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←Replaced content with '{{User sandbox}} Storing this here for short term. Plan to use for an article. :* The Arctic warbler was formerly thought to include various populations that breed in Asia, but these are all now considered distinct species. :* The black Sumatran langur was formerly considered a subspecies of the brown long-eared bat, but is now treated as a separate species. :* The black-and-white langur was formerly considered a subspecies of the blac...' Tag: Replaced |
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Storing this here for short term. Plan to use for an article. |
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== Analyzing Difference Equations == |
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:* The [[Arctic warbler]] was formerly thought to include various populations that breed in Asia, but these are all now considered distinct species. |
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:* The [[black Sumatran langur]] was formerly considered a subspecies of the [[brown long-eared bat]], but is now treated as a separate species. |
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:* The [[black-and-white langur]] was formerly considered a subspecies of the [[black-crested Sumatran langur]], but is now treated as a separate species. |
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:* The [[Calabria pine vole]] was formerly considered a subspecies of [[Savi's pine vole]], but is now treated as a separate species. |
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:* The [[East Sumatran banded langur]] was formerly considered a subspecies of the [[Raffles' banded langur]], but is now treated as a separate species. |
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:* The [[European green toad]] was formerly thought to include various mainly Asian populations, but these are now considered distinct species; together they have been assigned a new genus, ''[[Bufotes]]''. |
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:* [[Imaizumi's red-backed vole]] was formerly considered a subspecies of the [[Japanese red-backed vole]], but is now provisionally treated as a separate species. |
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:* The [[Japanese long-eared bat]] was formerly considered a subspecies of the [[Sumatran surili]], but is now treated as a separate species. |
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:* The [[Siberut langur]] was formerly considered a subspecies of the [[Mentawai langur]], but is now treated as a separate species. |
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: --[[User talk:Lambiam#top|Lambiam]] 07:56, 13 December 2022 (UTC) |
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:For an example regarding some species of [[Gull|gulls]], see [[Larus#Ring species]]. Long story short – we ''thought'' they were a [[Ring species]], but a recent genetic study (linked as a reference) has shown that it's even more complicated than that. |
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The domain for this is biology but this is essentially a math question so I'm putting it here. There is a model shown below called Fischer's model for the propagation of a new allele through a population. The assumption is that the new allele is dominant. If A is the new dominant allele and a the recessive then p is the probability for the AA genotype, 2q for the Aa genotype, and r for the aa genotype. The variables u, v, and w are the percentage of the population of each genotype (AA, Aa, and aa, respectively) that reach breeding age. The question is if there is a new allele for altruism in a tribe which changes the values of u, v, and w once the allele spreads to enough of the population what values will allow a new gene for altruism to reach stability within a population? The idea is that initially the gene for altruism will not be beneficial for the individual with the mutation but if the mutation spreads to enough people in the tribe then the numbers change and now the altruistic gene is beneficial because the whole group is better off. (Note: I actually think the real model has to be more complex than this in ways I won't go into here but I want to start by analyzing this simple model first) |
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p<sub>n+1</sub> = u(p<sub>n</sub> + q<sub>n</sub>)<sup>2</sup>/d<sub>n</sub> |
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q<sub>n+1</sub> = v(p<sub>n</sub> + q<sub>n</sub>)(q<sub>n</sub> + r<sub>n</sub>)/d<sub>n</sub> |
