tag:blogger.com,1999:blog-9746467069618683562024-03-13T03:24:53.504-07:00The Accidental StatisticianMy thoughts on Education and ScienceAndyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.comBlogger260125tag:blogger.com,1999:blog-974646706961868356.post-77215174034437107492022-01-06T03:12:00.001-08:002022-01-06T03:12:28.584-08:00Google Maps and catching criminals<p>The BBC had an <a href="https://www.bbc.co.uk/news/world-europe-59884803">interesting article about a Mafia boss who was supposedly caught in Spain by being seen in a Google Maps photo</a>.</p><p>This article raises a few questions about privacy, Google and law enforcement. As well as the power of computing available to the law enforcement and security services.</p><p>There are two possibilities for how the authorities captured the mafia boss:</p><p></p><ol style="text-align: left;"><li>They managed to identify him from the Google Maps image as proposed by the article.</li><li>They actually identified him via an informant but they are using the Google Maps idea to protect their source (a credible alternative that creates plausible deniability).</li></ol><div>I have some questions about possibility 1 and some reasoning that I hope it correct and that you can follow.</div><div><ul style="text-align: left;"><li>Google censors faces and so law enforcement must have had access to the uncensored data - you cannot just say oh its an old guy wearing clothes that could be this mafia boss who escaped 10 years ago.</li><li>If that is true then are Google routinely handing over data that they collect to the authorities?</li><li>If they are then to which authorities?</li><li>Given the amount of data that Google are collecting worldwide for all of their mapping services how did they find this needle in a very large haystack?</li><li>Do they have massive storage and computing power available to fun face recognition on all of the Google Maps data to identify suspects?</li><li>Even if they have the power to run the search over all the data they will be limited on how many of these searches they can carry out.</li><li>Why was this specific criminal identified and targeted for a search?</li><li>If they were not targeted then they must have the computer resources to carry out a face recognition search from all of the outstanding criminal mugshots against all of the Google Maps data.</li><li>That is a whole scale of computing power beyond what we consider law enforcement of being capable of doing.</li><li>Those are resources only available to the security forces and still that is more than you would expect that they have.</li><li>If they are letting law enforcement use that resource then the actual power for search controlled by the security forces must be even better.</li><li>That means that they can know where EVERYONE is at any time and privacy is more than over.</li></ul><div>All of this makes it more likely that possibility 2 is the reality. The security services are good but if they were as good as this article suggests then there would never have been a January the 6th attack on the Capitol and there would be no doubt that various politicians are Putin assets. It would be impossible for Russia to infiltrate anywhere. </div></div><p></p>Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-72752342829127450042021-03-15T00:46:00.003-07:002021-03-15T00:50:34.692-07:00A Mothers Day boomer and the Demon EU<p> I phoned my mum for mothers day and the discussion moved to sending post to my son who is living in Spain. I said that I have lost one package sent to him already and I have also had one parcel from Spain rejected by a UK courier because it couldn't clear customs. I blamed Brexit. Mum being the Brexiteer that she is said it will all sort itself out "We traded with them before we were in the EU". When I suggested that this will NEVER sort itself out as we will always need this paperwork she then went on with "We never should have joined" </p><p>My blood was by now boiling and luckily we said our farewells because she is a complete fucking moron whose mindset is sending the UK back into the dark ages. The final result will be an extremist, authoritarian, facist, racist government. Am I exaggerating? I wish that I was. Check out the list of signs of fascism and you can tick off most of them in the British public and the current British government. Just check the new Policing Bill, but that is the tip of a very fascist iceberg and is evidence that the descent into a failed democracy is speeding up.</p><p>But stepping back to be a bit more reasoned does her argument make any sense? </p><p>The reason for the delays and the rejection at customs are the new forms that have to be filled in. </p><p>For example if your product contains ANY COMPONENT of animal origin then it requires a vet certificate to be imported into the EU. That is because it could have come from another country without the correct quality control and supervision and just be passing through the UK and then on to the EU. While the UK was within the EU the boundary was anything coming into the country. Now the boundaries are between the UK and the EU. This is a massive amount of paperwork. It even applies to a packet of crisps if it contains cheese powder. Basically this means nobody from the UK can take any food to the EU unless they are a commercial supplier because individuals cannot complete all that paperwork. </p><p>For commercial suppliers there is a massive burden of form filling that makes exporting much more expensive. Sure there are no tariffs or taxes but the cost in time and manpower of completing the forms makes this hidden cost enormous. Will this ever get better? Yes it will get automated and more efficient as we get more familiar but will this extra burden and paperwork always be there? Yes it will and that means extra cost.</p><p>That is why we joined. To get rid of all this paperwork and to create a simple transparent and seamless trade union. That is the entire point of the EU. That is why there are regulations on weights and measures, on quality and standards. The British Conservatives joined precisely for these reasons as it allowed their chums in business access to a bigger market. The only reason that they got in a huff when these rules were extended to cover workers rights. This is to make sure that workers are not exploited in one member country to produce goods more cheaply for the entire market. That would mean that you could have a sweat-shop nation. Business like this as labour is a major cost but at the time the EU has a pre-dominance of social democrats as premiers and so they brought in Labour protections as well as goods protections.</p><p>This meant that the Conservatives became less happy about the EU and Labour became more supportive except the far-left who never liked all this free trade thing (they think that living in a cave making your own stone-ground bread is a wonderful thing). </p><p>This shows that some of the wrinkles will be smoothed out over time but it cannot get better until we rejoin and ditch the burden of all of this unnecessary paperwork. It is certainly going to be much worse for anyone travelling to the EU as an individual until we rejoin.</p><p>What about saying that we traded before the same as the argument that musicians toured before given by that brilliant economist Roger Daltry. Try a thought experiment about transport. Before we invented cars did people travel around? Yes they certainly did. We have shells from the Mediterranean in UK archaeological sites. But do you want to go back to walking/riding from one end of the country to the other? </p><p>No I didn't think so either. Yes you could do things in the past but the reason that we joined was because that was better. Cars are better than walking and horses. We should never want to go back to something that is worse. </p><p>But that is what 52% of the voters chose in the EU referendum. They chose to ditch the car and start walking and riding again. Why did anyone do this? Well because the liars in the Leave campaign said that we could keep the car and get a turbo-charger and get the money back that we paid for the car. This is an obvious lie to anyone who thinks about it. There are no free cars and no free turbo-chargers. </p><p>What they did was disguise the lies by making it about immigration. That is a dangerous genie to use. This is what Hitler used and once you activate the hate of other you divide your country and create a very nasty place. I work a lot with immigrants or children of immigrants and they are the best people I know. I am married to an immigrant which is why my son is in Spain. To play on immigration is to play on a fundamental genetic concept of superiority of some to others. It is to embody the idea of a selfish gene. This is what keeps the Royal Family and aristocracy in place. We have special blood/genes compared to the rest of you. Implicit in this argument is that immigrants are genetically different they are lesser people. </p><p>Sorry to break it to you but as someone who works in genetics they are no different. Where they come from is an accident of geography. It was an accident that Boris Johnson was born in the US because his parents were there at the time. It was an accident that Donald Trump's great grandfather went to the US to escape conscription to the German army and so the family became established there. Immigration is meaningless, as meaningless as nationality and passports. They are inventions of wars and dictatorial governments. </p><p>There is also no reason to have any special families or to believe that inherited wealth and power does anything useful for mankind. That means that a very high inheritance tax would level out the accidents of birth and we should all be Republics.