Tim Smith

Biomedical Engineering PhD student.
Presently: UC Irvine.
Previously: Vancouver, Boston, DC.

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PhD Student at UC Irvine (Biomedical Engineering)
Biotechnology | Greater Los Angeles Area, US

Summary

BS Engineering (Bioengineering); Franklin W. Olin College of Engineering, Needham MA. US citizen.

Skilled at integrating experiences across diverse fields, including nucleic acid processing, tissue engineering, microscopy automation/computer vision, software engineering, and user experience design. Familiar with teamwork, open-ended projects with realistic constraints, and communicating results professionally.

Work at Caltech in 2007 resulted in a first-author publication in Organic Letters. Presented research methods from his experience at UC Berkeley at the 2009 BMES Annual Meeting undergraduate poster session.
Specialties: DNA purification, tissue culture, microscopy automation, image analysis, histology, immunohistochemistry, fluorescence microscopy, confocal microscopy, software engineering, data analysis

Experience

  • Sept 2011 - Present
    Graduate Student / UC Irvine
  • Jan 2010 - Aug 2011
    Research Engineer / Boreal Genomics
    Applications engineering for the Boreal Genomics Aurora nucleic acid purification platform, which uses a novel electrophoretic technology to concentrate DNA and reject contaminants. Areas of particular focus include environmental and clinical samples.

    Skills emphasized include experimental design and analysis and quantitative PCR.
  • Jun 2009 - Aug 2009
    Amgen Scholars Summer Researcher / UC Berkeley
    Participated in the selective Amgen Scholars undergraduate research program in Dr. Song Li’s bioengineering lab.
    Implemented in vitro assays to compare performance of nanofiber materials for vascular graft applications.
    Isolated and characterized smooth muscle cells from rat aorta and expanded cells in tissue culture for use in assays.

    Presented research methods at 2009 BMES Annual Meeting.
  • Jan 2009 - May 2009
    Student, Tissue Engineering ENGR3699A / Franklin W. Olin College of Engineering
    Participated in a unique, open-ended project class at Olin with an emphasis on acquiring laboratory-based skills in tissue engineering and tissue culture. Students independently developed protocols and methods based on primary literature under the guidance of Professor Alisha Sieminski.

    With three other students, designed and conducted a 4-week experiment comparing differentiation behavior of bovine mesenchymal stem cells under common conditions in PGA mesh, collagen gel, and PuraMatrix 3D culture scaffolds.
    Shared responsibility for managing project resources, budget, and timeline, and selecting and implementing methods.
  • Jun 2008 - May 2009
    Biology Intern / Arsenal Medical
    Formerly WMR Biomedical. Employed as a full-time intern through the summer and stayed on part-time during school year.

