Capra Biosciences harnesses the superpowers of a biofilm-forming organism Marinobacter atlanticus to make fat-soluble products like retinol which is used in anti-aging face creams, and high-end industrial lubricants for electric car engines

Some startups, like MicroByre, have been working to domesticate those reluctant, recalcitrant, and rebellious microbes by adapting them for use in the lab and creating genetic tools to manipulate them

The SWW aimed to mimic the average conditions and nutrient proportions of conventional domestic wastewater.

McMaster's Stephen Girard(1918), he said, was a "series of anecdotes . . . without connection"and with little interpretation or analysis." In Rhodes's last twovolumes the facts rarely appeared "to have meaning or to be partsof a coherent structure." " "No simple theme, like that whichdominated his great work, is apparent here. Mr. Rhodes has notseen any constructive unity in the years he covers. Instead of mak-ing a synthesis that would of itself lead the reader to a clearerunderstanding of American history . . . , he has developed his topicsparagraph by paragraph, with often abrupt transition from themeto theme." 26 His failure in the final product followed,

With practice, your SourceNotes will become more like data and your Points moreanalytical.

Once I was started on the career of a social investigator,the manuscript books became a record of other people’scharacter and conversation; of their gestures and acts; infact, of human behaviour; and, as such, these entries havean interest of their own.

Synthesis notes are a strategy for taking and using reading notes that bring together—synthesize—what we read with our thoughts about our topic in a way that lets us integrate our notes seamlessly into the process of writing a first draft. Six steps will take us from reading sources to a first draft.

i was particularly struck by the fact that barry didn't say the mind is this this and that okay barry said well the mind is many things 01:19:18 uh look there's this and this this and this and there's a sort of layers also in some sense in which we can talk about it or or have some understanding partial media 01:19:30 understanding about it some wisdom about it and this layering i find it it's uh absolutely brilliant from my perspective 01:19:43 uh because it it dissolves the wrong question which is what is the mind period what is the thing which is the mind here is the thing which is mine uh let's just 01:19:55 define it characterize it and understand what it is that's a wrong that's a wrong way of thinking about it it's when we say when we think about our mind of course we think something you you unite somehow 01:20:09 it's the set of processes that happen into me and it's about my thinking my emotions but it's not one thing it's a complicated layer there's many layers of discussion possible about 01:20:21 that i don't want to enter into the specific but i found this fascinating and let me go to time immediately because uh it's it's deeply related i got the book of time which is a um 01:20:34 the audio of time in which i carlo this carlo is very timely because we're also kind of running low on time absolutely absolutely 01:20:46 and and and in the book i sort of uh try to collect everything we have learned about time from science from special activity from generative statistical mechanics from other pieces and and what we 01:21:00 tentatively uh learn about time with quantum gravity which is my uh specific field once again you have to sort of uh put your hands on the notion of time and the main message of the book 01:21:12 in fact the single message of the book is that the question of what is time is a wrong question because when we think about time we think about the single thing okay we think we have a totally clear idea about time time is a single thing 01:21:25 that flows from the past to the future and the past influence the president the president of the future in the present this is how things are the reality of the present entire universe is a real state in that and we learn from science that this way 01:21:37 of viewing times is wrong it's factually wrong okay it's not true that uh we all proceed in in in together from 01:21:48 moment a to moment b and the amount lapse amount of time lapses between a and b is the same for everybody and so on and forth because we learned from from experiences especially activity generativity statistical mechanics and 01:22:01 other things so the way to think about time is that it's a very layered thing but with this thing we call time is made by layers um conceptually and when we look at larger 01:22:14 domain the one of our usual experience some layers are lost so uh some aspects some some properties of what we call time are only good 01:22:25 uh are only appropriate for describing the temporal experience we have if we don't move too fast it doesn't look too uh to to to too far away if you don't look at the atoms too in detail as a single 01:22:38 degrees of freedom and so on so forth so the notion of time opens up in a in a in a set of layers which are become increasingly 01:22:53 uh general only if you go down to the bottom level um some aspect of time like the universality of time uh uh only makes sense if if we don't go too 01:23:06 fast velocities for instance um so this is a similarity and that's why the the opening up of what the mind is into layers seems to be uh 01:23:19 the right direction to go right when if if i ask uh does a cat has a mind or does a fly has a mind it seems to me that the only answer is uh to get out of the idea that the 01:23:31 answer is either yes or no i mean i i suppose that certainly a cat has a certain you know a sleepy feeling in the morning and the moment of 01:23:43 joy when he sees his fellow cats but i suppose a cat doesn't go through a complicated intellectual game of trying to understanding what is reality and debating about that so there is some aspect in common uh either not break up 01:23:56 this this notion in in pieces once again uh i mean the the topic is what is real uh 01:24:08 if we start by saying time is real it's a beautiful chapter why you cannot say that time is an intrinsic existence uh we just get it wrong if we think well then atoms are real or the mind is real 01:24:21 all these answers we got it wrong we can say that things are real in a uh in a conventional sense within a context within a within a um 01:24:37 and and then we when we try to realize what you mean by uh something is real this is certainly real in a conventional sense but we realize that um reality the reality of this object 01:24:49 itself it gets sort of broken up into interdependence between this object and else and its different layers 01:25:02 and and that's the reality that as a scientist i can deal with not the ultimate reality the the conventional reality of course conventional reality is real as uh perry 01:25:15 was saying this is not a negation of reality uh it's a it's a it it's a freedom from the idea of the ultimate reality uh 01:25:27 the ultimate uh sort of intrinsic inherent reality being there on which in terms of which building progress

