More broadly, we hope that others, especially the hundreds of new startups in synthetic biology, consider sharing pre-competitive ideas, methods, tools, etc. We think the community will be stronger as a result.
This is a great initiative. Hat's off to this company - Octant-bio for encouraging open sourcing of their hard work and optimization.
we usually need 400-1200 colonies, it’s still easier and faster to do this manually than by colony picker. Also, colony pickers typically cost >$100K and don’t seem appropriate for our scale.
Chemical inducers such as carbon sources, metabolites, and antibiotics, environmental signals such as light, pH, oxygen, or temperature, and autoregulatory quorum-sensing molecules can all be sensed by TFs
Common inducer molecule types
A final word: when we do not understand something, it does not look like there is anything to be understood at all - it just looks like random noise. Just because it looks like noise does not mean there is no hidden structure.
Excellent statement! Could this be the guiding principle of the current big data boom in biology?
blood circulate
The early modern English physician William Harvey (1578-1627) made several valuable contributions to the medical sciences, including the circulation of blood in the human body. In De Motu Cordis (1628), Harvey sets down his landmark experiments; in these, Harvey used ligatures to stem blood flow to better understand how the heart works to pump blood throughout the human body. This knowledge will be critical for Victor's creation of the Creature.
physiology
By 1818 physiology had become a controversial branch of medicine at the center of the dispute between vitalism, the idea that a divine spark energized animal life, and materialism, the argument that chemical processes alone give rise to life. Mary Shelley was well aware of the dispute since the Shelleys' family doctor, William Lawrence, was vigorously taking up the materialist argument in works like An Introduction to Comparative Anatomy and Physiology (1816). For a full view of this controversy as it relates to the novel, see Marilyn Butler, "Frankenstein and Radical Science" [1993] reprinted in J. Paul Hunter, Frankenstein, Norton Critical Edition, second ed. (New York: Norton, 2012): 404-416.
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
This cell is the simplest photosynthetic “machine” designed by nature – an attractive foundation for manipulation
key challenge is to quantify the functional roles of bacterial taxa in nature to understand how the properties of ecosystems change over time or under different environmental conditions
tools described here can be used to mimic complex expression patterns, such as the ones found for pneumococcal virulence factors, paving the way for in vivo investigations of the importance of gene expression control on the pathogenicity of S. pneumoniae.
It is challenging to study how pneumococci control virulence factor expression, because cues of natural environments and the presence of an immune system are difficult to simulate in vitro
includes creation of innovative solutions for bio energy, resource recovery, and emerging public health concerns by leveraging synthetic or molecular biology tools, novel biological systems (genetic circuits, enzymes, genetically engineered microbes), fundamental biological and chemical concepts, artificial intelligence, and big data science, as well as collaborations in Computer Science, Public Health, Plant Biology, or related fields.
Humans are worse at this because we all have different goals, whereas all ants work towards the survival of their colonies.
Ants are "immune" to traffic jams in their world
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
Download the complete Review Process [PDF] including:
</br>
CustoMem in the UK uses synthetic biology to create a granular material that attracts and sticks to micropollutants such as pesticides, pharmaceuticals, and certain chemicals in wastewater
MicroBio Engineering Inc., a research and engineering consulting firm specializing in developing improved algal strains and cultivation processes for wastewater reclamation, animal feeds, higher value products and, yes, biofuels.
In Japan, scientists are developing synthetically altered soy plants and yeast that produce glycyrrhizen, a compound in licorice root that is 150 to 300 times sweeter than sugar
expatiation
Actually, it's Exaptation - Wikipedia.
Fear of humans as apex predators has landscape-scale impactsfrom mount ain lions to mice (2019)
Apex predators such as large carnivores can have cascading, landscape-scale impacts across wild-life communities, which could result largely from the fear they inspire, although this has yet to be experimentally demonstrated.
Humans have supplanted large carnivores as apex predators in many systems, and similarly pervasive impacts may now result from fear of the human ‘superpredator’.
We conducted a landscape-scale playback experiment demonstrating that the sound of humans speaking generates a landscape of fear with pervasive effects across wildlife communities.
- Large carnivores avoided human voices and moved more cautiously when hearing humans,
- medium-sized carnivores became more elusive and reduced foraging.
- Small mammals evidently benefited, increasing habitat use and foraging.
