Dos Margaritas Por Favor: Science, Music, Photography, and Other Rants

Too Narrow a Focus?

Posted in Uncategorized by jheil on September 23, 2009
Jeff Actually has a job. I haven't asked him what he gets paid.

Jeff Actually has a job. I haven't asked him what he gets paid. It's probably something decent.

Disclaimer: This post is based on heresay and speculation. It is written in a casual tone and should be not be taken as an indication of my literary incompetence.

I was talking with someone today about what people do with degrees and they were saying “people with science degrees make the least amount of money”. Even less than art’s they said. “Hey I have a science degree” I thought. I was mildly hurt/offended. My degree… worthless? Worthless… like a BA you say? Even more worthless than a BA!?!? Way to trigger my inferiority complex.

It was a rather general discussion, but one of the themes was that if you work in Science with a B. Sc. you could be a lab tech making $16/hr or in quality at some food company.. blah blah.. the usual things that you can think of the apply to biology focused science degrees. I guess we are biased being in Biology. Anyway, I disagreed about the scope of jobs being that narrow. The counter argument I was given was that other jobs I mentioned, such as potential management positions, were jobs an arts grad could do and they would be more qualified, since they could write and understand social issues and stuff like that.


Well… no… I guess I’ve shown myself to be somewhat competent. I’m confident that I can go out and do well at a wide range of things. I took a wide range of courses in my undergrad. Oh, by the way… here is an embellished window into my regular inner dialogue… I mean monologue.

ANYWAY… ahem…Should undergrad science education (especially life sciences) get away from just pumping people full of results with a few methods sprinkled on top? I say yes. Make them all take english. I never took english, I opted for 2 sociallogies, 2 psychologies, 2 philosophies for arts courses, and I didn’t like most of those courses. I however managed to take useful things away from every one of them. Make science students take arts and arts students take science I say. Wheter it be english or whatever. Make them all write essays.

Anyway, by not thinking this through fully, or providing a very reasoned arguement, more of a gut feeling, I have left PLENTY of room for comments. Fire away!

What is Life? they asked

Posted in Science by jheil on September 11, 2009

I filled out a survey today for the TUdeft (from the Netherlands) iGEM team as part of their human practices project.

The theme of the survey was basically “is life sacred and is synthetic biology messing with it?” The last question was what do you think life is? I wrote a mildly poetic answer. I feel it captured the divide between “life” and the human experience and the perception of human life.

“Life is self replicating; life is evolving; life is chemically transforming its environment; life is not consciousness. Strangely enough, for us, consciousness is life.”

Although, sometimes life supports consciousness I might add. However, no one really knows the extent of that support. Yeah but is moral status an absolute or on a sliding scale? Is consciousness a requirement for moral status? Will I ever dust off that bioethics textbook?

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Nanopore sequenceing and DNA synthesis

Posted in Science by jheil on September 4, 2009

If you have ever tried to create a gene construct or make specific mutations to genes via cloning and PCR methods you would appreciate the potential time and sanity saving benefits of DNA synthesis.

As the ambitions of synthetic biology increase the limitations of the aforementioned methods become glaringly apparent. This is true even with standardization attempts, such as biobrick alpha ( which simplifies the process greatly. The problem with BBa (biobrick alpha) is that you have to standardize the part beforehand. For some genes doing this via PCR is rather difficult and time consuming. Then you still have to clone afterward.

I have been strugling to standardize a 1.8 kb gene for a while now. The PCR primers are designed to amplify the gene, add the BBa prefix and suffix, add a ribosome binding site, and make a synonymous mutation to get rid of an EcoRI site. Problem is… it still hasn’t worked. It’s been close, but close is still wrong. I got a quote to synthesize the gene at $1500 it was above our budget. The cost of synthesizing goes up dramatically above  lengths  of 1.0 kb.

Today’s DNA synthesis companies still work with phosphoramidite chemistry. Double stranded DNA is synthsized in the same way as oligonucleotides, but with a few costly steps afterward. To drive the cost down and make longer sequences cheaply obtainable a whole new approach is needed. I recently had a discussion with some colleagues (Andre, and Ricardo) about in vivo DNA synthesis, that would be a simple as shining different wavelengths of light at cells and having them assemble a molecule for you. This could involve an enzyme similar to a telomerase that would have an RNA function as a template. The input would align the nucleotide of choice with the active site of the enzyme, and it would function as a sort of DNA typewriter. I suppose that would be the holy grail, but there are going to have to be some intermediate steps toward that goal. I say an enzyme based in vitro approach could bridge that gap.

nanopore sequencing

Oxford Nanopore Technologies alpha-hemolysin nanopore (ribbon diagram) with covalently attached cyclodextrin (teal) transiently binds a base (red) traversing the pore.

