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Feynman on Biology

Feynman on Biology | SynBioFromLeukipposInstitute | Scoop.it
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By Christina Agapakis


"Richard Feynman was a brilliant, bongo-playing, lock-picking, eminently quotable physicist. His quips, on anything from the pleasure of findings things out to the key to science to how fire works are standard fare for science fans. For synthetic biologists, it’s a quotation he left on his last blackboard at Caltech before his death in 1988 that is most frequently quoted: “What I cannot create, I do not understand.” This statement gives quotable form to the “drive to make” that happens when engineers start doing biology. Feynman of course wasn’t an engineer, he was a theoretical physicist–a field less often associated with creating stuff than with creating equations. But Feynman also liked to dabble in other fields, including a sabbatical year in Max Delbrück’s biology lab at Caltech studying genetic mutations in viruses that infect bacteria. The chapter on this disciplinary dabbling in Feynman’s autobiography, Surely You’re Joking Mr. Feynman, is a fascinating look at what happens when a physicist starts doing biology. I read Surely You’re Joking during college, just as I was starting to work in a biology lab. I still vividly remember one tiny anecdote about the general applicability of a certain lab technique in everyday life, a technique I was just starting to get the hang of while I was reading the book: There was one useful lab technique I learned in that course which I still use today. They taught us how to hold a test tube and take its cap off with one hand (you use your middle and index fingers), while leaving the other hand free to do something else (like hold a pipette that you’re sucking cyanide up into). Now I can hold my toothbrush in one hand, and with the other hand, hold the tube of toothpaste, twist the cap off, and put it back on. For Feynman, these little tricks of the trade–the tacit knowledge that biologists gain through experience–end up being the focus of his biological excursion more than any facts about bacteria, phage, and DNA. He concludes that: I learned a lot of things in biology, and I gained a lot of experience. I got better at pronouncing the words, knowing what not to include in a paper or a seminar, and detecting a weak technique in an experiment. These stories of these lessons are told with Feynman’s quirky mix of charming arrogance and humility, the strange combination of traits that gave him the confidence and the curiosity to jump into a new field. Feynman discusses giving a presentation to fellow students in a biology class at Princeton, the other students “laughing hysterically” at his mispronunciation of common biology terms. Later, the class urges him to move on after an especially long introduction of background facts saying, “We know all that!” He replied: “Oh” I say, “you do? Then no wonder I can catch up with you so fast after you’ve had four years of biology.” They had wasted all their time memorizing stuff like that, when it could be looked up in fifteen minutes. The chapter’s title, “A Map of the Cat?”, comes from a short anecdote that captures Feynman’s humility and humor when confronted with too many new facts: I began to read the paper. It kept talking about extensors and flexors, the gastrocnemius muscle, and so on. This and that muscle were named, but I had not the foggiest idea of where they were located in relation to the nerves or to the cat. So I went to the librarian in the biology section and asked her if she could find me a map of the cat. “A map of the cat, sir?” she asked horrified. “You mean a zoological chart!” From then on there were rumors about a dumb biology student who was looking for “a map of the cat.” Rereading the chapter now after many years in biology labs, I’m particularly struck by they way Feynman describes experimental work, the early molecular biology tools and techniques that require “great care and a lot of tedious work.” More than the facts or the jargon or the disciplinary conventions for writing papers, this is where the biggest differences appear between the practice of biology and the practice of theoretical physics. Feynman’s legendary ability to think through problems in physics–his “problem-solving algorithm”–didn’t help as much in the lab, leading him at one point to say, “It would have been a fantastic and vital discovery if I had been a good biologist. But I wasn’t a good biologist.”..."


