 for the last talk of these Matlis first part before the lunch Jonathan it was enough The causal reality of entities the gene knocking and knock out Cases and it's a it's a common work Thank you so much, and yeah, I just wanted to start off by thanking Alexandra and Charles for organizing this workshop This is co-authored work, and I should just say up front that Ray Lynn did most of the work with this paper and so I might need some help from him during Q&A He's a good co-author Okay So I just wanted to start with a brief introduction to the scientific realism debate So on this paper is supposed to be some kind of contribution to that debate and one of the questions that philosophers ask in this debate is can we demonstrate the reality of unobservable entities and There are some paradigm cases of unobservable entities Philosophers love electrons. That's one of the standard cases, right? Also genes, and that's the case that we focus on in this work. So Basically To a first approximation You can say the scientific realists provide various arguments that we can Demonstrate the reality of unobservable entities While scientific anti-realists provide various arguments that we cannot So what we want to focus on is what we call the causal reality of entities and There's two parts to this idea The first part is that an entity that's taken as being a cause of some effect or phenomenon in some causal hypothesis or inference exists And the second part of it is the causal relationship Between the entity and the effect is real rather than a mere cognitive connection So it's kind of realism About an entity and about the causal relationship between that entity and something else And so what we want to say is in some cases in science We can demonstrate the causal reality of entities in this sense of one and two And the following methods can demonstrate the causal reality of genes in particular And the causal relationship between genes and phenotypic features and we focus on three methods here Transgenesis gene knock-in and gene knock-out So a little bit more on these three methods Transgenesis involves introducing a gene to the genome of an organism that does not have that gene in a natural state And then observe whether or not a new phenotype is expressed Gene knock-in is where you insert an exogenous gene in general at the NA sequence To a targeted locus of a genome in an organism or substitute an original gene in the genetic Focus with another new one and then you observe whether or not a new phenotype is expressed And then gene knock-out a targeted gene in an organism is deleted from or made inactive In the genome of the organism and then you compare the phenotypic difference between the knock-out organism and normal individuals So I'll say more about all of these methods very soon We'll start with transgenesis it Requires this technique of recombining DNA So science has used restriction enzymes to cut segments of DNA at the correct sites and then use DNA gaze to combine different segments of DNA To introduce a foreign gene into the new genome Science has used the technique of recombining DNA to link an exogenous DNA segment to a vector for the vectors and typically viruses or Plasmids and then the vector transports the exogenous DNA segment to the target cell and so an example of this You can cut DNA from plasmids and combine the DNA segments that encode various forms of antibiotic resistance to produce E coli cells with Okay, and so The argument that we want to give makes use of this concept that Raylin developed a number of years ago called experimental Individuation, so basically experiments that create or produce individuals in some sense And he has three conditions for what counts as experimental individuation The first is separation Sciences need to separate something from its surrounding environment or things that it's attached to in some way and so in this case Sciences cut or separate the specific DNA sequence from the genome of some organism for example E coli The second condition is manipulation where scientists after they separate something they use it to do something else So in this case Sciences link that DNA sequence with the DNA in a vector plasmids and inject the vector into new cells And then the third condition on maintenance of structural unity or maintenance of structural integrity This is you know Maintaining the structure of the thing that you've separated and manipulated and in this case Sciences makes themselves express a new feature for example antibiotic resistance But the specific DNA sequence is responsible for so the fact that it expresses the new feature Indicates that its structural unit is maintained because the function is preserved basically So science is thereby experimentally demonstrate that the transfer DNA sequence is an individual gene. Okay, so When Rayland originally proposed this idea He also suggested that when you experimentally Individuate something that provides the strongest evidence for the theoretical commitments The sciences have two particular individuals in the ontological structure of the world so it has Epistemic significance because it's the strongest evidence that we have for the existence of individuals In subsequent co-authored work we developed the idea that experimental Individualism is a criterion of reality. So if you can experimentally something that's a very good reason