Future Ben

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’être 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.

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.

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.

What does that look like? Huh? If you said, “a normal mouse brain,” you would be right. You would also be an insensitive dick who doesn’t know when it keep their damn mouths shut.

Well. Off to scan a half dozen brains just like that one, because whether you have a positive or a negative result, you need a statisticly valid n number. You can’t just fail an move on, you have to fail again and again and again.

I just want to send out a special message to the following programs.

PV4.0 (Came with MRI console) After spending several hundred thousand dollars on the extremely specialized piece of hardware you control, refusing to even start because of your licensing being locked into the network card.  Congratulations! You have protected yourselves from piracy! No unscrupulous hospital/research institute who drops a quarter of a million dollars on a new MRI console will even think about getting a cracked version of YOUR software.  And you’ve stopped all those punk kids from trying to reconstruct and analyze MRI data without giving you your due.

Amira (7000$/year) For crashing literally every 15 minutes and for the complete lack of thought given your file structures.  So sprawling and precarious that moving anything from anywhere can destroy even saved work.  I am sure there is some reason I have to carefully gather the dozens of random binaries you spew out just to crop a single 3D image, but clearly I am not smart enough to understand why you don’t just save it all in one fucking folder.

Analyze (5000$/year) What can I say? Not only do you not allow me to save files outside of your environment, YOUR DEFAULT EXIT ERASES ALL OF MY WORK!!! There is nothing I love more than the thrill that one careless click and everything I haven’t taken great pains to properly export one slice at a time will vanish. Wow what a rush! As a special bonus I am putting up the exception you threw when I was so idiotic as to try and open a file with the SAME NAME as one already imported! What was I thinking? Clearly not even the most advanced software engineers can work around such an insane twist of quantum logic. I should consider myself lucky that I merely had to restart my computer to get going again. I could have torn the spacetime continuum!

Vector NTI (1000$/year) Now I know you guys have been taking a lot of flack lately. Just because you offered your product for free to academic institutions and then 3 years later abruptly demanded a small fee for all your hard work, you have been accused of treachorous bait and switch tactics. Moreover how could you be called to task for intentionally obfuscating all the files in your database so that, unless we pay you your money there is no way we will be able to access the hundreds of sequences we generate each year. No user could be trusted with such a powerful thing as access to their data! You were saving us from ourselves! And for those of us that can’t afford to lose years worth of work or spend the months it would take to export all of our data as text files and reannotate them, you will continue to save us at 1000$/year.

Windows… you know what you are.

As a student I do not pay these ridiculous support fees, but I see what you are doing and I do not appreciate my lab being fleeced. The time will come when it is MY time to choose what tools I will use and develop. I will not be locked into your software just because their learning curve is not as steep as using open source scripts.  I will not allow my data to be held hostage.  I will always say, “no” to software that separates me from the work I do.  And no, we can’t all be programmers, and people should be supported for developing tools, but limiting consumer choice to protect your shoddy work will only alienate those who would buy your product.

This began as a sort of joke, but warrants deeper thought. If sexuality is a personal trait then we share a cultural metasexuality through media. Sex organs and their deliberate obfuscation. Make for an obvious example. There more culturally specific memes. Oysters carry a certain connotation in Eurocentric culture, but not in Asian societies. However it gets interesting when we move to octopus tentacles.

This very specific sexual reference dates back to 19th century Japan from a print probably by Yositishi, depicting a fisherman’s wife. Yet it is a central theme in the metasexuality of the Internet.

How and why does a 19th century artist influence the sexuality of digital culture and more importantly how can something as mercurial as the Internet have a definable sexuality?

Let’s explore tentacles next.

Oh hell yes. An MIT group has made a small sensor that is powered by the electrolyte gradient between the tree roots and the soil.

The Voltree power supply is a great idea. Can a tree power more than a small sensor? The engineering is there for harvesting a voltage potential. What about a plant engineered for an enhanced gradient to harvest. A biological solar panel? Not so far out.

Really I just wanted to get the Anarchy player running on the site. I can’t decide which is more obnoxious though. The Anarchy splashpage or the Youtube watermark.
Option A.
sany0076

Option B.