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Generating Effective Models and Parameters for RNA Genetic Circuits

Generating Effective Models and Parameters for RNA Genetic Circuits
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by

Chelsea Y. Hu Jeffrey D. Varner , and Julius B. Lucks *


"RNA genetic circuitry is emerging as a powerful tool to control gene expression. However, little work has been done to create a theoretical foundation for RNA circuit design. A prerequisite to this is a quantitative modeling framework that accurately describes the dynamics of RNA circuits. In this work, we develop an ordinary differential equation model of transcriptional RNA genetic circuitry, using an RNA cascade as a test case. We show that parameter sensitivity analysis can be used to design a set of four simple experiments that can be performed in parallel using rapid cell-free transcription-translation (TX-TL) reactions to determine the 13 parameters of the model. The resulting model accurately recapitulates the dynamic behavior of the cascade, and can be easily extended to predict the function of new cascade variants that utilize new elements with limited additional characterization experiments. Interestingly, we show that inconsistencies between model predictions and experiments led to the model-guided discovery of a previously unknown maturation step required for RNA regulator function. We also determine circuit parameters in two different batches of TX-TL, and show that batch-to-batch variation can be attributed to differences in parameters that are directly related to the concentrations of core gene expression machinery. We anticipate the RNA circuit models developed here will inform the creation of computer aided genetic circuit design tools that can incorporate the growing number of RNA regulators, and that the parametrization method will find use in determining functional parameters of a broad array of natural and synthetic regulatory systems.'


http://bit.ly/1CQEEX3

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SULSA 2015 Research Symposium | SULSA

SULSA 2015 Research Symposium | SULSA | SynBioFromLeukipposInstitute | Scoop.it
The heat is on, but SULSA server meltdown is fixed, so you can sign up for Life 2.0:The Synthetic Biology of New Life http://t.co/DWjmigiCXy
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How do I build an NOT gate in a biological arithmetic logic unit? - YouTube

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Deoxyribozyme based NOT gate: 


The deoxyribozyme (DNA based catalyst) is in an active form, if no input (in) is present (in = 0). Cleavage activity results in this case in a fluorescent oligonucleotid (F) as output. An oligonucleotide input (in) (in = 1) leads to hybridization of the input strand (green) with the closed loop strand, which is marked purple. This results in an inactive, open loop and the absences of a fluorescent product. 



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Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


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Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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How do I build an AND gate in a biological arithmetic logic unit? - YouTube

Arithmetic logic unit: Shown are four basic Boolean logic gates (AND, NOT, NOR, and XOR), their symbols and respective truth tables. 1 means that the input (...
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Engineered particles 'may become antibiotics of the future'

Engineered particles 'may become antibiotics of the future' | SynBioFromLeukipposInstitute | Scoop.it
Using synthetic biology, researchers have engineered particles called phagemids that cause harmful bacteria to malfunction and cease replicating without bursting open.
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High-Throughput Synthetic Biology: Synthesizing Designer Yeast through Automation and Acoustic Liquid Handling | Webinars | GEN

High-Throughput Synthetic Biology: Synthesizing Designer Yeast through Automation and Acoustic Liquid Handling | Webinars | GEN | SynBioFromLeukipposInstitute | Scoop.it
Get the latest in biotechnology through daily news coverage as well as analysis, features, tutorials, webinars, podcasts, and blogs. Learn about the entire bioproduct life cycle from early-stage R&D, to applied research including omics, biomarkers, as well as diagnostics, to bioprocessing and commercialization.
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Systems Biology

Systems Biology Adam Arkin, University of California, Berkeley and E.O. Lawrence Berkeley National Laboratory Over eons, evolution acts on organisms to ...
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Download PDF Microbial Synthetic Biology Volume 40

1.Browse And Download This Book now. 2.If you can't download change your ip adress. 3."Click here to download PDF Ebook now at http://bit.ly/1Kgs4Xk.
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How does a biological Input:/Output device work? - YouTube

Input/Output (I/O) device: In a “digital” biological I/O device input molecules induce due to a set of non-steady state chemical reactions (engineered cohere...
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Jay Keasling - 18th Heinz Awards - Technology, the Economy and Employment