</p><p>After looking at all this reason was I right to argue with my mum on Mothers Day?</p><p>Yes completely. Because this is a fight for the soul and future of a country and by extension to humanity. If we cannot get it into our thick heads that our differences are trivial to what we have in common, then humanity has no future. We either learn to work together or we all die fighting one another. We have all the resources, knowledge and technology that we need to create a utopia but we lack the political will. </p><p>While lying politicians divide us for their own self-interest then nothing will change. When people and nations work together in unions (not perfect by far) then there can be change. </p>Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-8294642872900307542020-03-27T09:27:00.003-07:002020-03-27T09:27:24.805-07:00The hydroxy-chloroquine paper for Covid-19There has been a lot of attention given to a paper on the use of <a href="https://www.sciencedirect.com/science/article/pii/S0924857920300996" target="_blank">hydroxychloroquine as a potential treatment for Covid-19,</a> especially after it was tweeted about by US President Donald Trump. As a researcher who has worked in Malaria and also Viral Research and as someone who carries out statistical analysis I was skeptical about the paper.<br />
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I downloaded the paper and the accompanying data in order to carry out my own analysis. As many people have already pointed out the study is a <a href="https://www.sciencemag.org/news/2020/03/insane-many-scientists-lament-trump-s-embrace-risky-malaria-drugs-coronavirus?fbclid=IwAR2x2SCkMmuMtPJcarsYylVQ_dHh-dFLlLEvjq-S9ITnnla3HiqgTtBXB2Q" target="_blank">particularly poor design</a> and does not meet even its own power requirements of 48 participants. It is not a randomised trial and it introduces confounding variables such a participant age, and it is not blinded so the placebo effect is also an issue. Elizabeth Bik also pointed out that the final measure is unreliable and patients go from being negative to positive because of a dubious threshold.<br />
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My main concern is the very large number of non-determined data-points in the dataset. I copied the dataset into SPSS as a binary set replacing the significant test measures with positive and the negative test results as negative. Non-determined values were marked as missing values as were undeterminable values such as time since symptoms developed for someone who was unsymptomatic.<br />
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I then carried out the Fishers Exact Tests for those taking the hydroxychloroquine and those left untreated for days 1 to 6. I could not reproduce ANY of the reported p-values. The results from my analysis are given below, but the key point is that there is no significant effect of hydroxychloroquine on the virus except for day 6 and by then because some of the participants had experienced symptoms for up to 10 days already you would have expected them to recover from the virus anyway. I sent my results to the corresponding author. My view as an editor for another journal is that if it had been soundly peer reviewed and the quality of its statistics assessed then it would never have been published.<br />
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This does not mean that hydroxychloroquine is definitely not a potential treatment. It may prove to be a treatment in a future study but this particular study presents no evidence that it is an effective treatment for Covid-19.<br />
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D1</h3>
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<a href="https://1.bp.blogspot.com/-QjV_sy3ZPqM/Xn4o03WKo2I/AAAAAAAAHf8/OcNRA1Cz7fgfW1QAnr2d0gBaBDElqPwWQCLcBGAsYHQ/s1600/FireShot%2BCapture%2B070%2B-%2BD1.htm%2B-%2B.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="253" data-original-width="648" src="https://1.bp.blogspot.com/-QjV_sy3ZPqM/Xn4o03WKo2I/AAAAAAAAHf8/OcNRA1Cz7fgfW1QAnr2d0gBaBDElqPwWQCLcBGAsYHQ/s1600/FireShot%2BCapture%2B070%2B-%2BD1.htm%2B-%2B.png" /></a></div>
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<table aria-label="Chi-Square Tests" class="Default PivotTable" data-col-labels="Value;df;Asymptotic Significance (2-sided);Exact Sig. (2-sided);Exact Sig. (1-sided)" data-collabelheight="1" data-column-dimension="Values;" data-decimal-char="." data-layer-dimension="" data-lookname="Default" data-maxcolwidth="72" data-numcols="5" data-numrows="6" data-row-dimension="Statistics;" data-row-labels="Pearson Chi-Square;Continuity Correction;Likelihood Ratio;Fisher's Exact Test;Linear-by-Linear Association;N of Valid Cases" data-rowlabels="Corner" data-rowlabelwidth="1" role="complementary" style="width: 582px;" summary="Chi-Square Tests, table, 1 levels of column headers and 1 levels of row headers, table with 6 columns and 10 rows"><tbody class="PivotBody defaultLayer innerFrameBd">
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D2</h3>
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<a href="https://1.bp.blogspot.com/-HcuSXhZA8gQ/Xn4pCW7L3YI/AAAAAAAAHgQ/Pc-SVkCf7mIwuDU4w2wUblJg8XJjyzkogCLcBGAsYHQ/s1600/FireShot%2BCapture%2B076%2B-%2BD6.htm%2B-%2B.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="265" data-original-width="679" src="https://1.bp.blogspot.com/-HcuSXhZA8gQ/Xn4pCW7L3YI/AAAAAAAAHgQ/Pc-SVkCf7mIwuDU4w2wUblJg8XJjyzkogCLcBGAsYHQ/s1600/FireShot%2BCapture%2B076%2B-%2BD6.htm%2B-%2B.png" /></a></div>
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D3</h3>
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<a href="https://1.bp.blogspot.com/-HC0iIxTDDPQ/Xn4pBcT-CrI/AAAAAAAAHgI/2Dy4bMox8wMaAk1zb2WgsTxIp-S_6VUHwCEwYBhgLKs0DAMBZVoB4Fr5gA-vHlmwGQUeMJDPN9fKHepgMnB993z3fCO_v07eyWsYhVtFsy0reT4gQAgC4vWlF30VLdyO6txVHcZ5j59j4XWikV6KkMtUi_mBQIWyJyawx7VoJETJ0Sb-3Q0hO0UZpCixduQ2akPTeNlA1fP2z22nQ-Xvl3_tSICtnNUSG8d_WOb3WmcP2yPn2eKS8bpHpaHh91V_ksoYtSrV_xGkOmOaeluDeUr3eFY5OxcUXVNQP-bKEzkUkKFb_qQ_aYJfBfnASjEY11bZth67rYw2EWFOGrYlUQRAVFmwXihDNfowQPylDDVMLZoEfAcjOyDB17h_wXz3juCumseoEMxSevgmVTOChzjaSv5OzbQBKRygJEhlW5kn_soJVkHcFuif14LTGUy0bq-frPddEFiiVAfH82Xl50xOgEpN9NVjj5OcZF4WAFr1m1aPi-amw3Rlc7IT1l2GbWImN6zogEgUvtBVje4k36jqoDeC26nqUH01vWZn9Mw_NBDg-tTkUrRFA5HGWxvBqti_lWTbUrtUrkK1aKn3jGC-oylNuyTc9GyyXGxOZrFCevD12kYV_1UgfXSiZ4dktCX1xNTFEj71Rwn-ZABkwh9f48wU/s1600/FireShot%2BCapture%2B072%2B-%2BD3.htm%2B-%2B.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="261" data-original-width="638" src="https://1.bp.blogspot.com/-HC0iIxTDDPQ/Xn4pBcT-CrI/AAAAAAAAHgI/2Dy4bMox8wMaAk1zb2WgsTxIp-S_6VUHwCEwYBhgLKs0DAMBZVoB4Fr5gA-vHlmwGQUeMJDPN9fKHepgMnB993z3fCO_v07eyWsYhVtFsy0reT4gQAgC4vWlF30VLdyO6txVHcZ5j59j4XWikV6KkMtUi_mBQIWyJyawx7VoJETJ0Sb-3Q0hO0UZpCixduQ2akPTeNlA1fP2z22nQ-Xvl3_tSICtnNUSG8d_WOb3WmcP2yPn2eKS8bpHpaHh91V_ksoYtSrV_xGkOmOaeluDeUr3eFY5OxcUXVNQP-bKEzkUkKFb_qQ_aYJfBfnASjEY11bZth67rYw2EWFOGrYlUQRAVFmwXihDNfowQPylDDVMLZoEfAcjOyDB17h_wXz3juCumseoEMxSevgmVTOChzjaSv5OzbQBKRygJEhlW5kn_soJVkHcFuif14LTGUy0bq-frPddEFiiVAfH82Xl50xOgEpN9NVjj5OcZF4WAFr1m1aPi-amw3Rlc7IT1l2GbWImN6zogEgUvtBVje4k36jqoDeC26nqUH01vWZn9Mw_NBDg-tTkUrRFA5HGWxvBqti_lWTbUrtUrkK1aKn3jGC-oylNuyTc9GyyXGxOZrFCevD12kYV_1UgfXSiZ4dktCX1xNTFEj71Rwn-ZABkwh9f48wU/s1600/FireShot%2BCapture%2B072%2B-%2BD3.htm%2B-%2B.png" /></a></div>
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</td><td class=" e dataAreaTop dataAreaLeft vCC" title="a. 3 cells (75.0%) have expected count less than 5. The minimum expected count is 1.14."></td><td class=" e dataAreaTop vCC"></td><td class=" e dataAreaTop vCC"></td><td class=" e dataAreaTop vCC"></td><td class=" e dataAreaTop vCC"></td></tr>
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D4</h3>
