tag:blogger.com,1999:blog-1812431336777691886.post3496910246843282163..comments2024-02-29T03:57:00.088-05:00Comments on The Mermaid's Tale: Faith in science? Industrialized agriculture and antibiotic resistanceAnne Buchananhttp://www.blogger.com/profile/09212151396672651221noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-1812431336777691886.post-24801146936432213842014-09-23T14:04:15.382-04:002014-09-23T14:04:15.382-04:00Thanks, Alex. I like the idea that the point is t...Thanks, Alex. I like the idea that the point is to make decisions about changing one's view. Or at least re-evaluating. And I like the idea of crowd sourcing truths. Anne Buchananhttps://www.blogger.com/profile/09212151396672651221noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-39310325469805896432014-09-23T13:58:28.445-04:002014-09-23T13:58:28.445-04:00Reply to Alex
I'm no expert but in the course ...Reply to Alex<br />I'm no expert but in the course of a career in genetics and evolution of course have come across or collaborated with people using Bayesian approaches. I agree with your comment and tomorrow will venture (hopefully not too far off base) my own view of how this applies to the idea of 'revolutions'.<br /><br />Earlier in my career, the big debate was between frequentists and likelihood advocates, and more recently Bayesian methods have gained fashion. Likelihood advocates, at the time at least, stressed that a likelihood ratio was just a comparison of two notions, not a test of truth.<br /><br />What I know of Bayesian approaches comes (as I cite tomorrow) from Jaynes' book. There is also Pearl's book Causality, but to me what I say tomorrow is relevant to that point of view.<br /><br />Basically, and I think we'd agree, if you have a well-posed question and its numerically evaluable and involves sampling etc., Bayes gives a good way to go--and no illusions about 'truth'.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-77913453632741918162014-09-23T13:22:04.776-04:002014-09-23T13:22:04.776-04:00Anne,
The point, as I see it, of Baysian statisti...Anne,<br /><br />The point, as I see it, of Baysian statistics is that by adopting an explicit prior we gain a lot of utility for reasoning about how much evidence we need to <i>change</i> our beliefs. And we can treat the process as iterative.<br /><br />A nefarious or utterly pig-headed bayesian can load the dice at the point of prior selection but that is explicit and open to critique. Anyone reviewing the conclusions can choose different (much more reasonable) priors and re-run an analysis to see <i>in quantitative terms</i>, what the data should lead them to conclude (or put another way - what the data should lead them to change about their beliefs.)<br /><br />I have enjoyed thinking about this stuff in light of the work (and frank advocacy) of Bayesian reasoning by John Kruschke. <br /><br />See http://www.indiana.edu/~kruschke/BEST/ <br /><br />and the article <br /><br />http://www.indiana.edu/~kruschke/articles/Kruschke2012JEPG.pdfAlex Stoddardhttps://www.blogger.com/profile/00700602554438046007noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-26207120712036439032014-09-22T17:29:44.180-04:002014-09-22T17:29:44.180-04:00Alex,
I'm not schooled in Bayesian statistics...Alex,<br /><br />I'm not schooled in Bayesian statistics, so here's a simple-minded question: why do we need statistics at all if we load the dice, so to speak, in favor of the answer we believe we should get?<br /><br /> Anne Buchananhttps://www.blogger.com/profile/09212151396672651221noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-91481118818627942102014-09-22T12:56:03.689-04:002014-09-22T12:56:03.689-04:00I think Anne was speaking figuratively about '...I think Anne was speaking figuratively about 'equal' in that one has no basis for preference of one over another (of course she may answer separately about this). <br /><br />It's true that the Bayesian approach is designed to 'disequify' hypotheses. Here the question (I think) is what the basis is for establishing the alternatives as priors for which one can establish a credible value, or the extent to which new data can adjudicate among very different hypotheses. In well-behaved situations, like coin-flipping, it's relatively clear. And this has been true in many areas of science, certainly, and whole theories of causality.<br /><br />We have a couple of posts upcoming on the relevance of this to scientific revolutions, but that's a somewhat different subject.<br /><br />This post was not about the Bayesian debate, but about more elusive and harder to evaluate explanations, I think.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-74977017074576215712014-09-22T12:10:04.816-04:002014-09-22T12:10:04.816-04:00In reply to Anne Buchanan,
I content all priors ...In reply to Anne Buchanan, <br /><br />I content all priors absolutely are not equal. That is why it is to the benefit of scientific reasoning to force there declaration and review.<br /><br />It is true that I may arbitrarily change the conclusion arrived at from the identical set of data by an arbitrary choice of prior (either its "shape" or its "strength"). However when I have done so my prior is stated and open to evaluation and criticism. <br /><br />What the prior is doing is encoding my initial belief along with how strong the evidence needs to be for me to change my belief. <br /><br />Often in practice one may choose a very non-committal and weak prior but it ain't necessarily so. See http://xkcd.com/1132/ Alex Stoddardhttps://www.blogger.com/profile/00700602554438046007noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-30241191704532841162014-09-21T19:17:42.932-04:002014-09-21T19:17:42.932-04:00Manoj,