    Implemented a cell-based immunofluorescence assay to evaluate material biocompatibility at a medical device startup.
    Designed data analysis programs to interpret and report results from cell-based assays and histology images.
    Independently developed automation tools for fluorescence and H&E microscopy image capture and analysis.
  • Jan 2008 - May 2008
    Research Assistant / Olin College; Joanne C. Pratt lab
    Developed proficiency with bacterial and human cell culture and transfection-related technologies while working towards a deeper understanding of interactions of tumor-suppressor protein RASSF1A. Skills emphasized included luminometric reporter gene assays, PCR, DNA agarose gel electrophoresis, Western blots, and sterile technique.
  • Dec 2007 - Jan 2008
    Nevada Field Organizer / Hillary Clinton for President
    • Responsible for organizing 41 precincts in advance of Nevada’s first-ever early Democratic caucus. Ultimately responsible for 15 precincts in Henderson on Caucus Day, after planned staff expansions.
    • Worked 100+ hour weeks to educate first-time caucus-goers, identify supporters, recruit volunteers, and build & manage caucus organizations in each assigned neighborhood through voter contact at doors and on phones
    • Prepared contact lists based for volunteers and interns from Voter Activation Network and managed communication with volunteers with The Donkey
  • Sept 2007 - Dec 2007
    Youth and Campus Outreach Intern / Human Rights Campaign
    Pioneered a new dimension of HRC's social networking strategy by designing and implementing an advocacy-oriented Facebook application. Integrated data from multiple sources including VAN (Voter Activation Network) lists and GetActive to prepare a database application for a state LGBT rights group. Prepared Convio/GetActive advocacy and messaging campaigns and managed HRC field team correspondence.
  • Jun 2007 - Aug 2007
    HHMI SURF Fellow / California Institute of Technology
    Self-directed research on the solvent dependence of conformations of small molecules, particularly ephedrine and structural analogs, in the lab of Dr. John D. Roberts. Extensive use of Internet research skills, 1-D nuclear magnetic resonance (NMR) methods, and chemistry lab techniques.
  • Jun 2006 - Aug 2006
    Volunteer / Commonwealth Coalition
    Contacted voters, recruited volunteers from phone lists, canvassed neighborhoods, and provided internal IT support to a Va. GLBT advocacy group for 2-4 hours a week in anticipation of the November 2006 "marriage referendum."
  • May 2006 - Aug 2006
    Intern for the General Counsel / Office of Compliance
    Designed, implemented, delivered training for, documented, and supported a web-based case tracking system for 20 users at a federal legislative-branch agency enforcing labor & safety law, with no technical supervision. Also analyzed legislation and assisted with miscellaneous office functions, including attending US Senate hearings. Extensive use of project management and Internet research skills; received Library of Congress training on legal research techniques.
  • Jun 2005 - Aug 2005
    Software Performance Intern / webMethods
    Designed and executed performance benchmarks for webMethods products and coordinated with program development teams to address product defects. Skills emphasized included Segue SilkPerformer BDL and Java programming, including JMS. Returned to position over winter break in January 2006.
  • 2002 - 2005
    Network Administrator / Kidz Online
    Coordinated with team to maintain Internet-facing media servers and internal workstations in a content-production environment. Skills emphasized included Windows 2000/XP/2003 and Debian Linux administration, PC hardware maintenance, IP routing including BGP configuration, Microsoft Class Server administration, and Python scripting.

Education

  • 2011 - 2016
    University of California, Irvine
    PhD in Biomedical Engineering
  • 2005 - 2009
    Franklin W. Olin College of Engineering
    BS in Engineering (BioE)
  • 2001 - 2005
    Thomas Jefferson High School for Science and Technology
    Activities: Japan Bowl, TJ Drama, Shakespeare Troupe

Additional Information

Websites:

Posts

I do not apologize.

YACHT - Shangri-La

“Well if I can’t go to heaven, let me go to LA.”

The Decemberist’s “Calamity Song” video is a surprisingly literal presentation of the YDAU Interdependence Day Eschaton scene from Infinite Jest. I was impressed by the attention to detail — Otis’ computer is even running Pink2 — and Colin Meloy is an entertaining, if quite not a convincing, Michael Pemulis. But it wasn’t as gripping as I wanted it to be — I couldn’t make myself feel the tension on the court. Is a four-and-a-half-minute music video too short? It took DFW several hundred pages to get to that point. (And if you haven’t read the book, do, but probably don’t bother with the music video until you have.)

(And I really wanted to see Otis’ head get stuck in the monitor…)

Update: Lol, the director actually mourns that he couldn’t end the video that way.

Seeing even a portion of the beloved novel brought to life was “like a weird dream fugue,” he said, though he reluctantly accepted that his video could not end as the passage from “Infinite Jest” does, with a child’s having his head crashed into a computer monitor.

“They’re all flat screens now, and you can’t put your head through a flat screen,” he said.

link (nyt)

I don’t feel that it is necessary to know exactly what I am. The main interest in life and work is to become someone else that you were not in the beginning. If you knew when you began a book what you would say at the end, do you think that you would have the courage to write it? What is true for writing and for a love relationship is true also for life. The game is worthwhile insofar as we don’t know what will be the end. My field is the history of thought. Man is a thinking being.
Truth, Power, Self : An Interview with Michel Foucault (via mfoucault)

Mostly I just want to point out Professor Noam Chomsky’s excellent use of the word “uncontroversially” below.