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<a href="https://1.bp.blogspot.com/-OIB_mHISG4A/Xn4pBUlBMVI/AAAAAAAAHgA/dMRyPmc77Rsa558ViPMui2hhnGExaXjPQCEwYBhgLKs0DAMBZVoBqX4AXKJKd4ANVw3hkXNurVO8t6DV9EPezzdHnbgFTFgSJW5hXPoyv8PDYYxiUARolKvAu9ijvgvXM61cH77ByaM6ogKy_vqytjeKcn9GCjLiXKDQuRCizJVoaSYfV7hrDH9dTNU6VohcH46vUXz1hXDyxkeNRB-73scS2b_EfSJhad8Gx33bmuPe21D22-ecuZxerlTq9lMuk87pbS-wtLWriwegm6vCELUT57hs6cDmpTOJo1UKNK-Ziu8e8_ECu1XSA7ZMLqc_DzzsBTiXYe-INeZsRyqumJzG21Hj3YYQZiUqaZyNlD_cz0saqKGTUuaTg4xryQtu_ArEiLFaG5SG69H2Mi_jzM0fKF7mO3E5AyqF4I-_JXj4yr7NsdntlDs6jpSCdn-AFSaPpQ4HU_5JWrwj6PThel_5PWuSpRNoya2fMbn_4xcoNUuZkiOiuYynQ_fttTvR3Fsegk0BAlbScPogpWHSFzDeplsQdtXSqJiWCNGg81WF3J7U4vQo6XXZRe1-LW_6AGUk4IJNF43e8UQiAiWgzkI6JFi_SBMO3bk9IfuvEycVT94_61Sw7GlemWF6VQuDMzCYpbHhS7xoM6-Nhl-Mwmdf48wU/s1600/FireShot%2BCapture%2B073%2B-%2BD4.htm%2B-%2B.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="244" data-original-width="646" src="https://1.bp.blogspot.com/-OIB_mHISG4A/Xn4pBUlBMVI/AAAAAAAAHgA/dMRyPmc77Rsa558ViPMui2hhnGExaXjPQCEwYBhgLKs0DAMBZVoBqX4AXKJKd4ANVw3hkXNurVO8t6DV9EPezzdHnbgFTFgSJW5hXPoyv8PDYYxiUARolKvAu9ijvgvXM61cH77ByaM6ogKy_vqytjeKcn9GCjLiXKDQuRCizJVoaSYfV7hrDH9dTNU6VohcH46vUXz1hXDyxkeNRB-73scS2b_EfSJhad8Gx33bmuPe21D22-ecuZxerlTq9lMuk87pbS-wtLWriwegm6vCELUT57hs6cDmpTOJo1UKNK-Ziu8e8_ECu1XSA7ZMLqc_DzzsBTiXYe-INeZsRyqumJzG21Hj3YYQZiUqaZyNlD_cz0saqKGTUuaTg4xryQtu_ArEiLFaG5SG69H2Mi_jzM0fKF7mO3E5AyqF4I-_JXj4yr7NsdntlDs6jpSCdn-AFSaPpQ4HU_5JWrwj6PThel_5PWuSpRNoya2fMbn_4xcoNUuZkiOiuYynQ_fttTvR3Fsegk0BAlbScPogpWHSFzDeplsQdtXSqJiWCNGg81WF3J7U4vQo6XXZRe1-LW_6AGUk4IJNF43e8UQiAiWgzkI6JFi_SBMO3bk9IfuvEycVT94_61Sw7GlemWF6VQuDMzCYpbHhS7xoM6-Nhl-Mwmdf48wU/s1600/FireShot%2BCapture%2B073%2B-%2BD4.htm%2B-%2B.png" /></a></div>
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D5</h3>
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<a href="https://1.bp.blogspot.com/-KZf4fvR_mr8/Xn4pCDXY0FI/AAAAAAAAHgk/L5AXtfHqCv4wWRDoIsiMAnvkIxMPxcfCwCEwYBhgLKs0DAMBZVoAty3O7ULWtoZPj4E2X8eHG6Fh_jFGSf9EP-_627quXhtyW4jobs-6fc6ZZZ664pet4lDI2wKh3EJ2_Td_X9tDdX280jXSaV-UagRUE720mKc5b-RW2-obkbaIKZp64Dtlhar1H-3oEOmmiElFDjBnFkMFPks-RCpWz4fQxyEzGpmmy1EqaWo1DiYL0V5wNQKwh35-PuT88oGPlKROsV-nUw2fRm1XisilUQn5-vDRK7J2mi3oY-Iu_Q7P9CPNIixKcerLdetA2722kNK0146W28LQuWOtwKNjVCp6BkPq4ONVTSMIMVUMnTw1h2aMMXVmy8VIIzKzVJBihBsSuNIU261mxK2xO4uIPzRwiOQxogQXEp3dVYnHHE2h0DQf70i5axe_iZ1nJP4QY1G6xRM_yWQYFiCrbdNAQ4LBHk7yoi237SovYyxB0AzQajqlsyvpGtniHKMtbDGfO9Nfv7ZfckyE7XqGSOQ08Uv6Z_wa6R8guv5dpyp8e0VVBu9lB-NRuQ5LmJGoUz8ahB3JTVNFbU4QTNJcuG5YsIhwK7Zh2tid0kdcXctOkHa1EWgBaGXX7TRZZfXSVo0mVKvZHtrximKwai9nXucswqNf48wU/s1600/FireShot%2BCapture%2B075%2B-%2BD5.htm%2B-%2B.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="266" data-original-width="647" src="https://1.bp.blogspot.com/-KZf4fvR_mr8/Xn4pCDXY0FI/AAAAAAAAHgk/L5AXtfHqCv4wWRDoIsiMAnvkIxMPxcfCwCEwYBhgLKs0DAMBZVoAty3O7ULWtoZPj4E2X8eHG6Fh_jFGSf9EP-_627quXhtyW4jobs-6fc6ZZZ664pet4lDI2wKh3EJ2_Td_X9tDdX280jXSaV-UagRUE720mKc5b-RW2-obkbaIKZp64Dtlhar1H-3oEOmmiElFDjBnFkMFPks-RCpWz4fQxyEzGpmmy1EqaWo1DiYL0V5wNQKwh35-PuT88oGPlKROsV-nUw2fRm1XisilUQn5-vDRK7J2mi3oY-Iu_Q7P9CPNIixKcerLdetA2722kNK0146W28LQuWOtwKNjVCp6BkPq4ONVTSMIMVUMnTw1h2aMMXVmy8VIIzKzVJBihBsSuNIU261mxK2xO4uIPzRwiOQxogQXEp3dVYnHHE2h0DQf70i5axe_iZ1nJP4QY1G6xRM_yWQYFiCrbdNAQ4LBHk7yoi237SovYyxB0AzQajqlsyvpGtniHKMtbDGfO9Nfv7ZfckyE7XqGSOQ08Uv6Z_wa6R8guv5dpyp8e0VVBu9lB-NRuQ5LmJGoUz8ahB3JTVNFbU4QTNJcuG5YsIhwK7Zh2tid0kdcXctOkHa1EWgBaGXX7TRZZfXSVo0mVKvZHtrximKwai9nXucswqNf48wU/s1600/FireShot%2BCapture%2B075%2B-%2BD5.htm%2B-%2B.png" /></a></div>
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D6</h3>
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Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-31693665889611751112018-10-31T09:08:00.001-07:002018-10-31T09:08:54.199-07:00Why I hate Fast Track ReclaimIf there is one company in the world that I truly hate and that i would tell everyone that I know to avoid like the plague it is Fast Track Reclaim (FTR).<br />
<br />
What do they do?<br />
They are there to get your overpaid payment protection insurance (PPI).<br />
<br />
I was pretty sure that I never had PPI but on the off chance I filled in the online form for FTR to check if I had had PPI. I did not pay much attention to the charge level of 30% that they charge and that they notified me about in the first call. To start this process you have to sign a letter of authority but as all their literature says we will do the check for free and only ask for payment if we are successful I did not pay particular attention when signing the letter.<br />
<br />
THAT WAS A SERIOUS MISTAKE.<br />
<br />
They did find that I had PPI with NatWest Bank and they called me to ask for the details so that they could send off my claim. I answered the questions and they posted the completed form to me asking me to return it so that they could make my claim. Now me thinking much more carefully now looked over the form for the fees and could not find any and so that was when I figured out that they sail close to the wind. It just says if they are successful in the PPI claim then they will charge a percentage fee. But there was no percentage. If I do not see a fee I am not signing. I then ignored their daily phone calls.<br />
<br />
THIS WAS A SECOND MISTAKE<br />
<br />
I just thought that they were (they are) pushy and definitely stretching what is legal to the limits. What I had not read was clause 1.5 of the letter of authority.<br />
<blockquote class="tr_bq">
1.5 If you do not return the Lender Questionnaire by post but complete it over the phone you will still be bound by the terms of this agreement.</blockquote>
This is a contract where in the ABSENCE of you doing anything the contract becomes active, because FTR know that many clients like me will become suspicious when they send out the questionnaire and it does not contain the fee schedule.<br />
<br />
Because that <b><u>fee schedule is hidden in the letter of authority and their fee is 30% in my version of the letter</u></b> (the government actually legislated against this level of fees but the legislation only applies to after July 2018). Not only are their fees extortionate but they apply to the full sum before tax. So once the tax is removed they will be over 40% and all they did was send a letter to the bank on your behalf.<br />
<br />
I was surprised when NatWest contacted me about my PPI as I thought not returning the questionnaire had ended the matter. they asked me to fill in the details over the phone - the same details that FTR had supposedly sent from my questionnaire. NatWest then sent a letter (a day after the legal deadline but dated before) to say that I had a claim and saying what the payment would be. Then to my surprise I got a bill from FTR asking for 40.5% of the payment as their fee even before I had anything from NatWest. I was very angry and followed their complaints procedure saying that I was not correctly informed. They said we did tell you in the letter of authority and on the phone. They were right yes they did. So I complained again suggesting that clause 1.5 flies extremely close to being an unfair contract term. Which it does. While the contract is specific there is a question in equity about that clause and whether it is fair to impose the terms for an inaction.<br />
<br />
FTR operate at the limits of what is legal. They grab as much as they can within the current system and as the government regulates them and legislates against their practices they move just enough to continue gouging clients. I made a mistake but I hope people learn from my experience.<br />
<br />
<ol>
<li>NEVER deal with FTR or any other PPI company.</li>
<li>Use the online tools now available for finding if you had PPI and drive companies like FTR out of business.</li>
<li>If you do decide to use one of these companies read everything and listen to everything. Watch out for clauses like clause 1.5.</li>
<li>If you do use FTR then make sure you never go over the questionnaire with them online OR if you do cancel their services in writing as soon as you have.</li>
<li>Just send the letter to the bank yourself when you (or FTR have done the search to find the PPI)- the template is on the <a href="https://www.moneysavingexpert.com/news/2017/03/ppi-reclaim-deadline-martins-5-must-knows/" target="_blank">Money Saving Expert </a>website. </li>
</ol>
<br />
Meanwhile I am going to send all of my interactions with FTR to the legal ombudsman in the slight hope that someone might do something about these companies. I am looking forward to the government legislation meaning that we can sue the PPI reclaims people for mis-selling us PPI reclaims.<br />