Thus, just the sound of a predator can have landscape-scale effects at multiple trophic levels.
Our results indicate that many of the globally observed impacts on wildlife attributed to anthropogenic activity may be explained by fear of humans.
Most of us are unaware of how our actions lead to self-organizing behavior.
This is what Adam Smith realized in a Wealth of Nations
The Two Sides of the H-LAM/T System
When I view this diagram, I am reminded of Robert Rosen's Modeling Relation, an image of which is here The Modeling Relation grew out of research in Relational Biology which was the first mathematical biology to recognize that relations among organism components and between those components and the environment are key to understanding complex adaptive systems.
In my opinion if you can get enrolled into a degree program for systems biology then that would be best. However, if you are just exploring the field on your own I would recommend going through these resources.Video lectures by Uri AlonVideo Lectures by Jeff GorePrinciples of Synthetic Biology (at edx)Coursera specialization on systems biology.If you are looking for mathematical intensive start with first 2 and if you are looking for biologically intensive begin with last 2. Either way go through all 4 of them as they provide diverse perspective on systems biology which is very important. As you will move through these materials all the necessary supplementary information like books, papers and softwares will be informed within these materials itself.Hope this helps!
performance curves beginning to level off – because of our inability to automate the design work needed to support further hardware improvements. Wed end up with some very powerful hardware, but without the ability to push it further
Addressing the question of singularity, the author takes on an interesting perspective. One rationalization or opposing view is that technology is only as informational and intelligent as the creator itself. Just as the Mores conclude, "the computational competence of single neurons may be far higher than generally believed" and that "our present computer hardware might be [] 10 orders of magnitude short [compared to] our heads". This means that AI cannot surpass human intelligence as popularly believed. Rather, the article conjectures the possibility that if singularity were to occur, further innovation and improvements could never be made. I assume this is a biological and anatomical argument. Thus, implying that the technological constraints of AI cause it to be inferior to the biological makeup of the human brain. Thus, the author suggests that singularity can never really be fully realized.
Butte Biology
Also, the existence of differences between men and women doesn’t necessarily mean they can’t be changed in the future, even some biological ones. How much of what we’ve inherited – biologically, psychologically or socially – is outdated and malleable?
Expand... posthumanism?
There are factors other than sexism or discrimination that could in part explain why Google does not have 50 percent female representation. There are differences between men and women on average, based on population level statistics. (He qualifies this by noting a number of these differences are small and there is significant overlap between the genders.) These differences may in part explain the gender gap in tech. Women and men may differ partly because of biological reasons.
Summary of Damore's claims.
This could help explain where so much of our body’s fluid goes. While our cells contain most of the fluid, and the circulatory system carries a whole load more, over a third went unaccounted for and was simply said to be “interstitial”, or just floating around between organs and cells. The researchers claim, in a paper published in Scientific Advances, that the “interstitium” should be defined as an organ in its own right.
The interstitium, a new organ, accounts for the body's "black matter" (unaccounted for fluids).
Statistical and integrative system-level analysis of DNA methylation data
perfectly fit for a blind, myopic, workaholic, trail-sniffing, and collective traveler"
Plus, while we think of ants as a hierarchical species (Queens>Drones>Workers, etc.), Queens really only exist to pump out eggs and don't give any oversight or leadership. The entire colony functions as a complex society without anything resembling discrete, individual deciders.
approaches have proven invaluable for understanding metabo-lism and improving metabolite production (Wiechert 2002;Patilet al. 2004), metabolic engineering ‘design principles’ are yet tobe fully elucidated due to our incomplete knowledge of livingsystems. Subsequently, it can take many iterations of the classi-cal design-build-test cycle to achieve engineering objectives,some of which may even be impossible to meet using availablebiological knowledge.An elegant way to overcome the challenges associated withengineering in biology is to apply a selective pressure to a genet-ically diverse population so that cells with the desired pheno-type can be isolated.
This is key!
This conclusion is not founded on this single instance, but on this instance compared with a general experience of the regularity of this clement in all its operations.
I am thinking here of Darwin's Moth, a species of moth Charles Darwin concluded must exist, from the shape of a certain orchid, 40 years before the moth itself was discovered. It is not the induction from orchid->moth, but dozens of moth-orchid interactions that lets you fill in the probable details.
e. Actually, I think this is better an example of analogy, now that I think about it.
e2. Moth-Orchid Dynamics would be a good name for a rock band
But should I from the same experiment infer the circulation of the sap in vegetables, this would be called an argument only from analogy.