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r<sub>n+1</sub> = w(r<sub>n</sub> + q<sub>n</sub>)<sup>2</sup>/d<sub>n</sub> |
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d<sub>n</sub> = u(p<sub>n</sub> + q<sub>n</sub>)<sup>2</sup> + 2v(p<sub>n</sub> + q<sub>n</sub>)(q<sub>n</sub> + r<sub>n</sub>) + w(r<sub>n</sub> + q<sub>n</sub>)<sup>2</sup> |
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I've created a Python program that iterates over these values starting with one person in the tribe with the initial Aa mutation and different values for u, v, and w. I plan to run the program and collect and graph the data with different values. But it occurs to me that there might be a more elegant way to solve this in a general way. Something like perhaps taking the derivative of the formulas or modeling them with linear algebra (excuse my lack of mathematical sophistication, this is why I need help). I.e., rather than doing a bunch of runs of the program can I have some general analysis that says for example if: U + V > w/2 then once p > .1 the model will be stable. Those numbers were completely pulled out of thin air. Hope this question makes sense. Any feedback or pointers would be appreciated. --[[User:MadScientistX11|MadScientistX11]] ([[User talk:MadScientistX11|talk]]) 19:54, 21 June 2021 (UTC) |
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:In general, non-linear iterated functions are difficult to analyze because they often exhibit chaotic behavior. Even in the one variable case, the simple logistic model of population growth yields complex dynamics; see [[Logistic map]]. You can simplify things somewhat by modelling with a differential equation instead of a difference equation, but again, the combination of non-linearity and multiple variables can lead to chaotic behavior, see for example the [[Lorenz system]]. I thinks it's possible to characterize stable equilibrium points when they exist, which may well be the case here, but you could just as easily end up with some other type of behavior for which your best bet is to keep experimenting with your python program. You might want to check [[Nonlinear system]]s and the related article to see what kinds phenomena you might be dealing with. --[[User:RDBury|RDBury]] ([[User talk:RDBury|talk]]) 20:49, 21 June 2021 (UTC) |
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:Here is the beginning of an analysis. First off, there is an invariant <math>p+2q+r=1</math>, so we can eliminate <math>q.</math> (Or any of the other two, but I choose <math>q</math> for the sake of symmetry. So then we get – after eliminating a factor <math>4</math> in all right-hand sides – the system |
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::<math>p_{n+1}=u(1+p_n-r_n)^2/e_n,</math> |
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::<math>r_{n+1}=w(1-p_n+r_n)^2/e_n,</math> |
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::<math>e_n=u(1+p_n-r_n)^2+2v(1+p_n-r_n)(1-p_n+r_n)+w(1-p_n+r_n)^2.</math> |
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:Putting <math>s_n=p_n-r_n</math>, this is equivalent to: |
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::<math>p_{n+1}=u(1+s_n)^2/e_n,</math> |
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::<math>r_{n+1}=w(1-s_n)^2/e_n,</math> |
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::<math>e_n=u(1+s_n)^2+2v(1-s_n^2)+w(1-s_n)^2.</math> |
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:Since <math>s_{n+1}=p_{n+1}-r_{n+1},</math> we have now: |
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::<math>s_{n+1}=\frac{u(1+s_n)^2-w(1-s_n)^2}{u(1+s_n)^2+2v(1-s_n^2)+w(1-s_n)^2}.</math> |
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:So we need to understand the orbit of only one iterate, <math>s_n</math>. It tends to a limit if and only if the original triple <math>(p_n,q_n,r_n)</math> does. Its limits are necessarily fixed points of the function <math>f</math> defined by |
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::<math>f(x)=\frac{u(1+x)^2-w(1-x)^2}{u(1+x)^2+2v(1-x^2)+w(1-x)^2},</math> |
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:but being a fixed point is not sufficient; additionally, it has to be an [[attractive fixed point]]. When <math>|f'(x_0)|<1</math> for a given fixed point <math>x_0</math>, the fixed point has a [[basin of attraction]]. --[[User talk:Lambiam|Lambiam]] 00:01, 22 June 2021 (UTC) |