for being a realist about it and then The connections of the causal reality of genes here Genes exist and the causal relationship between genes and phenotypic features is real The experimental demonstration of the individuality of a trans gene and the demonstration of the specific causal Relationship between the gene and the specific feature is something that's interdependent Experimental individuation gives you basically reason to think that genes exist and reason to think that the causal relationship between the gene and its Associated phenotype is real. So in other words Experimental individuation demonstrates the causal reality, but there might be some reason for skepticism here and You might think okay perhaps experimental individuation alone cannot demonstrate the causal reality of genes You might think that we need Theoretical knowledge or theoretical assumptions about genetic mechanisms to demonstrate the causal reality of genes For example knowledge and assumptions about the encoding of DNA the transcription of genetic codes from DNA to RNA the translation of codes from R.A. to synthesized proteins and so on and so basically our goal is to try to develop an argument that Minimally relies on theoretical knowledge and assumptions as much as possible So in order to eliminate or address this skepticism In addition to experimental individuation, we want to say something about causation too and our starting point is Water's concept of a cause is an actual difference maker and Woodward's manipulability theory of causation and causal explanation so We have this ADM which stands for actual difference maker. So Z or Or X is the action. No, sorry X causes Z or X is the actual cause of Z If it only if X actually makes Z happen and Z is an actual difference and then a criterion of an actual difference making X is the actual cause of an actual difference Z Y if I is intervened by the manipulating X and the actual difference Z and Y is made by this so When applied to the specific example of Transgenesis we get something like this right the trans gene for example the gene for antibiotic resistance is the actual cause of the phenotypic feature the antibiotic resistance and Y is the thing that's intervened by manipulating X the trans gene and then the difference Z the antibiotic Resistance in the experiment of organism is made by this intervention So based on the satisfaction of CADM We can say the trans gene X is the real cause of the antibiotic resistance Z And we thereby warrant belief in the reality of trans genes and the reality of the causal relationship Between a trans gene and its specific feature without appealing to theoretical knowledge or assumption So I think the idea here is we don't necessarily need to say anything about this we can talk about What happens when we do the intervention and what the outcome is? Okay, so there is still some room for skepticism and It concerns the limitations of trans genesis as a method so trans genes are not necessarily Incorporated into the genome of the organism the combination of a trans gene with the genome is a random And trans Genesis can't ensure that a trans gene is inserted at a proper site of the genome so that the gene can express its function Functional sequence of DNA can only be cut at the proper site by a proper restriction enzyme But if you don't have that you can't do it And it's also difficult to manipulate or transfer any gene from a gene of interest from eukaryotic Organisms for example mice by means of trans Genesis because they're more complicated So we have some more skepticism here Basically, how do you know that the trans genes have been incorporated in the genome of say experimented mice because they're more complicated And this leads to the next two methods that I'm going to talk about so There's gene targeting and this makes use of homologous Recombination, which is the exchange of genetic information between homologous chromosomes And it has two major functions Generating variation process of reproduction and also repairing defects in DNA And then gene targeting makes use of this principle of Homologous recombination in the process of cell division to alter a targeted gene by inserting a marking sequence To a target locus of the targeted gene and then we have these two methods gene knockout And gene knock in and I'll start by saying a bit more about gene knockout so There's two stages to producing knockout mice and the first stage Has four steps, which I'll talk about First you engineer copies of the gene in the test tube to produce targeting vectors By inserting a neo mice and resistance gene Into the targeted gene and then engineer the vector by attaching the herpes virus Thymidine kinase gene and that's one end and Pictures help so That's the neo R and this is the HSP TK So then you use DNA calcium phosphate co precipitate to introduce vectors into cells extracted from a mouse embryo Some vectors are inserted into the target site that the homologous chromosome by homologous recombination The neo R gene carried by the vector is successfully inserted into the target gene and Inactivates it which amounts to knocking it out Other vectors may be either randomly incorporated into some chromosomes So that the chromosomes contain the neo R gene and the HSP TK gene or not inserted into any chromosomes so Then you use two kinds of drugs to make a positive negative