<br />Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-70255946099082599072018-04-20T07:12:00.002-07:002018-04-20T07:33:20.146-07:00The golden ruleThe first point is that I am not a Christian, the second is that I am not a Marxist or really even a socialist. I am a rational humanist but not quite from the same view as Steven Pinker. I am a Liberal, a moderate a fence sitter and someone who moves with the shifts of contingency. I would say most that I am a pragmatist. I take ideas from when and where they are needed to fit the current situation. I understand that complexity makes long term inflexible beliefs dangerous and often counter-productive. I do not believe in straight-jackets of a particular political/social/economic belief system. However there are one or two fundamentals that we should apply.<br />
<br />
The golden rule from Christianity is "do as you would be done by". All other religions have equivalent versions of the basic idea that we should all be nice to one another and behave in ways that we would expect others to behave towards us. This is part of the basis on which we construct human society.<br />
<br />
There are those that argued and continue to argue that society is not actually fundamental and who use the arguments of evolutionary science to dispute that society is necessary. These people are an not just ignorant they are an abomination. Their arguments have long been refuted by Axelrod and his work on cooperation and the experiments based on the Iterated Prisoner's Dilemma.<br />
<br />
You may think that abomination is too strong a word to apply to them but it is not. These are the hawks and defectors in game theory. Why are they so dangerous? They are so dangerous because they not only pursue an egoistical view of the world where only their self-interest is served, they also undermine trust in general and between everyone else. They are a cancer in a social world and only ostracism is a fitting punishment for them. If they remain part of society then they are parasites taking from the majority doves. They are even deceitful enough to try and convince they population that hawks out-number doves but this can never be the case. Tit-for-tat proves this. Defection is the exception and not the rule.<br />
<br />
The difficulty is that most of our politicians, media moguls and financiers are these abominations and this has undermined trust in society so severely that we are now staggering from one crisis to another. I agree with Pinker that the world is significantly better now than at any time in the past. Where I disagree is that we are orders of magnitude worse off than where we should be because of these parasites in our midst.<br />
<br />
I was reading Marx and Marxism by Gregory Claeys when it became clear to me how we have strayed from the golden rule. It comes from his definition of what a socialist wants.<br />
<br />
<blockquote class="tr_bq">
Socialists seek to reorganize society to satisfy the needs of the majority without the poverty, inequality, competition and waste associated with capitalism. Like many of their Utopian predecessors they imagine ways of belonging to groups and of relating to other people which are more generous, kind and peaceful, and which minimize or abolish exploitation and oppression. They embrace values like friendship, trust, harmony, fraternity, unity, and solidarity, which seems to be waning in modern society, but which might be recaptured or created anew. p28</blockquote>
Who can argue that they think that generosity, kindness and peace are what we want to aim for in the future or that oppression and exploitation are to be avoided? Who will argue that friendship, trust, harmony and solidarity are bad things? If you are against this then you are opposed to the golden rule to do to others as you would have other do to you.<br />
<br />
That is what these abominations try to argue and they have sown their seeds of mistrust, deceit, inequality and exploitation for the last 50-60 years as they seek to roll back the post-war settlements. These are the neo-cons where con is the most appropriate word, they are deceivers. Sometimes they try to hide by using the term neo-liberals but they are not liberals. Liberals did not believe in unconstrained capitalism, they believed that there had to be a communal input even if there was to be as much personal freedom as possible. Look at the social housing of Cadbury's and all of the philanthropy of people like Carnegie etc. For them philanthropy was part of the business and not just an add on. Even Ford understood that he needed to pay his workers enough that they could become customers. Compare this to someone like Larry Ellison who is a philanthropist at gun-point.<br />
<br />
There is a golden rule and that is that society does exist and it does so because most of us believe in being nice to one another. Society does not triumph over the individual as we still do have individual needs. Instead they are locked together in the same way as waves and particles are locked together in physics. There is a complementary duality between the rights of the individual and the communal benefits that we all derive from society. Those that deny society are unnatural and wrong they are liars.<br />
<br />
I find it very hard to reconcile this golden rule with the behaviour of the current politicians in both the US and the UK. Brexit is the child of these abominations and Trump is these abominations personified. Both the UK Conservative party and the US Republican party have allowed these abominations to dominate and until they can cleanse themselves they deserve to have no future part to play in government.<br />
<br />
We can have another Utopia when we cut out these cancerous individuals. That does not mean the Leninist and Trotskyist view that violence is the answer. It is simpler than that we just need to ignore them, not vote for them or buy from them. Democracy means that in the end they depend on the community through capitalism as we are their consumers. We are their voters and we create their success. If we deny them this then they will wither and fail we just have to see past their deceptions and false promises.Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-58967783069002246182017-12-13T08:56:00.000-08:002017-12-13T08:56:17.556-08:00Roger StoneRead Jon Ronson - The Elephant in the Room<br />
<br />
Alex Jones is paranoid.<br />
<br />
Stone was introduced to Jones by Reeves - the grandson of the original superman<br />
Stone had a business with Mannafort and they also worked with Lee Atwater.<br />
<br />
Stone worked for Savimbi in Angola<br />
Bob Dole<br />
Landmines<br />
Marcos<br />
<br />
Stone knew Roger Ailes<br />
Anti-globalist/establishment<br />
<br />
Except Stone is part of the establishment - he was Nixon's Counsel.<br />
<br />
They have a cult mentality - they will kill the GOP<br />
This is a coup - they do not want to win hearts.<br />
<br />
Alex Jones hijacked the Young Turks<br />
Stone and Jones brought up Clinton rape accusations to the debates.<br />
<br />
Manages media - creates false flag confrontationsAndyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-49716108570563940632017-12-13T08:30:00.000-08:002017-12-13T08:30:49.056-08:00SuperHubsThis is a <a href="https://www.amazon.co.uk/dp/B01J1Z0C3O/ref=dp-kindle-redirect?_encoding=UTF8&btkr=1" target="_blank">slightly puzzling book </a><br />
<br />
p22 the author is partially wrong. Hierarchies do work and Herbert Simon showed why, but this was not because of top down control. They can be non-directed and spontaneously arise.<br />
<br />
p25 gatekeepers to the rich and powerful. Is this a good idea?<br />
<br />
p27 - why did the author write the book?<br />
<br />
<ul>
<li>potentially undermines her credibility.</li>
<li>makes people wary in talking to her.</li>
<li>obvious that she is a Soros fan.</li>
</ul>
<div>
p32 "Money is mostly created by banks offering loans" regulated by central banks interest rates and asset purchases (Gold etc.) At the minute with QE $17 trillion has been pumped into the markets and created huge asset bubble such as BitCoin. The intention was for the money to be used for investment and to kickstart growth but this has failed. It has remained in the markets and the banks and not been distributed to the wider economy. This is going to result in a very serious and drastic need for realignment. </div>
<div>
<br /></div>
<div>
Fundamentally commodities are more important than other markets because we cannot live without them. We depend on them for:</div>
<div>
<ul>
<li>Shelter</li>
<li>Warmth </li>
<li>Food</li>
</ul>
<div>
As Apple share price rises the return per share has fallen because this is pure speculation and not investment. </div>
</div>
<div>
<br /></div>
<div>
p53 power of the central banks is greater than the politicians. Brexit proves this wrong. You can get a populist vote in ignorance of how the central banks work and this can create a suicidal economic policy.</div>