I was thinking on the drive home yesterday and I remembered having read about nanopore sequencing. Nanopore sequencing is quite amazing, and works by using a hemolysin nanopore (essentialy a protein with a nice beta-barrel) as a scaffold to support a exonuclease and a cyclodextrin molecule. The exonuclease nicely deposits nucleotides into the pore where they transiently bind the cyclodextrin molecule. When the nucleotides bind the cyclodextrin they then block an electrical current carried by the cylodextrin. The degree to which they do this depends on which nucleotide is bound. That allows the sequence to be read.

Here is when I begin to speculate. What if the same process was doable in reverse. If the cyclodextrin would bind and release a specific deoxynucleotidetriphosphate (dNTP) depending on the amplitude of an electrical current it could work. The exonculease could be replaced with a DNA polymerase something like the DNA typewriter enzyme in the last paragraph. The electrical/magnetic field produced by the electrical current could be used to move the RNA template around, and the pore assembly would feed the polymerase the right dNTP. The whole thing could be designed to exclude random dNTPs from getting into the polymerase active site. With two dNTP specific steps involved in the incorporation of each nucleotide it could be a robust system. The reaction could also be carried out in a pyrosequencing mixture such that when a nucleotide was incorporated there would be a flash of light. This would give the computer controlling the process a way of monitoring the quality of the reaction. This would work in theory if the reaction was working with a single copy of the assembly, but with multiple copies it would be impossible to tell if one of the copies has missed the incorporation of a nucleotide. You would want multiple copies to get high yields of synthetic DNA.  Well I can’t think of a way to remedy that problem right now. This is still some crazy speculation anyway.

All thoughts on this wild speculation are welcome.


Cheap Third Generation Sequencing, Nature Methods 6, 244 (2009)


Posted in Staying Sane: Adventures through stupidity by jheil on September 4, 2009

“a series of individual faculty entrepreneurs held together by a common grievance over parking”

-The Definition of a University according to Clerk Kerr

I have bought a parking pass for the last 7 consecutive terms at UW. I somehow managed to get a parking ticket at the beginning of the term a fair amount of the time. Usually because I forget to buy a pass. This term they ticketed me the morning of September 1st because the pass expired the on August 31st. The silly thing is for the week of Sept 7th they aren’t ticketing people because they actually offer a grace period for people arriving on campus. What is with the on again off again ticketing I say?

I was not happy so I sent an email to the parking services manager. Only the subject line and the first line of the email were sarcastic after that it was relatively well written. She replied back with “Thank you for your insightful comments” which I can only assume was sarcastic. Then goes on to say “If you wish to discuss your ticket I will be happy to over the phone”; now this is a full blown lie.

I had already paid the ticket,  since the appeals board is a farce. I just wanted to have them acknowledge their policy was stupid and unfair. If I bought the pass valid from September 1st to December 31st on the evening of September 1st and had been displaying the pass valid May 1st to August 31st I am covered from May1st to December 31st no? The 8 hours I had an invalid pass should be covered in retro, therefore I should have that ticket voided. I told the parking manager this. She scolded me like a child for having so many tickets on my record (a whole 9, all of them paid). She then gave me the quasi-analogous but flawed scenario of me not paying a parking meter and getting a ticket, then paying the meter after the fact and expecting the ticket to go away. The main difference is that when I go park at the meter the next day and pay it I’m not paying for the preceding day! It’s also a short term thing over a mater of hours, not a 4 month pass for god sakes. So if they aren’t voiding my tickets, which they aren’t, I should ask for my 1 days worth of parking back. The pass is good for 120 days, and costs $120, So they owe me a dollar since I bought it on the second day! Then her dumb parking meter analogy would be accurate.

She also compared me to “people who have been there 30 years with no tickets”. Those are faculty who have the pass deducted off payroll and sent to them via inter office mail. If they get a ticket because they forgot to affix the pass, they have their ticket voided no problem. I actually witnessed this when I was complaining about my September 1st ticket. I asked if I could deduct my pass off my payroll (I am on the payroll now), and no, Graduate students can not do that.

I’ll remember that when the University calls asking for donations when I actually have money. I’ll cite those 9 or more parking tickets and tell them how much I have already contributed.

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