We might ask ourselves how we would be reacting if Iraqi commandos landed at George W. Bush’s compound, assassinated him, and dumped his body in the Atlantic. Uncontroversially, his crimes vastly exceed bin Laden’s, and he is not a “suspect” but uncontroversially the “decider” who gave the orders to commit the “supreme international crime differing only from other war crimes in that it contains within itself the accumulated evil of the whole” (quoting the Nuremberg Tribunal) for which Nazi criminals were hanged: the hundreds of thousands of deaths, millions of refugees, destruction of much of the country, the bitter sectarian conflict that has now spread to the rest of the region.

To be sure, a glance at http://www.iraqbodycount.org/ is sobering, but I don’t think that word means what Dr. Chomsky wants it to mean. ;p

Anyway, I don’t have very much to say vis-à-vis the legality of bin Laden’s assassination except to say that while we all know that assassination isn’t any kind of policy tool and if I were in charge of the US budget I probably wouldn’t have spent as many millions of taxpayer dollars on his head as we have, I’m having profound difficulty conjuring much sympathy for bin Laden’s fate. I’m cheered that people are willing to ask the tough questions about due process and international law because I think they’re important principles, but — and this is my American speaking — in this instance, I really just don’t care. I certainly don’t think bin Laden’s assassination was unjust or, well, surprising, and the relatively muted outcry seems to suggest it wasn’t exactly incompatible with American foreign policy goals.

It is the recognition that well-read is not a destination; there is nowhere to get to, and if you assume there is somewhere to get to, you’d have to live a thousand years to even think about getting there, and by the time you got there, there would be a thousand years to catch up on.

Success is always built on shifting sands, though. [via, ironically, everybody]

A 22-year-old North Vancouver man has said he is facing a death sentence because B.C. will not fund the only medical treatment that could save him. Garrett Shakespeare’s red blood cells have a protein deficiency that causes his immune system to attack them, but the drug to treat it effectively costs $500,000 a year.

We’re somehow going to have to get more comfortable, as a society, spending utterly absurd amounts of money on biologicals and being taxed accordingly (my entire annual Canadian tax liability, both federal and provincial, including HST and my Medical Services Plan premiums, would cover maybe a couple weeks of treatment for him)… or accepting some alternative.

Yeah … sort of, um, who do I live for? What do I believe in, what do I want? I mean, they’re the sorts of questions so profound and so deep they sound banal when you say them out loud.

I think the reason why people behave in an ugly manner is that it’s really scary to be alive and to be human, and people are really really afraid… . That the fear is the basic condition, and there are all kinds of reasons for why we’re so afraid. But the fact of the matter is, is that, is that the job that we’re here to do is to learn how to live in a way that we’re not terrified all the time. And not in a position of using all kinds of different things, and using people to keep that kind of terror at bay. That is my personal opinion.
Well for me, as an American male, the face I’d put on the terror is the dawning realization that nothing’s enough, you know? That no pleasure is enough, that no achievement is enough. That there’s a kind of queer dissatisfaction or emptiness at the core of the self that is unassuagable by outside stuff… . And that our particular challenge is that there’s never been more and better stuff comin’ from the oustide, that seems temporarily to sort of fill the hole or drown out the hole.
I think it’s probably assuagable by internal means. I think those internal means have to be earned and developed, and it has something to do with, um, um, the pop-psych phrase is lovin’ yourself.
It’s more like, if you can think of times in your life that you’ve treated people with extraordinary decency and love, and pure uninterested concern, just because they were valuable as human beings. The ability to do that with ourselves. To treat ourselves the way we would treat a really good, precious friend. Or a tiny child of ours that we absolutely loved more than life itself. And I think it’s probably possible to achieve that. I think part of the job we’re here for is to learn how to do it. I know that sounds a little pious.

David Foster Wallace, typed out by hand (just so you know) from “Of Course You End Up Becoming Yourself.”
Do you know what, it was cultural,” he concludes. “I never came from the place that those people came from, so to come in and go, ‘I’m just going to try and make this stuff’ was probably a bit naive.” He’s at pains to point out that the divide wasn’t racial […] but one of geography and background; Blake comes from Enfield, dubstep started 27 miles away in Croydon.

James Blake, from this Guardian interview.

As a North American, the concept of being an unwanted, uncomprehending outsider because you’re from twenty-seven miles away makes me boggle. I actually thought this might be a very deadpan joke; Dan Hancox has been kind enough to enlighten me about UK musical microregionalism.