Jay Keasling, our 18th Technology, the Economy and Employment recipient, talks about the power of synthetic biology, and how his work on the new science of ...
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T Cell Immunotherapy: From Synthetic Biology to Clinical Practice - Springer

T Cell Immunotherapy: From Synthetic Biology to Clinical Practice - Springer | SynBioFromLeukipposInstitute | Scoop.it
T Cell Immunotherapy: From Synthetic Biology to Clinical Practice - Springer http://t.co/oGF6fKBYvW
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What are biological microprocessor applications? Part 2 - YouTube

What are biological microprocessor applications? Part 2
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Conferences and events | Biochemical Society - Synthetic Biology UK 2015

Conferences and events | Biochemical Society - Synthetic Biology UK 2015 | SynBioFromLeukipposInstitute | Scoop.it
Check out the latest conference and events from the Biochemical Society. Our programme covers a wide spectrum of topics; with events held in the UK and abroad.
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How do I build a NOR gate in a biological arithmetic logic unit? - YouTube

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A RNA aptamer based NOR gate: NOR is an OR gate followed by a NOT gate. Two subsequent RNA devices consist, in this case, each of three functional components: a sensor, made of a RNA aptamer (brown), an actuator component, made of a hammerhead ribozyme (purple), and a cobbling sequence between these parts, the transmitter (blue). 

Translation of the gene of interest (here GFP), encoded upstream of the device, is only possible in the case of the absence of both inputs (a and b).


BTW

Our Leukippos community needs your financial support. We are all working for free and pay everything out of our own pockets, such as server costs and page registrations. If you like our work and wish that we produce more quality content, such as this video, you can donate some bitcoins to this address: 


1KnikzSG7fnRfG76DxjLZyrbvw8fS9nisw


Further info:

Review - THE BIOLOGICAL MICROPROCESSOR, OR HOW TO BUILD A COMPUTER WITH BIOLOGICAL PARTS http://bit.ly/YI13bF

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Dr. Alicia Jackson: Programming the Living World, DARPA BiT | CodonOps

Dr. Alicia Jackson: Programming the Living World, DARPA BiT | CodonOps | SynBioFromLeukipposInstitute | Scoop.it
Dr. Alicia Jackson: Programming the Living World, DARPA BiT
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A Versatile Microfluidic Device for Automating Synthetic Biology - ACS Synthetic Biology (ACS Publications)

A Versatile Microfluidic Device for Automating Synthetic Biology - ACS Synthetic Biology (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it
RT @ACSSynBio: Learn more about a versatile microfluidic device for automating synthetic biology here: http://t.co/gFQFmJRjxv
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Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance

Convergence of regenerative medicine and synthetic biology to develop standardized and validated models of human diseases with clinical relevance | SynBioFromLeukipposInstitute | Scoop.it
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Why Bio is the New Digital - Joi Ito keynote - YouTube

From the 2015 Solid Conference. About Joichi Ito (MIT Media Lab): Media Lab Director Joi Ito is a leading thinker and writer on innovation, global technology...
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Dr. Alicia Jackson: Programming the Living World, DARPA BiT

Dr. Alicia Jackson, Deputy Director of DARPA's Biological Technologies Office (BTO), discusses the potential of synthetic biology and describes new tools that ...
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Building a Fab for Synthetic Biology - Joe Jacobson keynote

From Solid Conference 2015: Similar to the way in which we use fabs to build microprocessors and software to program them, the field of synthetic biology offers ...
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Synthetic biology used to engineer new route to biochemicals

Synthetic biology used to engineer new route to biochemicals | SynBioFromLeukipposInstitute | Scoop.it
Living cells can make a vast range of products for us, but they don't always do it in the most straightforward or efficient way.
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What are the building blocks of a biological microprocessor? - YouTube

What are the building blocks of a biological microprocessor? A biological microprocessor consist of four units: the input and output device (I/O), the arithm...
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