulting in permanent numbness.’

posted by futureBen at 1:55 pm  

Monday, April 6, 2009

From the DART Biotech awards.

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.

posted by Futureben at 12:25 pm  

Friday, April 3, 2009

Rainy Day Activities

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!

posted by Futureben at 9:02 am  
Next Page »

Powered by WordPress