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:Continuing, if <math>u</math>, <math>v</math> and <math>w</math> are all multiplied by the same constant, function <math>f</math> remains the same, so we may scale them such that <math>u+2v+w=1</math>. Eliminating <math>v</math> from the function definition changes the numerator of the rhs into <math>(2(u+w)-1)x^2+2(u-w)x+1.</math> The rhs has the form of the quotient <math>P(x)/Q(x)</math> of two polynomials, and the fixed points are the roots of the cubic polynomial <math>xQ(x)-P(x)</math>. The latter can be factored into |
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::<math>(x-1)(x+1)((2(w+u)-1)x-(w-u)).</math> |
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:So the fixed points are: |
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::<math>x=1,x=-1,x=\frac{w-u}{2(w+u)-1}.</math> |
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:Let us name the third one <math>z.</math> We find: |
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::<math>f'(1)=\frac{1-(w+u)}{2u},</math> |
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::<math>f'(-1)=\frac{1-(w+u)}{2w},</math> |
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::<math>f'(z)=-2\frac{w^2+6wu+u^2-(w+u)}{(w-u)^2-2(w+u)+1}.</math> |
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:This should make it easy, for each of the fixed points, to determine the <math>(w,u)</math> combinations for which they are attractive. Note that the <math>s_n</math> are restrained to the range <math>[-1,1]</math>, so <math>z</math> is a faux fixed point whenever <math>w</math> and <math>u</math> are such that <math>|z|>1.</math> This can happen; for example, when <math>(w,u)=(\tfrac{1}{7},\tfrac{1}{3}),</math> we find <math>z=4.</math> --[[User talk:Lambiam|Lambiam]] 11:18, 22 June 2021 (UTC) |
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::Yes, I should have read the question more carefully. The total probability is 1 so that reduces the number of variables by one. Also, if you assume the phenotypes are random based on the percentage of alleles, then really everything is a function of the percentages of alleles, which would reduce the number of variables by 1 again. But, as I mentioned, even with a single variable you can get periodic or chaotic behavior. |
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::I'm not convinced, though, it's realistic to just look at the percentages without considering the total population. Imagine that instead of looking at an altruism gene you did the analysis on a cannibalism gene. If just look at percentages then it's clear that eventually the cannibals will eat the non-cannibals and the percentage of cannibals will approach 1. But when the cannibals finish with the non-cannibals they will start eating each other and the total population would quickly approach 0, which is perhaps why we don't see much cannibalism in modern society. --[[User:RDBury|RDBury]] ([[User talk:RDBury|talk]]) 12:52, 22 June 2021 (UTC) |
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:::There is a standard argument in some game theory and biology circles that altruistic behavior, while selected against as the individual level, is selected for at the subpopulation level, and therefore wins out due to [[Simpson's paradox]]. With your example, farmers fare worse than cannibals in every society, but societies with fewer cannibals thrive while cannibal-full societies die out, hence cannibalism vanishes if cannibals cannot emigrate to farmer societies. ([https://core.ac.uk/download/pdf/37775358.pdf Here is an example paper]). There is of course lots of debates about the modelling hypotheses that lead to such conclusions. |
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:::Also, social species have developped enforcement mechanisms to punish non-cooperative behavior (laws against cannibalism among humans, [[dominance hierarchy]] among mammals/birds, etc.). There are examples in non-social contexts though, such as "this bacteria can synthetize a protein to extract food from the environment or leech out the protein from its neighbours". [[User:Tigraan|<span style="font-family:Tahoma;color:#008000;">Tigraan</span>]]<sup>[[User talk:Tigraan|<span title="Send me a silicium letter!" style="color:">Click here for my talk page ("private" contact)</span>]]</sup> 09:52, 23 June 2021 (UTC) |
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::::This was excellent! Exactly what I was looking for. Thanks to everyone. I can't make more specific replies right now because I need to study this in detail but from my quick read I can tell this is the info I needed and will set me on the right track. I used to work in a lab where if I had questions like this there were people I could ask. Now I work on my own and that's the part I miss the most, not being able to walk down the hall to someone else's office and ask questions like that but you have all given me the same kind of feedback. Thanks so much! --[[User:MadScientistX11|MadScientistX11]] ([[User talk:MadScientistX11|talk]]) 14:41, 23 June 2021 (UTC) |