selection So the first kind of drug basically kills anything that does not carry the neo R gene and the second kind of drug kills the cells that contain the HSP TK gene and Then after you conduct the procedure only the cells containing the neo R gene inserted by homologous recombination survive and proliferate so this is basically what happens with Gene knockout right back on to is knocked out and replaced by the neo R gene So the neo R gene Interrupts the target and gene in the homologous chromosome and inactivates the gene It also serves as a marker to indicate the cells that successfully recombine the sequences at the target locus The HSB TK gene marks serves as a marker to indicate the cells that ran Okay, so we've been talking about cells How do you alter the genome of living mice? This is the backstage You select the targeted gene in the genome of embryonic stealth stem cells obtained from a mouse embryo and introduce an engineered vector into ES cells You inject the ES cells containing the modified gene into embryos in the blastocyst stage inject the embryos into surrogate mothers to reproduce mice and then crossmate the mice and You get your knockout mice and you can observe some of the features in the normal state Disappear when the genes responsible for those features have been knocked out. So the third method gene knock Is where you introduce an exogenous gene to the target locus of the genome of some organism The main difference between knockout and knock in concerns the engineering of the vector that carries targeting gene So you have complementary DNA An exogenous gene for example complementary DNA a marker used to indicate the complementary DNA P a sequence and then the me or gene which is again used to indicate that the vector is Successfully inserted at the target locus So again in terms of pictures Right, we have the complementary DNA and P a sequence the me or gene and then the HSB TK gene as before and Again that HSB TK gene is used to indicate the cells that randomly incorporate the vector So same as the knockout method Okay, and how does gene knock in different from transgenesis? With gene knock in an exogenous gene can be precisely inserted into a targeted locus Rather than a random locus as a transgenesis by employing the mechanism of homologous recombinations and unlike transgenesis Gene knock in Contract the knocked in gene in the experimenting process through an associated indicator So going back to the skeptical doubts about transgenesis You might ask, okay, how do you know or warm that the genomes of experiment of mice have been adequately intervened How do you know that the transfer genes have been incorporated in the genome of cells of the experiment of animals? And the method of knock-in can provide some answers to these skeptical doubts So you can track the locus of the knocked in gene by means of engineering of the vector used to introduce an exogenous gene Gene like me or art is used as a tracking marker to discern the ES cells that contain the knocked in gene from those that don't and the design of a trackable marker Strengthens the warrant for belief in the causal reality of the knocked in gene and the causal relationship between that gene and the phenotypic so going back to the knockout method We can also use some additional causal conditions To support the argument. So we have a causation condition If X were not to occur that why would not occur? Regularity condition why regularly occurs when X occurs and then putting these things together We can say X is the cause of why if basically both of those conditions are satisfied and By breaking the structural integrity of the gene in the original genome So as to make a mutation on the gene we satisfied this right when you knock the gene out You can satisfy this condition. You can show what happens if X were not to occur And then we warrant the causal relationship between a knocked out gene and the feature and mice that the gene is Responsible for by observing that the feature disappears in the knockout mice And we can also apply CADM to knocked out genes So in this case Knocked out gene is the actual cause of the difference the phenotypic feature that disappears when you knock it out and then the experiment mice Plug in for why and based on the satisfaction of CADM. We can say that knocking out the gene X is the actual cause of the disappearance of the phenotypic features okay comparison with other views I Should say The last like four slides are my contribution So really did like basically everything up to this point and I Tried to situate this within the realism debate by kind of comparing some other views so I'll compare it with three sorts of views. So there's a hacking manipulation argument for the reality of entities and then inference to the most probable cause as Proposed by Cartwright and developed further by Clark and then this idea of causal warren from Suarez So here's a quote from Hacking's book Experimental work provides the strongest evidence for scientific realism. This is not because we test hypotheses about entities It's because entities that in principle cannot be observed are regularly manipulated to produce a new phenomena And to investigate other aspects of nature. They are tools instruments not for thinking But for doing and so I mean there's a lot of this that that we agree with but I guess the point that we Would