<br />
<br />Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-77794694797822052402017-12-13T08:20:00.000-08:002017-12-13T08:20:24.845-08:00Creating Research ObjectsThere is a serious problem with scientific fraud and the reproducibility problem. We need to think about ways in which we can check the integrity of a study.<br />
<a href="http://www.researchobject.org/" target="_blank"><br /></a>
<a href="http://www.researchobject.org/" target="_blank">http://www.researchobject.org </a><br />
<br />
This is also a way of encoding know how.<br />
<br />
Metadata is too time consuming to create at the minute. It needs to be built into the planning and research process itself (GitHub?)<br />
<br />
Want to create a knowledge exchange report<br />
Open Research Data - Manyika<br />
Rules for growth - Stodden<br />
<br />
Data management plans are required by research councils<br />
<br />
<ul>
<li>Integrity checking</li>
<li>Hashing</li>
<li>What are open file formats?</li>
</ul>
<div>
<br /></div>
<div>
Blockchain for the trust layer</div>
<div>
<ul>
<li>Politicians - regulations and policies</li>
<li>Qualifications</li>
<li>Medical Records</li>
<li>Passports</li>
<li>Forensics</li>
<li>Risk assessment and rating</li>
</ul>
<div>
Restoring trust is essential</div>
</div>
<div>
(Byzantine General's Problem)</div>
<div>
<br /></div>
<div>
Money is a trust system representing work done</div>
<div>
Reputation is also a trust system but this is only as strong as the weakest link.</div>
<div>
<br /></div>
Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-66181364807323674712017-12-13T07:21:00.000-08:002017-12-13T07:21:21.871-08:00Thinking about the bootstrap<br />
<ol>
<li>Bootstrap samples experimental units but in phylogenetics you sample the VARIABLES - sites.</li>
<li>How should we treat sites?</li>
<ol>
<li>Remove totall variant?</li>
<li>Remove sites where a row is missing?</li>
</ol>
<li>You cannot say that parametric and non-parametric are the same thing. They are correlated but not directly comparable.</li>
<ol>
<li>Carry out FastTree with H5N8, then H5 then N8</li>
<li>Use the parametric and non-parametric bootstraps</li>
<li>Use the CONSEL measures as well.</li>
</ol>
<li>Having more bootstraps than 100 makes NO difference to the bootstrap values. They converge quickly empirically.</li>
<ol>
<li>This is far below the theoretical numbers needed by Efron says that this is usual.</li>
<li>Suggests that sites are linked and so there is less independent variability than it appears.</li>
<li>Need to experiment with conserved sites.</li>
<li>Need to experiment with the substitution models to look at sensitivity and also gamma.</li>
</ol>
<li>There is a lack of independence between sites in the evolutionary models but this is IGNORED in the bootstrap calculations. You should bootstrap codons and not individual bases.</li>
</ol>
<div>
<br /></div>
<div>
Need to create synthetic data where the true tree is known. This can be used to test:</div>
<div>
<ol>
<li>Effects of sampling by censoring the data.</li>
<li>Evaluate modeltest.</li>
<li>Check trees from bad evolutionary models against the best models (probably the same!!!)</li>
</ol>
</div>
Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-76678308421161881042017-12-13T06:48:00.000-08:002017-12-13T07:09:58.883-08:00The process of learningGenetic: Very slow learning and wasteful because it depends on selection. This works between generations.<br />
<div>
<br /></div>
<div>
Taught: Fast learning that sums up what happens in a community.</div>
<div>
<br /></div>
<div>
Exploration: Novel learning by experiences. This is learning through interaction<br />
<br />
<h3>
Distances in psychology.</h3>
</div>
<div>
not transitive</div>
<div>
not symmetrical</div>
<div>
<br /></div>
<div>
Tversky 1977 - features of similarity</div>
<div>
AI cannot make human decisions until it gets beyond clustering distances.</div>
<div>
<br /></div>
<div>
Undoing Project p 107-114.</div>
<div>
<br /></div>
<div>
Belief in the law of small numbers - The Undoing Project p157-163</div>
<div>
<br /></div>
<div>
Pundtits (illiterate "experts") p 168</div>
<div>
<br /></div>
<div>
<br /></div>
Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-21128511218527690102017-11-18T02:57:00.001-08:002017-11-18T02:57:53.349-08:00The Virus Gene PapersI think it unlikely that I will be submitting to Virus Gene again in a hurry. We had written a few papers that we knew would be unpopular and sent them to a meeh level journal where we expected to have an easier ride through peer review. The first hint this wasn't going to be the case was the editor assigned who happened to have collaborated with a group that was in direct competition in H9 phylogenetics lead by Cattoli who I had insulted previously.<br />
<br />
Anyway, they are now in PeerJ and public so that nobody else runs off and starts using USEARCH in flu phylogenetics and claiming priority.<br />
<a href="https://www.blogger.com/goog_113893411"><br /></a>
<a href="https://peerj.com/preprints/3166/">https://peerj.com/preprints/3166/</a><br />
<a href="https://peerj.com/preprints/3396/">https://peerj.com/preprints/3396/</a><br />
<br />
I just wanted to put the referee's comments for the first paper that was rejected here, because they are laughable and in the context of the referee's comments on the second paper they are probably wrong or at least not consistent. I have put my responses here as with a straight reject I get not response to the editor, who is not going to be on my Christmas card list.<br />
<br />
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">Reviewer #1: General comments<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">The paper presents the method of classification of H9 lineages using clustering and compares the results with classification based on other methods.<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">The paper would gain if some practical aspects were added. The title suggests the method is fast, so an approximate time of analysis would be useful, especially that cluster analysis after each run is required and repeated clustering if necessary is suggested.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">Specific comments:<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">Introduction<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">Explain HMM and SVM abbreviations.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:20">Hidden Markov Models and Support Vector Machines<o:p></o:p></ins></span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">Materials and methods<o:p></o:p></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">Please add the information on the chain length in the BEAST analysis.<o:p></o:p></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:20">2 million<o:p></o:p></ins></span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="font-family: -webkit-standard, serif;">Results<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Lines 37-43: "USEARCH identified 19 clusters …" - does it refer to H9 HA? It should be indicated in the text to avoid confusion with subtype identification described above.<span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:20"><o:p></o:p></ins></span></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:20">19 H9 clusters</ins></span><o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Lines 43-44: "The subtype originated in Wisconsin in 1966 and this clade continues to be in circulation" Do the Authors mean that H9N2 subtype was first detected in Wisconsin in 1966?<span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:20"><o:p></o:p></ins></span></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:20">H9 is first detected in 1966 as part of H9N2</ins></span><o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Lines 37-39 (2nd page of results): The sentence "The phylogenetic trees…" is confusing, as only fig. 4 shows tree for clade 12 and it was not divided into subclades.<span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:21"><o:p></o:p></ins></span></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";"><span class="msoIns"><ins cite="mailto:Andrew%20Dalby" datetime="2017-10-01T11:21">Easily changed</ins></span><o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Lines 50-51 (2nd page of results): Were there 3 or 4 subclades of 14 clade identified?<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">Easily checked<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Discussion<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">First sentence "The clustering of the influenza viral hemagglutinins using USEARCH proved that clustering can correctly identify the viral subtypes from the sequence data" - the subtype identification was partially correct, as it did not detect H15, and H7 was split into two clusters, so this statement should be revised. It would be interesting to mention with which subtype the H15 sequences were clustered.