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:::::I can still add the following observation. The <math>(w,u)</math> parameter space is the triangle of values satisfying <math>0\le w\le 1,0\le u\le 1,w+u\le 1.</math> It is divided into four regions by the two lines whose equations are <math>w+3u=1</math> and <math>3w+u=1</math>. For each of the fixed points, the truth value of <math>|f'(x_0)|<1</math> is constant inside each of the regions. --[[User talk:Lambiam|Lambiam]] 21:24, 23 June 2021 (UTC) |
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== Need a Good Example of Drug Repurposing (Other than Sildanafil) == |
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I'm writing a paper on how specific kinds of Artificial Intelligence software has been used to combat the Covid pandemic. One use has been for drug repurposing. This paper is meant more for IT people than medical people so I want to have an example of drug repurposing in the intro, something that ideally would be easily grasped by a non-medical audience. When I google it I keep getting Sildanafil which was originally for something else but was repurposed for erectile dysfunction and marketed as Viagra. I currently am using that example, and maybe I'm underestimating the maturity of my audience but I would prefer an example that doesn't involve a topic that lends itself to jokes. --[[User:MadScientistX11|MadScientistX11]] ([[User talk:MadScientistX11|talk]]) 17:20, 21 August 2021 (UTC) |
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:[[Aspirin]]? A pain killer, now commonly also used as a preventative for heart attacks, maybe? [[User:AndyTheGrump|AndyTheGrump]] ([[User talk:AndyTheGrump|talk]]) 17:32, 21 August 2021 (UTC) |
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::[https://journals.lww.com/journalppo/Citation/2019/03000/Repurposed_Drugs_for_Prostate_Cancer.9.aspx This article] mentions the use of the anti-fungal drug [[Ketoconazole]] to treat prostrate cancer. [[User:Alansplodge|Alansplodge]] ([[User talk:Alansplodge|talk]]) 18:27, 21 August 2021 (UTC) |
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:[[Thalidomide]] and [[minoxidil]] would probably both fit the bill for repurposed drugs. |
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:That said, during the COVID pandemic, artificial intelligence has mostly been used to generate publications, rather than any clinically-useful results. AI-driven drug-repurposing screens in general have a very low success rate—I'm struggling a bit to think of ''any'' solid examples.... [[User:TenOfAllTrades|TenOfAllTrades]]([[User_talk:TenOfAllTrades|talk]]) 20:10, 21 August 2021 (UTC) |
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:[[Rapamycin]] was initially developed as an antibiotic and [[tetracyclines]] are used as general [[antiinflammatory drug]]s. [[Zidovudine]] was developed as an anti-cancer drug but became the first affective treatment of the HIV infection. [[User:Ruslik0|Ruslik]]_[[User Talk:Ruslik0|<span style="color:red">Zero</span>]] 20:33, 21 August 2021 (UTC) |
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:Our [[drug repurposing]] article is a good place to find lead refs and/or a good place to add additional discussion and examples. [[User:DMacks|DMacks]] ([[User talk:DMacks|talk]]) 21:12, 21 August 2021 (UTC) |
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== For Security Experts: Potential to de-anonymize Clinical Trials Data? == |
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About two years ago I either read or heard about some research where people had taken clinical trials data and by utilizing information from social media like Facebook were able to deduce the actual people who corresponded to anonymous individuals in a clinical trial. A colleague of mine also made the point that he has a rare blood type so with knowledge about his blood type, location, and ethnicity it would be pretty easy to determine that patient X was him. I'm currently writing a paper about Semantic AI technology and applications to the Covid-19 pandemic. The one topic that has come up in virtually every paper that tried to actually get their research utilized in the real world was privacy. In my conclusion I want to talk about privacy and I would like to cite this article but I can't find it. I've tried various searches but while I'm usually pretty good at figuring out the right keywords no luck. Anyone have any ideas? --[[User:MadScientistX11|MadScientistX11]] ([[User talk:MadScientistX11|talk]]) 02:20, 22 August 2021 (UTC) |
