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BioBuilder: Synthetic Biology in the Lab
Today’s synthetic biologists are in the early stages of engineering living cells to help treat diseases, sense toxic compounds in the environment, and produce valuable drugs. With this manual, you can be part of it. Based on the BioBuilder curriculum, this valuable book provides open-access, modular, hands-on lessons in synthetic biology for secondary and post-secondary classrooms and laboratories. It also serves as an introduction to the field for science and engineering enthusiasts.
Developed at MIT in collaboration with award-winning high school teachers, BioBuilder teaches the foundational ideas of the emerging synthetic biology field, as well as key aspects of biological engineering that researchers are exploring in labs throughout the world. These lessons will empower teachers and students to explore and be part of solving persistent real-world challenges.
Learn the fundamentals of biodesign and DNA engineeringExplore important ethical issues raised by examples of synthetic biologyInvestigate the BioBuilder labs that probe the design-build-test cycleTest synthetic living systems designed and built by engineersMeasure several variants of an enzyme-generating genetic circuitModel "bacterial photography" that changes a strain’s light sensitivityBuild living systems to produce purple or green pigmentOptimize baker’s yeast to produce ?-carotene
Developed at MIT in collaboration with award-winning high school teachers, BioBuilder teaches the foundational ideas of the emerging synthetic biology field, as well as key aspects of biological engineering that researchers are exploring in labs throughout the world. These lessons will empower teachers and students to explore and be part of solving persistent real-world challenges.
Learn the fundamentals of biodesign and DNA engineeringExplore important ethical issues raised by examples of synthetic biologyInvestigate the BioBuilder labs that probe the design-build-test cycleTest synthetic living systems designed and built by engineersMeasure several variants of an enzyme-generating genetic circuitModel "bacterial photography" that changes a strain’s light sensitivityBuild living systems to produce purple or green pigmentOptimize baker’s yeast to produce ?-carotene
240 pages, Kindle Edition
First published March 25, 2015
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April 7, 2023Antoine de Saint Exupéry encouraged for ship-building in The Little Prince, namely “If you want to build a ship, don’t drum up people to collect wood and don’t assign them tasks and work, but rather teach them to long for the endless immensity of the sea.”
synthetic biologists, or biobuilders, want to engineer living cells to do something useful; for example, treat a disease, sense a toxic compound in the environment, or produce a valuable drug.
Ultimately, synthetic biologists would like to be able to build specialized living organisms from scratch using designed DNA. The field isn’t there yet. Currently, most endeavors involve the modification of organisms that already exist rather than building all-new organisms to behave in novel ways.
synthetic biology’s solutions offer a few unique advantages. Most strikingly, cells can make copies of themselves. Cars can’t copy themselves
example of synthetic biology’s potential scale is the genetic reprogramming of a tree so that it will grow into a fully functional house based on the genetic instructions designed by a synthetic biologist. Such a system would take advantage of the tree’s natural program (to grow by taking in a few nutrients from the environment) and put it to use for society’s needs.
a mechanical engineer might design a pot with an unevenly weighted round bottom. When the reservoir in the bottom is full of water it acts as a counterweight and keeps the pot standing straight. As the plant absorbs the water, the counterweight decreases and the pot begins to tip over. This visual indicator would be an obvious reminder to the owner that the plant needs water. Perhaps the leaning plant could even turn on a faucet to water itself.
some plants require more water than others, so the designers might need to create many different pots with different weights in the bottom
An electrical engineer might come up with a completely different solution to the watering problem, one involving electrical moisture sensors and automatic watering.
one solution might use a gene discovered in chameleons that is responsible for changing color in response to stress. It’s possible that this gene could be inserted into plants; thus, they then could change their color to alert us when they need water.
The International Genetically Engineered Machines (iGEM) competition applies the concepts of standardization to DNA parts. This competition brings together college and high school students from around the world to answer the question, “Can simple biological systems be built from standard, interchangeable parts and operate in living cells?” The first competition, held in 2004
“finding a way to eliminate only malaria-infected mosquitoes” will set you on a better path than the more vague “curing malaria,”
arsenic contaminated water, which is a problem in Bangladesh and West Bengal.
• A cell that produces an odor when exposed to arsenic
• A cell that begins growing and dividing very quickly when exposed to arsenic
• A cell that displays a distinct color when exposed to arsenic
One of the key research publications that launched the field of synthetic biology built a NOR gate to operate in a living system. The work was from the laboratory of Dr. James Collins at Boston University. His research group built two NOR logic gates using genetic parts and cross-wired them to create a latch.
the availability of standardized parts has allowed engineers to more rapidly prototype new ideas. Commonly standardized features include the size, shape, material properties, and behavior of components.
part of the power and beauty of building biological systems is that cells can change their molecular composition based solely on the DNA sequences they contain. In this way, they behave somewhat like computers reading software, except that instead of interpreting zeros and ones, cells read instructions that appear in the language of DNA.