<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">I can show that H15 separates out at slightly lower identity. H7 is two groups adjacent so it is correctly identified. It gets 14 out of 15 clusters this is 93% accuracy the method works. 93% is more accuracy than typical for clustering algorithms.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Lines 27-30 (2nd page of discussion): "…small sub-clades of four or less sequence were merged for phylogenetic analysis…" Please explain it in Results.<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">You cannot make a tree of less than 3 sequences.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Supplementary Figure 3: There are branches labeled with subclade number and some with individual sequence. Please explain it. It is also associated with the comment above.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">That would be because labelling a cluster containing one sequence with a cluster name would be stupid. As these clusters were grouped for tree generation it would be misleading to use the cluster number but I can edit them to have both.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Table 3 - missing data in the 5th line<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">No that does not exist – it is unsupported data in the LABEL paper that is not public and cannot be verified. This was data given to Justin Bahl but not available to anyone else.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Reviewer #2: The automated detection and assignment of IAV genetic data to known lineages and the identification of sequences that don't "fit" existing descriptions is a challenge that requires creative solutions. The authors present a manuscript that proposes a solution to this question and tests it on an extensive H9 IAV dataset. <o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Though I find the general question intriguing there are a number of issues. The two major items are: a) as a study on the evolutionary dynamics of H9 IAV, this is missing appropriate context, and the results are not adequately presented or discussed; and b) as a tool to identify known and unknown HA, it generates results that appear to be no different to BLASTn, it isn't packaged so that others may use it in a pipeline/web interface/package, and the generated "clusters" aren't linked to any known biological properties. I elaborate on a few of these issues below.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">1) This is not a novel algorithm: USEARCH has been in use for over 7 years and it has been previously used in IAV diagnostics. Consequently, I would expect the authors to present a novel implementation of the algorithm (e.g., a downloadable package/pipeline, or an interactive interface on the web) or a detailed analysis and discussion of the evolutionary history of the virus in question. Unfortunately, the authors do not achieve either.<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">This reviewer is lying you may search for IAV and USEARCH in Google and you will find NOTHING except the two papers I mentioned both of which are more recent. It was first used by Webster in 2015 and for a different approach. It is mostly used for analyzing metagenomics projects. It cannot be packaged because as the paper shows you have to make decisions about the clustering. It is not just automatic you have to analyse the appropriate identity and clustering.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">2) The introduction is not adequately structured - after reading, I was left confused as to why dividing the H9 subtype into different genetic clades was necessary, i.e. there is no justification provided for the study. The discussion of clades and lineages is particularly convoluted and given the presented information, it is not clear what the authors are trying to achieve (i.e., they move from identifying subtypes, to identifying clades, to lineages, to reassortment, and all possible combinations). Additionally, there are entire sections of the introduction that consist entirely of unsupported statements (lines 39-48 on alignments and tree inference: lines 52-60 on lineage evolution). This section needs to be revised to provide appropriate context and justification for the study.<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">The reviewer is obviously completely oblivious as to why you want to carry out lineage analysis in influenza. As such they are not competent to review the paper. As the WHO actually has a working party to create these nomenclatures for H5 this argument is ridiculous. <o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">3) There are many figures associated with BEAST analyses. The goals of these analyses are not introduced, and the trees are not presented or described in any meaningful detail. Further, and more concerning, the presented trees appear to be wrong, i.e. the tip dates are not in accordance with the temporal scale.<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">That would be because the editor had the number of figures reduced. The BEAST analysis is not particularly important other than to show the consistency of the clustering. If the reviewer bothered to read then they would see that one of the trees does not use tip dates and is a maximum likelihood tree and so dates WILL NOT be consistent with the temporal scale if there is variation in mutation rate along one of the branches. This is actually an interesting point as BEAST FAILS completely to generate a reasonable tree with tip dates for that cluster of data. It produces a network with cycles over a wide range of initial parameters.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">4) One of the major results (lines 6-16 in the results) is that the USEARCH algorithm can identify the correct subtype of a sequence, most of the time. How does this compare to BLASTn? And, failing to classify a subtype (line 16) is problematic. The authors should consider what the goal of the analysis is, and then present it along with results from similar algorithms, e.g., with the same data, is BLASTn able to identify subtypes?<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">I am intrigued by how the reviewer thinks that BLASTn works? To do the same task I would need to identify prototypes of each cluster and then use BLASTn to find the rest of the cluster. I would then need to apply some sort of cut-off in order to identify when BLASTn was finding members of other clusters and not the current cluster. In short this is nonsense. They perform different functions as USEARCH identifies the clusters not just related sequences. USEARCH produces the results in about 1 minute. Just to even set-up the BLAST searches would take 10 times longer than this and to analyse their results and do the correct portioning will take hundreds of times longer. The title of the USEARCH paper is actually “Searching and clustering orders of magnitude FASTER THAN BLAST”<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">5) I do not understand the significance of USEARCH identifying 19 clusters (line 37); and these data are not linked in anyway to a larger more comprehensive description of the evolutionary dynamics of H9 IAV. The authors should refine their hypothesis, and discuss the results - specifically, if a cluster is identified, what does it mean? What is the significance of the previously unidentified clusters? How closely does this align with phylogenetic methods (and the discussed LABEL)?