if we've looked at the synthetic a priori of time he also addresses the synthetic a priori of 00:15:46 space and one very interesting distinction he draws is between animals who have semi-circular canals in their heads somewhere and animals which don't now we do fishes do 00:15:58 limpets don't for an animal with semicircular canals the word this the nature of space is to have right left up down forward backwards it's to be suspended or the 00:16:11 head to move through a volumetric space that we is so familiar with us we think of that as space as simply existing an animal not so endowed with no 00:16:24 semicircular canals encounters space in an entirely different way and he discusses how space arises for something like a limpet or a paramecium so he has taken the synthetic a prioris 00:16:36 of time and space and reconsidered them in a manner appropriate to the 1920s and 30s paying keen attention to the structures and processes of the body 00:16:48 this is work that we still need to do

he's built a little toy he's built a treadmill for a snail isn't that wonderful he's a genuine scientist he's doing lots and lots of experiments with 00:11:27 animals they're very creative experiments in this case he's built a treadmill for a snail so the snail is held by a vice on a rotating ball and the snail is then um approached by 00:11:40 the investigator who chucks it under the chin like this and if you chuck the snail under the chin like this the snail will recoil not surprising i 00:11:52 would recall it as well but as you speed up the frequency of these chucks under the chin at about five hertz once you pass a frequency of about five chucks per second 00:12:05 the snail's behavior changes remarkably instead of being perturbed and trying to withdraw it tries to crawl onto onto something the qualitative nature of what's happening 00:12:18 to the snail has changed for the snail and its response or it's it's um sense making is altered and it's tried it perceives seems to perceive now a constant surface onto which it might 00:12:32 crawl now that might seem strange to you but i'll remind you that if we flash a light for you five times a second you'll see a light flashing and if we speed up the interval 00:12:44 then we shorten the interval between flashes to make them faster there comes a critical point at about 20 site flashes per second where you no longer perceive individual flashes but you 00:12:54 perceive a continuous light something like this underlies the magic that happens with moving pictures as well where you know that the action you see in the cinema is a bunch of projected still pictures 00:13:09 but they um have this character of continuous movement for you likewise in sound if we play that for you you hear a bunch of disconnected claps but if we shorten the 00:13:22 interval between the claps and speed it up there comes a point at which it changes into a continuous low pitch and that happens again about 20 hertz at about 20 cycles per second now for this snail 00:13:35 that border is at a different place it's at about five cycles per second what this shows is quite profound remember kant's synthetic a prioris 00:13:46 time for this snail is different than time for you the time that arises as a function of the body of the snail has this border at about five hertz where you have one at about 20 hertz 00:14:01 his basic insight is that worlds arise for snails that are not commensurable with worlds that arise for humans with which are not commensurable with worlds that arise for earthworms 00:14:15 the notion of an umvelt we get to determine a minute is used to describe this bodily specific arising of a world together with time and space 00:14:28 now i said it's rather weird to think of time being fundamentally different for an animal of a different constitution but i'll remind you that we can use our cinematic tricks to make ourselves aware of our own 00:14:41 limitations on the left there through high-speed photography we managed to make perceptible an event which we cannot otherwise see the event that you see there with the splash is 00:14:53 perfectly real but we can only make it manifest through high-speed photography similarly whoops there are processes going on around us 00:15:05 that we do not perceive and we can use time-lapse photography to make those to speed them up so that they become perceptible to us something like the blooming of a flower or the battles intricate battles fought 00:15:16 between brambles and hedges these make us aware that we perceive time as unfolding at a rate dictated by our own metabolism and bodily processes so this idea that time and space 00:15:32 are considered very different from count but very much tied now to the body this is quite radical