It suddenly occurred to me that one of the best support sources for open source biotech would be the open source software movement. Google offers scholarships to students to take on summer coding projects with open source foundations. Is there any Bioinformatics in there? Just two that I can see.

GenMAPP (Gene Map Annotator and Pathway Profiler):

an academically based organization that develops and supports GenMAPP (Gene Map Annotator and Pathway Profiler), a visualization and analysis tool for biological data. GenMAPP illustrates the relationships between various genes and proteins to help researchers understand their data in terms of connected, biological pathways. Over 18,000 people from >70 countries have registered to download the GenMAPP program. There are over 360 publications that reference GenMAPP or use GenMAPP to display data in the context of biological pathways. GenMAPP is 100% open source. All new development is in Java, MySQL, Derby, XML, and Web technologies such as MediaWiki in collaboration with the UCSF library, BiGCaT Bioinformatics, and the Cytoscape Consortium. Our development team is composed of individuals who are both biologists and programmers, providing a unique perspective on building and using open source tools.

The NESCent (National Evolutionary Synthesis Centre):

NESCent facilitates synthetic research on grand challenge questions in evolutionary biology and also works to address critical needs in software infrastructure and education through promoting open, collaborative development of interoperable and standards-supporting open-source software. The Center is located in Durham, North Carolina, is jointly operated by Duke University, the University of North Carolina at Chapel Hill, and North Carolina State University, and receives its core funding from the National Science Foundation (NSF). Together with developers from open-source life-science programming toolkits (BioPerl, Biojava, Biopython, Bioruby, BioSQL; collectively referred to as the Bio* projects), evolutionary software packages, and recently developers of comparative phylogenetic methods NESCent has so far run two Hackathons, which continue to have significant and lasting impacts on the landscape of collaborative software development in our field. The Center is committed to FLOSS and sharing of scientific data (see for example the NESCent Data and Software Policy at http://www.nescent.org/informatics/data_software_policy.php); all software products of the Center are released as open source and established as collaborative projects on sites such as SourceForge. Members of the Center’s Informatics team are lead developers in several open-source projects, and one of our organization administrators has been active on the Board of the Open Bioinformatics Foundation (http://open-bio.org/), the umbrella organization for the Bio* projects, since seven years.

Well it’s a start. I need to look more into what these groups are doing.

So started reading anAleister Crowley and honestly I am inspired. The poor bastard has so much about the universe and yet he admits that it is all just symbolism. He doesn’t even attempt to rectify astrology with astronomy. And honestly I don’t really care very much about either circa the 1920’s. The massive failing I see in Qabbalah or any occultism is the presupposition that the universe is crystaline and all we have to do is find the patterns. As if algebra could even get you past even the most basic model of nature.

So here is Crowley who can’t make it to trans-humanism because his cannon of reason and practice, the Qaballah, is based only on algebra and could never be a dynamic, ergo functional, model. Hence the inspiration. Trans-humanism is based on a dynamic model with complexity. But how to understand complexity. I don’t know enough about network theory or graph theory, or probability math, or statistics, or discrete, or any math really. I don’t have any sort of grasp on object oriented programming, or C for that matter. This is all foundation level stuff and I just don’t have it. I was too impetuous as a youth. Why oh why did I while away my time with RPG’s and hallucinagens? The rhetorical answer is so that I take the flights of fancy needed to ask that very question.

Is it too late to crack a book and actually get a grasp of the fundamental concepts behind all the junk that I know is important but I don’t really understand? I fear that impetuousness has never gone away. I spend my day worrying about viral gene transfer and T1 weighted images, why would I start on something that I won’t be good at for more than a year. And this is how the brain grows old dear reader. It isn’t that you can’t form new dendritic connections. You are just to lazy. If I really believed this was important I would stop reading this dull ass Aleister Crowley reader and go study the real secret language of the universe!

Oh look at me! I am putting Crowley on a shelf and replacing it with a review paper of BAC transgenics and on Melanosomes. That is a start, but where to begin on network theory? Oooh a hyperlink!