<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">Um really this is now getting to be a bad joke. The paper compares to LABEL a method based on totally subjective cluster names created by influenza researchers. The entire discussion is carrying out exactly what this referee is suggesting in this paragraph. Do they need glasses? Are they suffering from a reading problem? Do they have a brain injury? USEARCH produces some of the clusters from LABEL, faster more efficiently and correctly. It is completely objective and based on mathematical criteria. There is no bias dependent on convenience sampling because it uses all the data not just the data a particular lab collects at a particular time. This is a MAJOR step forward in trying to sort out the mess that is influenza nomenclature and shows that most existing attempts are biased, partial and use rules that are not appropriate such as the need for clades to be homogeneous in subtype e.g. only H9N2 and not other H9 containing subtypes. The hypothesis is that existing nomenclatures are bad arbitrary, subjective and not based on mathematical rigour. We have proved this in this paper and in two more analyzing H7 and the internal influenza genes. All show exactly the same point, sound maths, rigorous systematic approaches and excellent biological agreement. <o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">Minor comment:<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">1) Using my laptop, I aligned all non-redundant H9 HAs (n=5888) in ~2 minutes, and inferred a maximum likelihood phylogeny in ~6 minutes. The argument that phylogenetic methods are slow, particularly given modern tree inference algorithms and implementations on HPCs (e.g. Cipres: </span><span lang="EN-US"><a href="http://www.phylo.org/"><span style="color: blue; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">http://www.phylo.org</span></a></span><span lang="EN-US" style="font-family: -webkit-standard, serif;">) is not accurate. Additionally, alignment issues - particularly within subtypes is a trivial issue. <o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">Yippy for you referee 2. Now put them into clusters. Just edit that tree with 5888 sequences and see how long it takes. Meanwhile USEARCH will have done it after 1 minute and it will be mathematically correct and not depend on how you cut the trees. Alignments of large numbers of sequences are unreliable. Regardless of this referee stating that this is unsupported this is actually supported by a very large literature and best summed up in the work of Robert Edgar who wrote Muscle and who says DO NOT DO LARGE ALIGNMENTS WITHOUT USING MY USEARCH PROGRAM FIRST. But then it is unlikely that referee 2 actually RTFM for the alignment program. I am sure they ran it without bootstrap and it could not have used tip dates as only BEAST does this.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">2) There are a number of methods, e.g, neighbor joining and UPGMA, that use agglomerative clustering methods.<o:p></o:p></span></div>
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<span lang="EN-US" style="color: red; font-family: "-webkit-standard",serif; mso-bidi-font-family: "Times New Roman"; mso-fareast-font-family: "Times New Roman";">Yes there are well done referee 2 for being a genius and knowing that actually all of phylogenetics is related to clustering. This is the one and only correct statement that they make. All nomenclature and lineage methods depend on agglomerative methods but this is a divisive clustering method which is much less susceptible to convenience sampling. USEARCH is the fastest and best clustering method you can use and it is divisive and not agglomerative.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-family: -webkit-standard, serif;">My comment is that I have NEVER encountered a more partial incompetent and ignorant referee than referee two. I think that they protest too much because they have too much invested in current methods such as LABEL which this paper show to be at best poor and at worst completely wrong.<o:p></o:p></span></div>
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Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-84264657700101394412017-11-18T02:42:00.000-08:002017-11-18T02:42:02.926-08:00The state of Influenza PhylogeneticsI really was not particularly interested in viral phylogenetics for most of my research career but I started my research in the area when I joined the Institute of Animal Health. I have a background in synthetic organic chemistry and protein crystallography and so I am well aware of how vicious and petty academic politics can be (ask me someday about the MRC skiing anecdote, or the Ribosome Nobel Prize story, or maybe the Rubisco saga or you can ask me about Nicolaou and Taxol ).<br />
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But I can honestly say that I have never met a more political, corrupt and inept field than influenza phylogenetics. It is staggering how bad it is, and that might be what makes it interesting. I come to it from a statistics perspective as I spent five years on my Damascene transformation in the statistics department at Oxford. I am very interested in bad science, people doing science badly in order to get grants and power but who really have no idea what they are doing. I was inspired by the work of John Ziman and the growth of the field of reproducibility (scientists like to suggest that this only applies to social sciences although psychology is acknowledging it has a problem too and biology in general definitely has a reproducibility problem). In viral phylogenetics there is a lot of bad science.<br />
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First I want to set out the main problems I have are:<br />
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<li>Most biologists in the field have no idea what they are talking about from a theoretical perspective. They don't get the maths, they do not understand the assumptions and they ignore any results that do not fit with their expectations instead of asking themselves why it happened.</li>
<li>Sampling is terrible, It is all a convenience sample and this cannot avoid being a biased sample. Why are we focused on China when we collect almost nothing in Africa and the last swine flu pandemic came from Mexico?</li>
<li>People horde data and do not collaborate. There are 3 main databases which all have data in different formats with different annotations that you might or might not want. They are designed to make it difficult for researchers to use data from all three.</li>
<li>Peer review is intensely political and there are cliques which cite each other's papers excessively and which block publication of other groups. There are some government laboratories that have > 50 cites on a scientific note paper that says ... well not very much. Everyone is playing the citation game to keep their government laboratory funding. </li>
<li>There is a lack of communication between the analysts and the laboratory scientists. For example how many analysts know that the virus was often passaged through hen's eggs for amplification before sequencing the result was that the sequences mutate to have chicken specific variations and so the sequences in the original sample are not the same as those they submit to the database. This is exactly the same as the cowpox vaccine for smallpox - it is NOT cowpox Jenner got lucky and also the problem of cell culture where the cell cultures are no longer the genotypes originally collected.</li>
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Why do I think these are problems?</div>
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<li>I told a referee that phylogenetics is just a clustering method based on a metric. They assured me that this is not always true. For example parsimony and maximum likelihood are not distance based methods says the referee. Except fundamentally they are. To calculate a parsimony you need an alignment. To get a multiple alignment you need to build an alignment you use a progressive alignment based on a guide tree which will often use UPGMA a distance-based method. Distance is fundamental to progressive alignment. Parsimony itself depends on the smallest number of changes - a distance. The scoring models you use as evolutionary models for measuring changes and calculating likelihoods are metrics for finding distances. Probability is a metric in measure theory it is a distance. You could use information theory but the difference in information is again a metric and a distance. Whatever way you try and cut it phylogenetics depends on distance and a metric and groups based on those metrics. It is clustering it does use metrics and because it uses metrics it is not completely objective it is subjective and metric dependent. People who do phylogenetics would do well to read Kaufman and Rousseeuw to understand why clustering needs care and why metrics are very interesting (I have a story about one of the authors as well which makes me reluctant to suggest reading his book but it is foundational).</li>
<li>The BOOTSTRAP - I don't know where to start. Nobody who is a biologist has bothered to do some simple experiments to check what is does and what it means with real data. For example to know how many bootstraps you need to use run it on your data with 50, 100, 150 and 200 and see if it has converged - you get the same numbers each time. From my experience 100 is more than enough. All of these referees and experimentalists using 500 or 1000 or 10,000 are wasting their time. If you read Efron's book he says 100 is empirically often enough although, in theory, the number should be something like the square of the number of sequences. If they had read Efron's book they might grasp the issues. That means going beyond his simplified paper saying what the bootstrap is and definitely going beyond taking Felsenstein's word for it. There is some fantastic work on this by Susan Holmes who worked with Efron. This is really great stuff but under-read and poorly understood. So much so that she has moved on to other things.</li>