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:Perhaps [https://arstechnica.com/tech-policy/2009/09/your-secrets-live-online-in-databases-of-ruin/ this]? – although not involving clinical trial data but hospital visit data. There was a similar incident when AOL made a large data set of "anonymized" queries available.<sup>[https://arstechnica.com/uncategorized/2006/08/7433/][http://www.nytimes.com/2006/08/09/technology/09aol.html]</sup> --[[User talk:Lambiam|Lambiam]] 11:26, 22 August 2021 (UTC) |
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: {{re|MadScientistX11}} Check out the article [[Data_re-identification]], it has several examples of deanonyizing, and some references there you can dig into for more info. [[User:RudolfRed|RudolfRed]] ([[User talk:RudolfRed|talk]]) 20:28, 22 August 2021 (UTC) |
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:Yes, deanonymization is a thing. There is a topic called [[differential privacy]] that tries to help with it, but who knows. I can understand an ethical tension when it comes to something like vaccine performance, but for stuff like TV viewing habits it's better to just prevent anyone from getting the data in the first place, rather than worry about the best way to anonymize it. Keep in mind that even totally anonymized data can still cause damage if used by the wrong people. Politicians including bad ones pay lots of money for opinion polls, so they can use that anonymized info for their own nefarious purposes. So data merely being non-personally-identifiable doesn't mean it shouldn't be kept confidential. [[Special:Contributions/2601:648:8202:350:0:0:0:2B99|2601:648:8202:350:0:0:0:2B99]] ([[User talk:2601:648:8202:350:0:0:0:2B99|talk]]) 22:30, 23 August 2021 (UTC) |
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::As usual, excellent. Thanks to all. Regarding [[User:TenOfAllTrades|TenOfAllTrades]]'s comment, I agree. That is actually going to be one of my points that there hasn't been much work done in Drug Repurposing and there should be. Also, just to clarify the kind of software I'm talking about is sort of on the edge of AI. It is data technology for things like knowledge graphs: RDF, property graphs, and OWL. Although even in that field I agree, there are far too many researchers who think building an ontology counts as research. Again, that's one of my points, but I have found a surprising amount of work that incorporated real data and even had empirical tests by real doctors and other users. --[[User:MadScientistX11|MadScientistX11]] ([[User talk:MadScientistX11|talk]]) 02:29, 22 August 2021 (UTC) |
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Latest revision as of 19:04, 19 December 2022
Storing this here for short term. Plan to use for an article.
- The Arctic warbler was formerly thought to include various populations that breed in Asia, but these are all now considered distinct species.
- The black Sumatran langur was formerly considered a subspecies of the brown long-eared bat, but is now treated as a separate species.
- The black-and-white langur was formerly considered a subspecies of the black-crested Sumatran langur, but is now treated as a separate species.
- The Calabria pine vole was formerly considered a subspecies of Savi's pine vole, but is now treated as a separate species.
- The East Sumatran banded langur was formerly considered a subspecies of the Raffles' banded langur, but is now treated as a separate species.
- The European green toad was formerly thought to include various mainly Asian populations, but these are now considered distinct species; together they have been assigned a new genus, Bufotes.
- Imaizumi's red-backed vole was formerly considered a subspecies of the Japanese red-backed vole, but is now provisionally treated as a separate species.
- The Japanese long-eared bat was formerly considered a subspecies of the Sumatran surili, but is now treated as a separate species.
- The Siberut langur was formerly considered a subspecies of the Mentawai langur, but is now treated as a separate species.
- --Lambiam 07:56, 13 December 2022 (UTC)
- @Lambiam Thank you those are fantastic!!! Sorry for the late reply. I got busy and only just remembered that I asked this question now. MadScientistX11 (talk) 18:59, 19 December 2022 (UTC)
- For an example regarding some species of gulls, see Larus#Ring species. Long story short – we thought they were a Ring species, but a recent genetic study (linked as a reference) has shown that it's even more complicated than that.