we need to understand what the tradition is that he is feeding from and how what his orientation is he is 00:01:21 taking his own work to be an extension of the work of immanuel kant now if you have not noticed anything in the history of philosophy of mind please 00:01:33 notice descartes and kant those are the two principal landmarks so many others but kant had died at the very start of the 19th century kant was working within a 00:01:46 physical framework that was newtonian in which space and time are simply blocks containers within which things unfold mechanistically that was the metaphysics available to 00:02:00 kant was asking with that metaphysics how do we come to know anything now he had the cogito of descartes very much on his mind but also the the empiricists 00:02:14 concerns with the role of the senses following the tradition of hume and kant attempted to resolve this by noting that there were some things that could not be learned from the world that had 00:02:27 to be in place before any knowledge of the world can happen at all he called these the synthetic a prioris those things that well nothing forces the manas but we can't begin to make 00:02:38 sense of the notion of knowledge without prior notions of time and space and causality this is a difficult position to occupy and can't argumentation was developed in very many ways and gave rise to very many 00:02:53 different kinds of science thereafter for the thing in itself this shell is not knowable rather i encountered a phenomenon of the shell the phenomenon of the shell 00:03:11 through mediated through the senses and the body and i can never thus get to the shell itself this is of course the paradox underlying all representational theories 00:03:22 of perception which is that they seem to leave you estranged from the world and not in contact with the world all knowledge seem to be mediated through the sensors so it need you need 00:03:34 to bootstrap knowledge with these synthetic api ras for accounts this is immanuel kant dies at the start of the 19th century and then about 00:03:45 1870 something like scientific psychology starts to emerge and there's a wide variety of approaches they're drawing among other things from kant but they're not following one 00:03:58 unified agenda funux comes in here and he sees himself as taking kant seriously and he's going to develop in his context in the 1920s and 1930s 00:04:10 the notion of a synthetic a priori changes now instead of the physicalist model of time and space and as containers that we have with kant the body is the ultimate synthetic a 00:04:22 priori for von neux cool epistemology or how a being comes to know the world will only be ever understood through careful attention to the structures of and processes of the body

Your efforts to capture content for future use will be tremendouslyeasier and more effective if you know what that content is for.

Mixup Method of Synthetic Idea Generation: Write out 3 sentences from past notes. Write a new sentence made of the 1st, 2nd, and 3rd part of each respective sentence. Repeat total of 3 times. Now look at the 3 synthesized lines & ask if wrong or right and why. Clarifies a lot.

There are four essential capabilities that we can rely on a SecondBrain to perform for us:1. Making our ideas concrete.2. Revealing new associations between ideas.3. Incubating our ideas over time.4. Sharpening our unique perspectives.

Even thoughelaboration works verifiably well for deep understanding, it might notbe the best choice if you just want to learn isolated encyclopaedicfacts (Rivard 1994).

Typically, double terminators are used to stop transcription. Because these parts can be up to ∼168 bp of DNA, this use of double terminators can lead to homologous recombination when used at multiple locations in a design

A spacer could compensate for any steric hindrance effect on recruiting the transcriptional machinery at the promoter of the next module in the assembly line; such an effect could be induced by the supercoiling that results when the transcription of the previous module is taking place. However, there is no direct evidence that this may cause a problem, and therefore the argument in favor of using a spacer remains speculative.

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.

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

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.

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

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.