Gibson assembly, which enables the simultaneous assembly of many pieces of DNA, is considered by many to represent the future of DNA assembly, but as yet it has not achieved the standardization required for a mature engineering method. One day, Gibson assembly, like BioBrick assembly, might become a standardized technique,
satisfying work is found in creating something you value and in solving a difficult problem
scientists are trained to speak in probabilities rather than absolutes
The Glowing Plant developers chose to work with the gene that encodes luciferase, an enzyme from the firefly that produces a visible glow from its chemical substrate, luciferin. They also chose to work with the plant Arabidopsis thaliana, a common laboratory organism that is widely used for academic and industrial research.
synthetic biologists, or biobuilders, want to engineer living cells to do something useful; for example, treat a disease, sense a toxic compound in the environment, or produce a valuable drug.
Ultimately, synthetic biologists would like to be able to build specialized living organisms from scratch using designed DNA. The field isn’t there yet. Currently, most endeavors involve the modification of organisms that already exist rather than building all-new organisms to behave in novel ways.
synthetic biology’s solutions offer a few unique advantages. Most strikingly, cells can make copies of themselves. Cars can’t copy themselves
example of synthetic biology’s potential scale is the genetic reprogramming of a tree so that it will grow into a fully functional house based on the genetic instructions designed by a synthetic biologist. Such a system would take advantage of the tree’s natural program (to grow by taking in a few nutrients from the environment) and put it to use for society’s needs.
a mechanical engineer might design a pot with an unevenly weighted round bottom. When the reservoir in the bottom is full of water it acts as a counterweight and keeps the pot standing straight. As the plant absorbs the water, the counterweight decreases and the pot begins to tip over. This visual indicator would be an obvious reminder to the owner that the plant needs water. Perhaps the leaning plant could even turn on a faucet to water itself.
some plants require more water than others, so the designers might need to create many different pots with different weights in the bottom
An electrical engineer might come up with a completely different solution to the watering problem, one involving electrical moisture sensors and automatic watering.
one solution might use a gene discovered in chameleons that is responsible for changing color in response to stress. It’s possible that this gene could be inserted into plants; thus, they then could change their color to alert us when they need water.
The International Genetically Engineered Machines (iGEM) competition applies the concepts of standardization to DNA parts. This competition brings together college and high school students from around the world to answer the question, “Can simple biological systems be built from standard, interchangeable parts and operate in living cells?” The first competition, held in 2004
“finding a way to eliminate only malaria-infected mosquitoes” will set you on a better path than the more vague “curing malaria,”
arsenic contaminated water, which is a problem in Bangladesh and West Bengal.
• A cell that produces an odor when exposed to arsenic
• A cell that begins growing and dividing very quickly when exposed to arsenic
• A cell that displays a distinct color when exposed to arsenic
One of the key research publications that launched the field of synthetic biology built a NOR gate to operate in a living system. The work was from the laboratory of Dr. James Collins at Boston University. His research group built two NOR logic gates using genetic parts and cross-wired them to create a latch.
the availability of standardized parts has allowed engineers to more rapidly prototype new ideas. Commonly standardized features include the size, shape, material properties, and behavior of components.
part of the power and beauty of building biological systems is that cells can change their molecular composition based solely on the DNA sequences they contain. In this way, they behave somewhat like computers reading software, except that instead of interpreting zeros and ones, cells read instructions that appear in the language of DNA.
Gibson assembly, which enables the simultaneous assembly of many pieces of DNA, is considered by many to represent the future of DNA assembly, but as yet it has not achieved the standardization required for a mature engineering method. One day, Gibson assembly, like BioBrick assembly, might become a standardized technique,
satisfying work is found in creating something you value and in solving a difficult problem
scientists are trained to speak in probabilities rather than absolutes
The Glowing Plant developers chose to work with the gene that encodes luciferase, an enzyme from the firefly that produces a visible glow from its chemical substrate, luciferin. They also chose to work with the plant Arabidopsis thaliana, a common laboratory organism that is widely used for academic and industrial research.
January 24, 2025
A very readable introduction to synthetic biology, I found it fascinating and exciting to see how many undiscovered things there are. The book particularly emphasises practical applications of biotechnology which I enjoyed and the majority of the book is practical labs you could carry out in a classroom after explaining some of the theory first.
November 10, 2017
What a fantastic read for people interested in synthetic biology.
March 15, 2023
Very fun book. haven't tried the experiments, so idk how accurate it is
August 28, 2016
Interesting introduction to the topic and yet the book is too technical for an average reader (like me)
Displaying 1 - 5 of 5 reviews