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hi my name is harrison smith and i want

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to talk to you today about my research

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the title is called seeding biochemistry

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in other words enceladus is a case study

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and the first thing i'd like to mention

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is that this work was done

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um not by myself but also with

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co-authors alexa drew jamboy and sarah

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walker

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so the first thing i want to talk about

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today is the concept of habitability

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which is pervasive in astrobiology

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and i want to talk about it because it's

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something which

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i'm a little bit passionate about and

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the idea that only environments like the

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one shown above where you have

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water on the surface of an environment

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these are currently the only types of

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environments which are currently labeled

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as being habitable

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but of course we know that that's not

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necessarily the case

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there are places in our solar system for

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example on enceladus where

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a subsurface ocean seems like a

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completely reasonable habitable

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environment

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but this language that we use to define

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habitability kind of pigeonholes us into

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thinking about the concept in a kind of

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biased way

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even in places like earth and antarctica

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for example

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the south pole lake bostock is a

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subglacial lake

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where life has been found and

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this is an interesting fact because this

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environment on earth would be deemed

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non-inhabitable by the definition and

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that's pervasive in astrobiology

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and one of the reasons i'm talking about

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this for so long

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is because um i think habitability is a

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concept which

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is hard to quantify um it's kind of

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specific

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to the environmental context and you

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remove the concept

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of individual organisms or types of life

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when you talk about habitability

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it's implied but it's not explicit

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instead i think it makes more sense to

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talk about the concept of viability

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and viability is specific to the type

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of life that you're interested in

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so you can actually quantify whether or

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not a particular type of organism or

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particular type of life

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is viable in a given environment and

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it's a little bit more

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rigidly explorable scientifically than

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the concept of habitability which is at

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some levels intentionally vague

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so the question that i have is kind of

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how can we predict if earth life can be

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viable on other planets

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um and i'm going to list a kind of set

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of features

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that it'd be nice um to have when we

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want to test this question

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and they're going to be biased by the

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fact that i'm a computational

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estrobiologist

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so ideally if you want a predictive

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earth life as well on their planets

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we don't have to require growing

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anything in the lab it's more easily

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scalable to ask this question this way

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it'd be nice to vary kind of the big

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unknowns so things like catalytic

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properties of organisms

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basically the reactions which are

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catalyzed by the enzymes encoded in the

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organism's genomes

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it'd be nice people vary the growth or

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sustainability requirements of organisms

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as we learn more about those things

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and having a first order model is

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probably good enough we don't want to

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really over constrain ourselves with

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thinking about things like reactions

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stoichiometries

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kinetic constants more environmental

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concentrations where we don't have to

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so the way that i approach this

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is using this technique called network

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expansion network expansion

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ideally gets around all of the issues or

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has the advantages that were listed on

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the last slide so

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the concept behind network expansion

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which is a computational approach

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is that you initialize possible

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reactions based on organism's genome or

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possibly a community's metagenome

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you look at the compounds which are

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available

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in the environment so in the case of

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enceladus for example these are

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observed based on spacecraft

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measurements

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you come up with a target you can come

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up with a target compound set so

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basically you define

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predefined the compounds which you think

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are required

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to define an organism an organism's

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viability

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in order to actually execute the network

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expansion what you do is you check

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if reactions are possible based on

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compounds in the environment so

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you say this organism can catalyze this

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set of reactions

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particular compounds

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and if these compounds are available we

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assume that the reaction is possible

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and what you do then is you add the

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products

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of whatever reactions are possible back

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into the seed set that you used to start

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out with

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and what you do what ends up happening

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is you start collecting compounds over

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time over the iteration of this

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simulation you repeat this process

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until no new compounds can be produced

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and at the end of the simulation you

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check

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how many target compounds are produced

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based on this predefined list

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that we're using to measure viability

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so this this meets all the requirements

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that i was listing before

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conveniently enough um and i want to

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point out that this is a technique which

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has some history and being used

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in particular studies in the origin of

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life but this is a really prominent

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paper that it was

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recently used in from a few years back

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looking at how

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we could use network expansion kind of

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at a global level to understand

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uh what reactions might have been

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possible in a world before

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phosphate okay so to kind of jump to the

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punch line

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when i asked the question could earth

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biochemistry be viable in enceladus

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uh if the answer is yes then a

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natural follow-up question might be kind

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of what organisms or combinational organ

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organisms are viable and if no what

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things would you have to add in order to

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make organisms viable

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and again the viability is something

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that we pre-depo predefined based on a

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list of target compounds and this comes

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from the literature and comes from

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studies on organisms and what types of

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environments they can grow in and

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what things they produce which are

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necessary for them to continue to

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survive

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okay so again here's just a reminder

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of the initialization process and going

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over a little more detail

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in kind of where the genomic data comes

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from we look at these genomic databases

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for example jgi which i show a

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screenshot of here we also get some data

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from

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phimat2 we're picking a kind of

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reasonable starting point for

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organisms for enceladus so we look at

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high ph

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we found about 307 organisms mostly

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bacteria

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that meet the condition of living these

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high ph environments

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um yes what you can do is you can go in

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and you can select an

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organism where you can select a

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metagenome

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and you can get the list of ecs which

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are enzymes associated with an organism

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or a community and you can tie these

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seeds to particular reactions through a

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database called keg

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and you can turn these reactions into a

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network that looks something like this

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um okay so that's how we initialize the

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possible reactions

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like i said to initialize the compounds

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what you do is you take um

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observations from enceladus taken from

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spacecraft measurements and this gives

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you the

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compound set the target set comes again

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from previous literature okay so here's

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jumping to the punch line

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um we find that none of the prokaryotes

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that

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we studied were viable even when you add