disagree about is whether manipulation on its own is enough we think not and I Think there are plausible counter examples to this. So Hasak Chang has talked about Experimental work in you know late 18th early 19th century Chemistry and physics where it's arguable that you know, you're manipulating caloric or manipulating logista so In order to rule out those kinds of cases We'd like to add something more than manipulation. So Manipulation is one condition of experimental individuation, but if you add maintenance of structural unity and separation I Think you can get rid of these potential counter examples And then we've also added the causal criteria that we introduced earlier Okay Inference to the most probable cause is another sort of similar view Basically you infer the reality of a cause from its effect and a non redundant causal explanation So non redundant means there's no alternative causal explanation that's incompatible with the proposed explanation and At least it's good or better And then the idea of causal war the idea is that inferences to the best explanation that satisfies certain criteria Generate causal warra the explanation must be non redundant Empirically adequate causal explanation and the inference must be a material inference rather than a formal inference so this has to do with the properties that you would Change when you're you know doing things like interventions and stuff like that there has to be a well-defined property and A way to understand how it could change and so on so I think a big difference between These sorts of views in our view is that they ground the reality of entities in causal explanatory considerations and One of the reasons you avoid doing this sort of thing is it's not gonna Persuade Anti-realists who are generally skeptical about appeals to causal explanatory relations or considerations to ground realism Our view grounds the causal reality of genes and experiments that satisfy certain conditions for example Experimental individuation causal criteria manipulation intervention Another difference here their views focus primarily on demonstrating the reality of entities And we've tried to do something a bit more than that since we've also Tried to demonstrate the reality of causal connections and this idea that Demonstrating the reality of entities and demonstrating the causal connections is something interdependent Okay, thank you This is joint work as you know if you have questions for us Please feel free to email us You have any questions about genetics? But yeah, thank you Yes, thanks. I very much like The separation criteria and I think I think that's an important one But I wonder if it's also not itself subject to doubt whether you have really separated an entity I mean take take the example of the prions for example, which cause certain diseases such as Kreuzfeld-Jakob or ESE I If I have their history right, but it was very difficult to prove that there was no nucleic acid Responsible for the transmission of the disease. So how can you make sure that you have no? Nucleic acid in your sample in an experiment that was designed to isolate or separate prions from From the place it yeah, good. I will talk to Ray Lin about that case But yeah, that's that's a good case to that for us to consider. Thanks a lot Yes Sure, okay Thank you very much really interesting, and I'm I know a few of us here recently just read Chang's New book. Oh cool. I'm gonna be talking about it tomorrow. So this tells me very beautifully And so I want to ask Yeah, I want to first ask you to expand a bit on what separates your account You mentioned the introduction of the separation criteria and how this Distinguishes your account from somebody like Chang's realism for realistic but then I also want to You know, maybe just accountants a Responsible his behalf the CB think namely his his Account allows us to do something like this. We can say well look Reality realism actually comes in degrees So something like just on Was for some time crucial to operationally go here into practice So if you just on this real now oxygen realer, right? It's more real because it's central to More operationally coherent practices or whatever it's superseded Yeah But so that's that's Just yeah, if you want to respond to that sort of line of argument from from Chang. Yeah. Yeah good so Maybe I should start off by saying like house on check is one of my favorite You know, we just read his new book last semester too, so I love this question and Yeah, as far as like what separates our account from his account I think a lot of people their reaction to his realism for realistic people is probably that it's not actually realism so You know, I think I understand what he's trying to do and I think I understand why he wants it to call it realism because he thinks that You know traditional kind of realism is just not gonna work at all So why not just take the name realism and apply it to something that is going to work which is his proposal and I think what we're trying to do and I don't know if we're gonna be successful or not is try to get something more like the traditional realism than you know Something that's not like the kind of pragmatist view that the Chang offers And I think Chang's response to us would probably be like you guys are trying to do something that's impossible and Our response I guess would be We're gonna keep