Georges Canguilhem actually has a lot to say about how much of the history of physiology works under different mechanical analogies, thinking of the heart as a pump and the arm as a lever, but he cautions this, arguing that Science and Technique are two distinct things that borrow and influence each other, but are not extensions of one from the other. Still, the analogy logic of how we understand the long-standing human body in terms of the thing we just invented seems relevant here.
Part of a dinosaur tail with feathers was found trapped in amber. It is 1.4 inches, with 8 vertebrae. (Apparently a very tiny dinosaur.) They think its from a flightless dinosaur called a coelurosaur.
We compare our assembly to a recently published one for the same species and do not find support for massive horizontal gene transfer. Additional analyses of the genome are ongoing.
They are contradicting another study that claimed that a certain species of tardigrade had about 17.5 percent of its DNA borrowed from other organisms through horizontal gene transfer. http://www.sciencealert.com/the-tardigrade-genome-has-been-sequenced-and-it-has-the-most-foreign-dna-of-any-animal
studies show changes in gene expression after 8 hours of meditating in the lab
According to set point theory, our attitude and behaviors have a bigger effect on our happiness than our external circumstances – and that’s good news for mindfulness. Mindfulness shapes our brain by increasing gray matter in areas related to attention, learning, self-awareness, self-regulation, empathy, and compassion.
Mindfulness literally changes our brains, making some areas more responsive, interconnected, and dense. In particular, these are areas related to empathy (the insula); memory, emotion, and emotion regulation; and reward circuitry. In response to distressing stimuli, meditators see more activation in their prefrontal structures (for awareness) and less in their fear-driven amygdala.
They have helped people reduce chronic pain, improve psoriasis, and increase their immune response to the flu shot. One study of mindfulness/compassion meditation out of Emory University showed reductions in stress markers, and even a simple long exhale (ahhhh) increases vagal tone. And – last but not least – a three-month meditation training program boosted telomerase activity, indicating longer telemores and perhaps a longer life expectancy.
In one version of this experiment, if we gave participants synthetic oxytocin (in the nose, that will reach the brain in an hour), they donated to 57 percent more of the featured charities and donated 56 percent more money than participants given a placebo. Those who received oxytocin also reported more emotional transportation into the world depicted in the ad. Most importantly, these people said they were less likely to engage in the dangerous behaviors shown in the ads. So, go see a movie and laugh and cry. It’s good for your brain, and just might motivate you to make positive changes in your life and in others’ lives as well.
When people watch Ben’s story in the lab—and they both maintain attention to the story and release oxytocin—nearly all of these individuals donate a portion of their earnings from the experiment. They do this even though they don’t have to. This is surprising since this payment is to compensate them for an hour of their time and two needle sticks in their arms to obtain blood from which we measure chemical changes that come from their brains.
(Ben's story is a very sad story)
when rats are sizing each other up in the moments before a potential fight, which may mean that laughter can help diffuse situations that might otherwise escalate into physical conflict. Similar behavior has been documented among chimpanzees.
As rats age, their chirping generally becomes less frequent. (A similar phenomenon seems to occur in humans: Research done by William Fry, a professor emeritus at Stanford University School of Medicine, has found that kindergarteners laugh 300 times a day, whereas adults laugh just 17 times.) However, rats who were tickled often when young usually retain their tendency to chirp later in life.
It is precisely this more childlike, instinctive form of laughter that scientists believe they have uncovered in rats. Panksepp, the Baily Endowed Chair of Animal Well-Being Science at Washington State University, has found that rats emit their high-pitched chirps when tickled, especially in areas, such as the nape of the neck, that are targeted by fellow rats during playful bouts. They make the same sounds when playing or anticipating playtime with one another, as well as when anticipating a reward. Other research has found that this chirping is common when rats enter new environments or encounter new animals; Panksepp likens this to nervous laughter in humans.
scientists have probed the brain circuits involved in human laughter, but this research has faced a number of limitations. For one, though researchers have used sophisticated equipment to observe people’s brain activity while they read cartoons or jokes, this equipment is quite sensitive to movement—a major drawback when you’re trying to induce a hearty belly laugh.
Why rats, which do have a form of ultrasonic laughter, have been used in laughter research.