(via zedequalszee)

27 miles was like my daily commute to high school! I guess Centreville just wasn’t a happening scene on its own?

Telekinesis - Dirty Thing

This is essentially a Death Cab song (cf. “Photobooth”, “Summer Skin”, lIterally like half of their catalog) but it’s really well done and if you don’t like it there isn’t anything I can do for you, I don’t think.

Join Dana Milkbank's Sarah Palin moratorium

I feel powerless to control my obsession, even though it cheapens and demeans me. But today is the first day of the rest of my life. And so, I hereby pledge that, beginning on Feb. 1, 2011, I will not mention Sarah Palin — in print, online or on television — for one month. Furthermore, I call on others in the news media to join me in this pledge of a Palin-free February. With enough support, I believe we may even be able to extend the moratorium beyond one month, but we are up against a powerful compulsion, and we must take this struggle day by day.

YES THIS DEAR GOD

CAFFEINE NICOTINATE

it’s not quite what you expect it to be (it’s a niacin [nicotinic acid] salt, not a nicotine salt) but it’s a pretty good name anyway

Why is alcohol so widely available if it is so toxic and what can we do about it? … I think it is time to use the now-considerable knowledge of the neuropsychopharmacology of alcohol to develop safer, alternative intoxicants whose effects can be reversed by antidotes.

The Scientist; free registration required.

File under: pretty things you can see from my window, some days.

My window, which I am desperately hoping the building is going to have cleaned, soon.

It is facile and mistaken to attribute this particular madman’s act directly to Republicans or Tea Party members. But it is legitimate to hold Republicans and particularly their most virulent supporters in the media responsible for the gale of anger that has produced the vast majority of these threats, setting the nation on edge. Many on the right have exploited the arguments of division, reaping political power by demonizing immigrants, or welfare recipients, or bureaucrats. They seem to have persuaded many Americans that the government is not just misguided, but the enemy of the people.

NYT

Pretty much my thoughts exactly.

Late update: … and The Shrill One jumps on board:

It’s important to be clear here about the nature of our sickness. It’s not a general lack of “civility,” the favorite term of pundits who want to wish away fundamental policy disagreements. Politeness may be a virtue, but there’s a big difference between bad manners and calls, explicit or implicit, for violence; insults aren’t the same as incitement.

(via langer)

Revealing the layers of fraud and deception behind the Wakefield MMR jab paper that sparked the autism-vaccine hysteria that refuses to die no matter how extensively it’s debunked. This blog entry serves as an introduction to the article published in BMJ; read both.

REQUESTED STATEMENT OF INTEREST PROGRAM OBJECTIVES

DRL and NEA invite organizations to submit statements of interest outlining program concepts and capacity to manage projects that will foster freedom of expression and the free flow of information on the Internet and other connection technologies in East Asia, including China and Burma; the Near East, including Iran; Southeast Asia; the South Caucasus; Eurasia, including Russia; Central Asia; Latin America, including Cuba and Venezuela; and Africa. Programming may support activities in Farsi, Chinese, Russian, Burmese, Spanish, Vietnamese, Arabic, French, and other languages spoken in acutely hostile Internet environments. Concepts may be global in nature, regional or country-specific.

Statements should clearly address a) support for digital activists and civil society organizations in exercising their right to freedom of expression and the free flow of information in acutely hostile Internet environments, or b) support for ongoing evaluation and research to enhance global Internet freedom policy and diplomacy.

One could make catty remarks about your choice of a) network neutrality or b) Wikileaks, but let’s instead actually just meditate in the warmth of how cool it is that the State Department cares about this at all. The Internet, man!

Posts

Pea pesto on linguine with purslane and tofu

Guess who just stemmed three pounds of spinach leaf by leaf.

Mushroom Bourguignon, from Smitten Kitchen. Satisfying!

Okay, so it doesn’t look like much, but it’s really tasty! From Ottolenghi. Bread from Bon Chaz.

Parsnip and pumpkin mash

Or, you know, buttnernut squash.