trying What what he might say right is that you can't escape The the mind framing of the concepts that you're calling real. Yeah, so genes are Concepts that are framed by human experience and interaction with the world And so it's gonna prevent you from you can talk about you know, how useful those concepts are in practice But can you access? Yeah, yeah, yeah, so I really like what he has to say about mind framing and I'm kind of Sympathetic to the idea that like there's no escape from mind framing. Yeah, so Yeah, I think Rayleigh and I need to talk more about this and figure out like what do we say against Chang and then yeah, this is Directly relevant to like what some of the stuff I want to do within the realism debate coming up, too So I hope someday I will have a way to answer your questions Like the fact that a philosopher of science was just reinventing It's completely new well, you like to be fair to him That's a general comment He says that in the book I became a bit of a physician because I was unable to live with philosopher of science reinventing the wheel every time But okay, back to the primes Back to the primes. We are ready to your answer. Yeah Semi-version is one of the three conditions for reality You separate the S-prime is in my mind Then you might demonstrate it's reality However, if you cannot separate the S-prime is in my mind Then you cannot stay. It is not real Right, yeah, so so is it some kind of an inductive argument or an Ibe type argument that you infer well with with we've done so much to try to separate them There's no no I mean So you sort of induce on the failures to to separate them and you conclude therefore there is no such contamination or So I know what we want to say we want to say that it's not based on I be okay And it's not based. It's not supposed to be based on induction. Okay. It's supposed to be based on Experimental results, but then there's the question like how do you know from the results that you've actually done it or not and I guess one of the things that I was thinking to I don't know if Rayland would agree with this or not but maybe there's some interdependency like among the three conditions, so like For example separation and maintenance of structural unity, right and if you see like For example the same function being expressed or you know, if there's some kind of other If you have some evidence that like you haven't broken it Maybe that's also evidence that you've separated it from something else. Okay, I need to think more about that So I guess I only have one trip So I'm going to go back to I'll go I'll try to go back to Yuriyushikora's distinction between methodology and methods here which it seems to me that your your and Rayland's discussion of individuation is a methodological precept to say that in order to do my science I need to Individuate and then the methods come when when they talk about methods. They're talking about How do we individually? How do we establish the criteria by demonstrating? So It's when you look at it that way you've stepped back from the realism as such Which strikes me as being much harder to do just from Going to talking about methods and methodology does that I don't this is not phrases a question But I just wanted to point out that there is a way of talking about the exact things that you talked about absent quite far away from the realism and And that there I There might need to be some more work here to say to connect these two Areas of the philosophy science I Yeah, so I guess is another way to put the point like the idea of using Experimental individuation as some kind of criterion for reality like within the realism debate there's kind of Some kind of gap there that needs to be bridged in some way Yes, okay. Yeah, I got it Um Yeah, good. So that's that's another thing that we'll have to think about. Yeah, thank you You have one trick and I have zero Taiwan read French, but there's a nice book of French philosopher that is exactly depending the reverse of your position It's it builds a complete books explaining that experimental data is a it's just a higher source of authority That's it. You don't think about real not real It's a higher level of authority in scientific discussion. Oh, this is the essence of Realities just authority more dirty there less authority there And it's applied to imagery and all kind of stuff It's a nice book, but that's only in French. I don't know why did not publish it in the kitchen Yeah, I'll get the wrap that's that's the enemy. Yeah That's the exact reverse. Wow Cool, I don't know. Yeah, we will translate me He knows really good Other questions comments We have a very short Well, I just wanted to say I mean, I was really interested in this exchange And I'm just wondering what happens if you just say response. Look the way they bridge those two fields just I'm radically empiricist by metaphysics Who is the red key in person? Okay, so so the question is how do we get from experimental and emituation to the realism at real estate? So, what if the response then is just What's real? It's what I what's real is what I can do science It is that is that British the Gabbard is there's something more needed Sounds good to me For you Okay, so but I'm just one person I know lots of people care I think you care and I think there's just There's like a step or a step and a half Yeah, yeah So let's thank you