W03V - Doyle Systems Biology Lab

Post Reply
glegrady
Posts: 160
Joined: Wed Sep 22, 2010 12:26 pm

W03V - Doyle Systems Biology Lab

Post by glegrady » Thu Oct 16, 2014 3:44 pm

W03V - Doyle Systems Biology Lab

Housed in the Chemical Engineering department at UCSB, the Doyle group is comprised of a diverse group of researchers coming from backgrounds such as computer science, biology, mechanical engineering and chemical engineering.

The Doyle group is a leading force on the computational side of the field of systems biology. Our ongoing work on circadian rhythms continues to probe at the sources of regulation that give rise to highly precise periods in the mammalian ‘biological clock’. We have also begun to make preliminary links between clock performance and cognitive function. http://thedoylegroup.org
George Legrady
legrady@mat.ucsb.edu

akshay
Posts: 12
Joined: Tue Oct 14, 2014 10:55 am

Re: W03V - Doyle Systems Biology Lab

Post by akshay » Thu Oct 16, 2014 11:55 pm

These are the things that I found most interesting about the visit:

Computational methods, being the area of expertise of the team, is applied to biological research. They are trying to push forth a (possibly) different way of measuring, predicting and diagnosing biological phenomena. Hence, their work is interdisciplinary in the sense that they are looking into ways in which one field 'fits' into the other, as opposed to symmetrically fusing the fields.

Yet, their methodology borrows aspects of both the bio-chemical sciences, and computation. It tries to create a sort of symbiotic mechanism where each side gains an understanding of the other: biological processes are understood better from computational modelling, in turn, giving a better understanding of how to design computational models for biological data. The fact that they work alongside medical professionals in clinical trials gives further credence to this.

Peter mentioned that he sees it all in his head prior to working out the nuts and bolts. From what Peter said, it seems that in addition to understanding how to work with data, it also requires a visceral understanding of the phenomenon at play.

The person in the PTSD room (I didn't quite catch his name) mentioned that he picked up programming quite easily even though his background lacked the use of it. I'm wondering if this was because he had some direction as to how much he *needs* to learn in order to go about his research. As opposed to approaching programming as the vast body that it is. (I just found it curious considering how easy it is to develop a mental block against computer programming.)
Last edited by akshay on Wed Dec 03, 2014 12:50 pm, edited 1 time in total.

kurt
Posts: 16
Joined: Tue Oct 14, 2014 10:57 am

Re: W03V - Doyle Systems Biology Lab

Post by kurt » Tue Oct 21, 2014 12:56 am

It was fascinating to go to a biology lab where there are no biological experiments being done in the classical sense. There were no microscopes, pipettes, beakers, centrifuges, or any other telltale biological equipment. The fact that discoveries are being made about complex systems in the human body from workstations in an office is inherently interesting. Granted, the data they're working with is being generated in more familiar laboratory settings elsewhere, this sort of outsourcing relationship gives Mr. Doyle's lab a heavy lean towards the engineering and computation side. One can only presume that this will be more common, if not the norm, in the near future. In this regard, we should all be aware of a Google X project announced earlier this year- their effort to define what is a healthy human:
http://news.sciencemag.org/biology/2014 ... lthy-human

This was a densely packed visit, almost like visiting 3 labs in one. It was unfortunate that we didn't get to spend some more time with Peter and the circadian rhythms research. I latched on to his experience of being scientist. First there's a vision, a boundless idea which illuminates a problem in a new way. Then to express this idea in a physical context presents both new insights and challenges, and a cycle of work is started. This to me bears an uncanny resemblance to the artistic process. Perhaps this cycle of generating an idea, working on the idea, modifying the idea with insight from the work, and injecting new ideas into the work is a kind of rhythm unto itself?

saharss2533
Posts: 19
Joined: Tue Jan 17, 2012 4:10 pm

Re: W03V - Doyle Systems Biology Lab

Post by saharss2533 » Thu Oct 23, 2014 9:49 am

Inaccuracy of Data---Failure or Athleticism of Technology:

One thing that grabbed my attention was the acceptance of inaccuracy as one of the premises in chemical and medical based research projects. As it was mentioned during the initial discussion in Frank Doyle Group, the scientists are not in search of “the right solution”, but a better or user-friendlier solution. The raw data that they were using was quite inaccurate to begin with. Therefore, they had to differentiate between different levels of inaccuracy: whether it was based on the inaccuracy and the errors of the evaluation technologies and machines, or if the error was in the visualization of the data, their post-processing and machine learning techniques or in their scientific approach in handling the data for example in creating their network connection for their DNA data. In some cases like the research group working on the detection of the blood glucose concentration for Type 2 diabetes, the data was to some extent more accurate than the data used in the two other research threads. In this group, the data was obtained directly from the chemicals in the blood at the times of observing specific symptoms in the body, while in the other two the data was strongly influenced by the subjective descriptions of the patients and not-fully reliable psychological methods and questionnaires. Since there is no way to control some of these inaccuracies, their challenge becomes how to approach different levels of inaccuracy and how to optimize their system.