But, you're looking at the history of ...Manoj,<br /><br />But, you're looking at the history of belief about mitochondria with the benefit of hindsight. We can dismiss earlier ideas as naive, and wrong, because we know better now. But what we don't know, and can't know, is whether what we now consider to be true will be overturned at a later date. It's possible that future scientists will consider us naive to have believed what we now believe. Knowledge about epigenetics has overturned some of what we thought we knew about gene expression, discovering miRNA expanded our knowledge of gene expression, etc. Increasing knowledge _has_ to mean that some of what we think is true now won't be true in the future. For me, that makes it difficult to disentangle 'belief' from 'knowledge.'Anne Buchananhttps://www.blogger.com/profile/09212151396672651221noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-8628377201597175962014-09-21T18:42:09.312-04:002014-09-21T18:42:09.312-04:00I think it is a mix. Religions often have a belie...I think it is a mix. Religions often have a belief in what is taken to be an unchanging truth (a 'received wisdom', or sacred text). Science has theories in which sometimes a comparably strong belief rests, but it can be titrated by facts. There are possibilities of change (of course, religions also produce sects), but consensus is one of many criteria for what is accepted. The sociocultural aspect has to do to a great extent with funding, jobs, and so on. So there are differences, I think, but there are also similarities. <br /><br />And we have no rigorous criteria for inference; instead we have a set of things we use in ways a consensus accepts; these can change.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-11888041420686505012014-09-20T12:07:42.490-04:002014-09-20T12:07:42.490-04:00"Someone asked me the other day on Twitter wh..."Someone asked me the other day on Twitter whether I thought that the words "science" and "belief" were compatible."<br /><br />Let's see. In 1960s, scientists believed that all eukaryotic organelles evolved through slow modifications, when Lynn Margulis hypothesized that mitochondria and chloroplast were symbiotic bacteria. A decade later, DNA evidence showed that mitochondria and chloroplast have own chromosomes. Margulis also hypothesized that eukaryotic cilia came from outside.<br /><br />"mitochondria originated inside cell through slow evolutionary process" - belief<br /><br />"mitochondria came from outside" - strong hypothesis in 1970, based on microscopic data<br /><br />"presence of genome show mitochondria were independent bacteria" - strong hypothesis, starting a new belief system<br /><br />"cilia was another bacteria - (spirochete)" - belief/weak hypothesis<br /><br />"earth is alive as in gaia" - belief/weak hypothesis<br /><br />I think scientists can believe in anything, but that belief part should not be treated as science. Here is the real problem. When science turns into 'scientific consensus' in a democratic system, the beliefs of many naive people turn into scientific fact. <br /><br />Manoj<br /><br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-14571630770111044572014-09-19T16:43:35.381-04:002014-09-19T16:43:35.381-04:00Reply to discussion
I think I'll draft a post...Reply to discussion<br /><br />I think I'll draft a post, maybe for Monday, about scientific revolutions. On thinking about it, I don't think I agree after all that 'revolutions' are changes in priors; at least to me that that isn't their major feature. I think that most real 'revolutions' (or 'paradigm shifts') are something else, and I'll try to say what I'm thinking when there's more space--to see if it's cogent or not.<br /><br />Even without toss-up priors, I agree that this doesn't seem to get us closer to knowing what 'truth' is, without the very strong prior, that this whole enterprise of science gets us there (and that there is one, objective truth). But that now gets us into philosophy....Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-77515835121222800382014-09-19T16:25:50.814-04:002014-09-19T16:25:50.814-04:00I like your description of revolutions in science,...I like your description of revolutions in science, one prior replacing another. But if all priors are equal, in effect, this doesn't answer the question of how we know if we have found a 'truth', does it? Anne Buchananhttps://www.blogger.com/profile/09212151396672651221noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-76369609502621880422014-09-19T16:17:42.643-04:002014-09-19T16:17:42.643-04:00Reply
That makes sense, and if we had to make our ...Reply<br />That makes sense, and if we had to make our priors explicit a lot of them might seem too generic (or, one might say 'faith-based' to be of much use at least relative to the claims of knowledge that are made. But it would perhaps show people more about their thinking.<br /><br />Of course whether 'probability' is even the right way to think of one's predispositions (or, often, even of one's results) is to me a serious but deeper question.Ken Weisshttps://www.blogger.com/profile/02049713123559138421noreply@blogger.comtag:blogger.com,1999:blog-1812431336777691886.post-34924076855043556022014-09-19T15:01:08.482-04:002014-09-19T15:01:08.482-04:00I posit we are all implicitly Bayesians in any rea...I posit we are all implicitly Bayesians in any reasoning when we admit (on going) observations to the discussion. Very loosely "faith" may be taken as the strength of our belief in a prior probability. It is also entirely reasonable to critique an adopted prior. <br /><br />Many a revolution in science could be described in terms of one prior replacing another as that commonly believed by scientists.<br /><br />There may be a lot of benefit to being more explicitly Bayesian in a lot of our scientific endeavors, perhaps especially when seeking scientific support and guidance for policy. At least it would force us to get the priors out on the table where they can be reviewed by all.Alex Stoddardhttps://www.blogger.com/profile/00700602554438046007noreply@blogger.com