Ingredients

  1. 600 g (peeled weight) pumpkin or butternut squash, in 2-3 cm dice
  2. 3 tbsp olive oil, plus extra for drizzling
  3. 1 bulb of garlic
  4. 5 medium parsnips, peeled and cut into large chunks
  5. 200 ml sunflower oil
  6. 2 onions, sliced into rings
  7. 80 g unsalted butter
  8. 1 tsp ground nutmeg
  9. 300 g creme fraiche, at room temperature
  10. 15 g chives, roughly chopped
  11. salt and pepper

Directions

  1. Preheat the oven to 200 C / 400 F / Gas Mark 6. Toss the pumpkin or squash with olive oil and a little salt and pepper and spread out in a roasting tray. Roast 30-45 min, until soft and mashable. Once out of the oven, keep somewhere warm. Meanwhile, using a serrated knife, cut about 1 cm off the top of the garlic bulb and place the bottom part in the oven next to the roasting pumpkin. Bake for about 30 min or until the cloves are completely tender.
  2. While the pumpkin is roasting, cook the parsnips in boiling salted water for 30 min, until completely soft. Drain and keep warm.
  3. Yet meanwhile, pour the sunflower oil into a medium saucepan, heat well, and fry the onion rings in 2-3 batches. They should turn brown, almost burnt. Transfer to a colander and sprinkle with salt.
  4. Take a large bowl that can accomodate the whole mixture. Hold the bottom of the head of garlic and gently press upwards to erlease the cooked flesh into the bowel. Add the butter, nutmeg, some seasoning, and then the parsnips. Crush well, using a potato masher (or pastry blender). Add the cooked pumpkin and mash very lightly (use a fork). Don’t over-mix; the mash should remain chunky and the pumpkin and parsnip distinct.
  5. Gently fold in the creme fraiche and chives to form a ripple in the mash. Spoon a mound on to each serving plate, garnish with the fried onions and a drizzle of olive oil, and serve at once.

Mushroom artichoke marsala and Ottolenghi’s Jerusalem artichoke and rocket soup, which, incredible.

 Jerusalem artichoke and rocket soup

 

Ingredients

  1. 400 g Jerusalem artichokes
  2. 45 g rocket, roughly chopped, plus extra for garnish
  3. 1 L chicken or vegetable stock
  4. 10 cloves garlic, crushed
  5. 6 scallions
  6. 1 egg
  7. 350 g Greek yogurt
  8. salt and pepper

Directions

  1. Peel the artichokes with a potato peeler, wash, and cut into irregular 1 cm dice. Put in a large saucepan with rocket, stock, garlic, and a couple pinches of salt. Bring to a boil and simmer lightly for 25 min until artichokes are tender; test one with a knife to make sure it’s totally soft.
  2. While the soup is cooking, cut the spring onions in half lengthways and then cut across these lenghts into slall dice. Set aside. Break the egg into a large mixing bowl and whisk well with the yogurt.
  3. When you are ready to serve the soup, reheat it to boiling point. Take a ladleful of hot soup and add it to the yogurt mix, stirring constantly. Repeat a few times, using about half the soup. You need to bring up the temperature of the yogurt. Now pour the warm yogurt into the soup pan, whisking constantly. Bring back to a very(!) gentle boil and leave there for a minute or two.
  4. Taste and season with plenty of salt and pepper. Stir in the spring onions and serve garnished with rocket.

Leek and Swiss chard quiche

Mushroom japchae!

May not look like much… but sure is good. Spaghetti with chickpeas courtesy smitten!

Cauliflower cake omg

Potatoes in dashi stock.

This week’s haul: garlic cheese bread, daikon, Sieglinde potatoes, and shiitake mushrooms.

Thanksgiving aftermath.

Yakisoba Japadog from the Burrard St cart.

NO JAPADOG, NO LIFE!!!

Alien produce from the market…

1.5lb spinach is a lot of spinach.

Brussels sprouts with bacon and boiled Sieglinde potatoes.

Catching up on older food. Veggie skewer with tofu last night at the Fringe.

Sakura roll and wakame from Kadoya on Davie

Couscous with roasted tomatoes and olives from Smitten Kitchen ca. 2007, with orzo instead because I couldn’t find pearl couscous! I wish you could have some. It is delicious.

Macchiato and biscotti at Cafe Citadella - brand new shop on Ash St in Fairview!

Audio

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