While it is acceptable to have noise and inaccuracy in the system in many fields of research, in some (art and engineering) fields and some industry applications, it is not at all tolerable. In the industry or even some institutions, the accuracy in obtaining and processing data can cause them millions of dollars. And in many art, performance or engineering productions, any sort of inaccuracy and malfunction in the system is considered as a failure of the project. This made me think of Raffaello D'Andrea’s lecture on athleticism of the machines. Does the athleticism of technology applicable to all the fields or that level of accuracy, consistency and reliability in the system is only limited to specific fields? Is it worth our time in this society to invest so much to make a system in an art project work like an athlete?

saharss2533
Posts: 19
Joined: Tue Jan 17, 2012 4:10 pm

Re: W03V - Doyle Systems Biology Lab

Post by saharss2533 » Thu Oct 23, 2014 10:01 am

Pictures from the Doyle Group's Lab Visit
Attachments
IMG_0214.JPG
IMG_0213.JPG
IMG_0212.JPG
IMG_0211.JPG
IMG_0210.JPG
IMG_0209.JPG
IMG_0208.JPG
IMG_0207.JPG
IMG_0206.JPG
IMG_0205.JPG
IMG_0204.JPG
IMG_0203.JPG
IMG_0202.JPG
IMG_0201.JPG
IMG_0200.JPG
IMG_0199.JPG
IMG_0198.JPG
IMG_0197.JPG
IMG_0196.JPG
IMG_0195.JPG

intae
Posts: 19
Joined: Tue Oct 14, 2014 10:56 am

Re: W03V - Doyle Systems Biology Lab

Post by intae » Thu Oct 23, 2014 12:17 pm

Yeh, it was interesting for me, especially the US ARMY funded the research of PTSD. PTSD is also a big issue in my country where there is still conscription existed since the Korean War. Every year Korea Army have had in trouble with some soldiers decided to suicide themselves or rampage inside barracks with grenades and rifle. I met several US MP soldiers who were decided to being deploy to the Iraq in 2005. They were suffered severe "Pre -Traumatic Stress Disorder" even there were 10000 miles away. At some points, the research in Doyle lab brought lots of questions for me because it is almost impossible to objectify the relation ship between after memory effect and their change of body. But I think that it is worth to spend energy and money on it. For future and life.

fabian
Posts: 13
Joined: Tue Oct 14, 2014 10:58 am

Re: W03V - Doyle Systems Biology Lab

Post by fabian » Fri Oct 24, 2014 2:19 pm

As everyone else I was fascinated by a biology lab consisting only of computers. I knew about the idea of "computational biology" before but I was not aware that computation and biology in this field are actually that much detached (happening in two completely different physical spaces even).

What struck me as particular about the group's diabetes research was the whole topic of feedback systems and their real-life implications, especially as the concerns the FDA has about the group's insulin device are based on it being a feedback system. Although in this specific case the probability of human error in a non-feedback system* - the patient reading the sensor data and adjusting his or her dosage accordingly - has to be much higher than in a working feedback system, granted there is some level of error control and calibration involved, there seems to be some kind of general reservation (let’s call it anti-cybernetics) involved that could be interesting to explore both from a systematic and historic perspective.

* Chernobyl 1986 comes to mind, where human interference with a feedback system led directly to catastrophe.

rluo
Posts: 21
Joined: Tue Oct 14, 2014 10:57 am

Re: W03V - Doyle Systems Biology Lab

Post by rluo » Sun Oct 26, 2014 6:01 pm

Can everything be computational?

The Book of Change, an ancient Chinese philosophy book, believes that the universe began as a whole, then divided into two, then three, then everything. Hence, the fundamental part of Chinese culture believes that the universe evolves following a pattern, and so as human beings.

In Doyle Systems Biology Lab, an interesting problem they are trying to conquer is applying the computational methods to diagnose PTSD, which is supposed to be a psychological issue in a traditional view. If Doyle’s Lab can find a pattern to detect PTSD, is it also possible to identify Depression, or other psychological diseases? Or ultimately, is it possible to develop an application for fortune telling by entering some basic parameters of a person? It probably sounds like pseudoscience, but maybe we are limited by the current computational ability that we cannot deal extreme lager amount of data?

There is a science fiction book called Three Body Program (http://www.amazon.com/The-Three-Body-Pr ... dy+problem ) which may answer some of the questions above, and I highly recommend it.

Post Reply