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phosphate phosphate is something which

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is missing in detections that enceladus

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people think mostly just because

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of instrument sensitivity and low

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concentrations but not because it's

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completely absent

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what we find here this is just going

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into a little bit more detail on kind of

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how we're defining the viability of an

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organism

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all these 65 global target compounds

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that they could possibly produce in

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their their

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metabolic network and so instead what we

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do is we don't penalize the organism for

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not having

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the possibility to produce those

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compounds based on the reactions that

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are coded for

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um through the proteins that are coded

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for in the genome instead what we do is

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we take the overlapping list

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of all the compounds which an organism

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could possibly produce with that target

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list

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and so for example this bacteria here

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its goal

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is producing 60 target compounds not the

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65 because 65

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and 4 aren't possible

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same example here is the other extreme

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so there's ikea that

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only overlap with 32 of these 65 target

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compounds and if it can produce all 32

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of these target compounds we say that

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it's 100 viable

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um so then the next follow-up question

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becomes

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what compounds would be necessary to

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enhance organismal viability if you

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could add particular compounds to the

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environment and solids could you

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generate

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environments which allow these organisms

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to be viable

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so what we do here is we generate what

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are called irreducible

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compound seed sets for each organism so

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basically working backwards to figure

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out

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um what are the seeds that need to be an

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environment in order

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for an organism to produce the full

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um intersecting set of target compounds

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necessary for viability

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and here's some details in that

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algorithm you can pause the video and

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look back at it later

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if you'd like so asking the questions

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which compounds would be necessary to

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enhance organizational viability

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if we just look at a particular organism

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there's a set of organisms and ask

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kind of how many additional seeds are

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required for viability

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and we ask this question independent of

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environment we get a result like this

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on the x-axis is the number of seed

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compounds and the y-axis is the

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molecular weight so kind of a proxy for

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the complexity of the compounds and you

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see that

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in general there are archaea for example

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on the left hand that plot

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that only need 50 uh kind of

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compounds for viability um

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if they're the right compounds and these

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tend to be very complex things

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on average based on what you can see the

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y-axis there

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and the dash the vertical dashed line is

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the um

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just number of compounds which are

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observed in the environment on enceladus

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that were incorporated into our seed set

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and so you can also break this plot by

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not looking at the seed sets with the

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fewest number of compounds but instead

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looking at seed sets with lowest mean

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molecular weight so if we want to kind

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of bias our results for

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simpler things you notice that now the

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left-hand side of the plot

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the archaea which requires the fewest

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number of seeds is actually 18 instead

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of 15 because here we're looking

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specifically at things that are less

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complex

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maybe a more relevant question though is

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to ask based on what we already know in

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enceladus

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what additional compounds would you need

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to add to the environment so not just

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not thinking environmentally

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agnostically but thinking particularly

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to the environment that we're interested

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in here

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so what are the seed sets with the fused

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compounds how many

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seeds do we need to add to those

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environments and we see that

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you have to add a minimum of seven seeds

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for some bacteria

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but it the average seems to be something

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more like about

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adding about 17 seeds and we can make

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the same plot where instead of

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looking at the seed sets which produce

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viability for the

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fewest number of compounds instead

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looking at kind of the

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least complex environments that produce

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viability in different organisms and you

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see these require slightly

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more compounds so kind of the takeaway

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is for viability you can get away with

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fewer compounds which are more complex

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or much larger number of simpler

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compounds and depends kind of what your

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constraints are going into

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things um we can do some other just kind

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of looking at interesting statistics of

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the data for

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viability for organisms so for example

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we can look at the jaccard index which

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is kind of the self-similarity of the

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seed sets

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for each organism and so what we find is

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even

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within organisms that irreducible seed

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sets can vary considerably they only

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have about 10 to 25

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overlap which is what that y-axis is

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there so there's many paths to viability

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and um the similarity between seed sets

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tends to be a lot higher

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when you compare archaea to archaea than

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than when you compare keto bacteria for

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instance

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um so that's not too surprising so

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kind of revisiting the question which

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compounds would be necessary to enhance

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organized liability

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um kind of from a very high level we

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find that

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uh prokaryotes can be viable using

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fewer compounds than what's on enceladus

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but if we're really

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curious in in terms of the particular

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environment of enceladus you still have

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to add

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at least seven compounds usually more

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especially if you limit yourself to

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simpler compounds and then to kind of

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answer the ultimate question of

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course earth biochemistry would be up on

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another planet

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i would say yes but with a big caveat

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which is you know

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if complex compounds are present in the

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environment or

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the organisms have sufficiently

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extensive catalytic capabilities we

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didn't limit ourselves to

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organisms which are known to be found in

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these high ph environments

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we might be able to find organisms which

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are viable or if we assume that there's

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more complex compounds in the

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environment that haven't been observed

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yet

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there may be organisms that are viable

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but out of the organisms that we tested

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none were viable with with what we know

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to be present and that's all it is

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so kind of the takeaway here is that

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this network expansion technique can be

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um useful for conservatively

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conservatively bounding

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environments for viability of organisms

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and that is implications for things like

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accidental panspermia and it could even

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help guide things like

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directed panspermia thinking about the

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big picture questions in astrobiology

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and here's some follow-up questions of

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of things that we're interested in

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exploring in future work related to this

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so thinking about ecosystems thinking

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about

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more details in the environment more

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constraints related to thermodynamics

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and concentrations for instance

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i'd just like to thank everyone today

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for listening um the

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reference for the paper that this is the

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00:14:21,910 --> 00:14:19,680
talk is based on is on the right there

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and i'd like to thank um kenny for

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sponsoring this work and

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the wpialc and the work that i did to