Experiments on humans have found that laughter can increase blood flow and strengthen the heart, much like aerobic exercise does. Laughter also helps decrease one’s threshold for pain, although not all humor is the same in this respect. According to Weems, positive humor—humor that looks for the bright side of troubling situations—is beneficial to our health, while darker, sardonic humor is not.
Take for example an old Groucho Marx joke: “One morning I shot an elephant in my pajamas. How he got in my pajamas, I don’t know.” Our brains will read the first sentence and be taken down a path imagining Grouch Marx on a safari in his pajamas, before we get the new image of the elephant actually inside his pajamas. That process of moving from one possible solution to the next involves a part of the brain called the anterior cingulate, or AC, which becomes more active when there are conflicting interpretations in the brain. The AC helps to quiet down the “louder” parts of the brain (associated with the expected response) to allow other quieter answers to emerge, and it’s particularly active during jokes. It helps us to figure out the novel solution, which, when resolved, gets incorporated into the brain and gives us that spike of dopamine. This is why we feel so good when we get a joke, and why jokes are not funny the second time around.
he grouped humor preferences into three types: “incongruity-resolution,” which involves “violating one’s expectations in novel ways;” “nonsense humor,” “which is funny only because it makes no sense;” and “sexual humor,” which is offensive or taboo. Although not everyone finds the same type of humor funny, the common thread in these joke types is that they all involve dealing with surprise and resolving the ensuing cognitive dissonance. “What elicits laughter isn’t the content of the joke but the way our brain works through the conflict the joke elicits,” writes Weems. Basic Books, 2014, 230 pages
Apparently fMRI was used in this work, though it isn't immediately clear how.
Weems explains what humor is, how things become funny, and why evolution gave us laughter. According to Weems, laughter and humor help us process conflict in our environment through the dopamine that is released in our brains when we find something funny. Dopamine relieves tension—which I discovered with my son—but it’s also implicated in motivation, memory, and attention, affecting processes as varied as learning and pain management.
laughing, probably through its effects on breathingwhich makes you breathe more deeply, actually calms your cardiovascular system. So, it reallyseems to be altering your stress profile as a pathway to physical health.
In answer to why awe would be a potent predictor of reduced pro-inflammatory cytokines, this latest study posits that “awe is associated with curiosity and a desire to explore, suggesting antithetical behavioral responses to those found during inflammation, where individuals typically withdraw from others in their environment,” Stellar said.
In addition to autoimmune diseases, elevated cytokines have been tied to depression. One recent study found that depressed patients had higher levels of the pro-inflammatory cytokine known as TNF-alpha than their non-depressed counterparts. It is believed that by signaling the brain to produce inflammatory molecules, cytokines can block key hormones and neurotransmitters—such as serotonin and dopamine—that control moods, appetite, sleep and memory.
There are new psychophysiological findings finding that cytokine levels, cytokinesreally reflect an inflammation in response in your body, which is very tough news onyour health, the only positive emotion that really lowers levels of cytokines is provingto be awe.
E.O. Wilson’s writing about biophilia.And it’s really this very rich hypothesis that we have this evolved love about naturalbeauty. So if you’re out in the woods, you’re in the mountains, you’re watching patternsof light on the ocean, it triggers this feeling in us, this feeling of beautiful delight ifyou will. And E.O. Wilson makes the case that that is an evolved preference because whenwe attach to beautiful things in nature, we’re finding kind of resource-richenvironments that have food and water and shelter as a way to orient towards thelandscape.
busy regions of the brain start stitching new connections with each other. Existing synapses—the connections between neurons that are very busy—get stronger, they get more sensitive, they start building out more receptors. New synapses form as well.
more activation in the left prefrontal cortex is associated with more positive emotions. So as there is greater activation in the left, front portion of your brain relative to the right, there is also greater well-being. That’s probably in large part because the left prefrontal cortex is a major part of the brain for controlling negative emotion. So if you put the breaks on the negative, you get more of the positive. On the other hand, people who routinely experience chronic stress—particularly acute, even traumatic stress—release the hormone cortisol, which literally eats away, almost like an acid bath, at the hippocampus, which is a part of the brain that’s very engaged in visual-spatial memory as well as memory for context and setting. For example, adults who have had that history of stress and have lost up to 25 percent of the volume of this critically important part of the brain are less able to form new memories.