<li>The need to make everything quantitative. Biology is NOT always quantitative. If I see a clade in a tree and it is monophyletic to a geographical location I believe that tree. I do not need to put a number on it. I could work out by permutation test how likely it is to get a clade that is monophyletic to a location but given the sampling is convenience sampling that is not probably going to be meaningful.</li>
<li>Creating trees for distinct species should make sense. We know and I mentioned before that influenza undergoes rapid change to obtain host specific mutations when it is introduced to a new host, such as passaging it in chicken eggs. We know this experimentally for ferrets as well. Why would a host specific tree be a bad idea? A referee and an editor thought so in my H9N2 work until a paper taking the same approach was published in Nature and then what I had done was Ok and they allowed my appeal after stalling publication for 18 months and two journals with the same editor in both.</li>
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Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-70581389968145290452017-10-01T10:55:00.001-07:002017-10-01T10:55:50.694-07:00How would you hack an election?If I wanted to win an election how would I do it?<br />
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In areas where there is no voter id what I need first is a list of past voting records. I need to know who doesn't vote. I need this because I am going to vote for them and I don't want any of them turning up by accident. People who are on the register but cannot vote because they are dead or incapacitated look like great candidates as well BUT these are too easy to check so actually I want to avoid this or someone might detect my fraud quite easily.<br />
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Once I have a lost of non-voters who are on the roll and alive and who could vote but never do what do I do next? I go to the polling station on their behalf and vote for them. Remember that they never vote and they are likely not to be recognised. I need to do this in small numbers at all of the polling stations. The more stations the better to spread the load and hide what I am doing. I don't want to do more than 50-100 votes in each of the stations. This means that my voting team needs to be at a maximum of 100 people. I do not want to have the same person voting at a station twice. These teams then move from station to station over the day. I can also do postal votes and absentee votes and these help. This is a big logistical operation but I don't care if I win the prize and control the government. You are talking thousands of operatives but they will target only a few key areas which can be flipped. Only marginals matter.<br />
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This is certainly possible for the swing states like Pennsylvania, Wisconsin etc. if I have Russian man-power available but I would need a forward base and a long term plan to get the people in place over time. Combine this with analytics, targeted media a big fake news operation and you can win the election.<br />
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How would you recognise this in the results? Can it be detected? The only thing that you see is a higher than expected turnout, unexpected demographic shifts and a high turnout from previous non-voters. But all of this is plausible deniability. There is not way an audit can say that this fraud exists unless you corroborate all of the suspicious votes. This is the perfect undetectable hack. Oddly enough Trump and Brexit both depended on previous non-voters.Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-11138161391919048622017-10-01T04:38:00.000-07:002017-10-01T04:38:02.937-07:00Is it just me or does seasonal flu not make sense?The NHS are warning that the UK is going to have a bad flu season this winter because there has been a bad flu season in the southern hemisphere this year.<br />
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But maybe they got a bad season this year because we got a bad season last year. Surely if this bad season alternates between northern and southern hemispheres one affecting the other then once a bad season starts all seasons have to be bad after that.<br />
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What is more puzzling is how is their bad season going to become our bad season? If it is being spread by air travel then why didn't we have a bad summer flu season? Why does it only kick off in our winter after their winter and flu season is over. The idea was that we get more flu and colds in winter because we spend more time in doors passing it to one another in the winter. I agree in an agrarian society where behaviour changes with seasons but I spend as much time in my office in the summer as I do in the winter. That is apart from the summer vacation but if I went to New Zealand won't I bring back the flu?<br />
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A big factor in my job and exposure is schools. The new school term brings colds and flu. Now we have much shorter summer holidays for schools in the UK we should see longer flu seasons if this is part of the cause for flu being seasonal. Seasonal flu is reality but our models as to why it is seasonal don't fit very well. We need to get some better models as to why it is seasonal and how it spreads between hemispheres.<br />
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Humidity and temperature have been shown to have effects but I suspect that there are more factors to take into account and imagining how flu seasons spread between hemispheres is another factor to consider.Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-63340868908155726562017-10-01T04:07:00.000-07:002017-10-01T04:07:51.023-07:00How not to develop analytic talentI wrote a review of the book Developing Analytic Talent by Vincent Granville and gave it a good bashing. But I could not do it justice to the total incompetence. Vincent Granville PhD is a perfect example of a snake-oil salesman. He speaks about his papers, his experience and the investment he has attracted, he talks about his books but a quick Google of his name just turns up a website which he set-up and which engages in some shady practices, including him writing articles pretending to be other authors, especially women in order to make it appear more gender neutral.<br />
<br />
The review could not capture the many gems within the book so here are some of his best bits of writing.<br />
<blockquote class="tr_bq">
Compound metrics are to base metrics what molecules are to atoms. Just like as few as seven atoms (oxygen, hydrogen, helium, carbon, sodium, chlorine and sulfur) can produce trillions of trillions of molecules and chemical compounds (a challenge for analytical and computational chemists designing molecules to cure cancer), the same combinatorial explosion takes place as you move from base to compound metrics. </blockquote>
p110<br />
<br />
Very nice but Helium is a noble gas and does not form compounds on Earth although it might do in special environments. His PhD is not in chemistry<br />
<br />
Apparently he also thinks that an app for pricing in amusement parks would be a good venture<br />
<blockquote class="tr_bq">
Increase prices and find optimum prices. (Obviously, it must be higher than current prices due to the extremely large and dense crowds visiting these parks, creating huge waiting lines and other hazards everywhere - from the few restaurants and bathrooms to the attractions).</blockquote>
p105<br />
<br />
Alternatively they could build more bathrooms and more restaurants and make even more money from the large crowds rather than reducing foot-fall as people go elsewhere. Who are richer the owners of WallMart or the owners of Tiffany's? <br />
<br />
This however is the best and saved for page 174<br />
<br />
<blockquote class="tr_bq">
The number of variables is assumed to be high, and the independent variables are highly correlated.</blockquote>
What? Wait let me see what the definition of independent variables is. That would be whose variation does NOT depend on the variation of another. That would mean not correlated. This is more than a slight howler this is so elementary that you cannot believe a single thing the author says. He then goes on to do regression in Excel.<br />
<br />
On page 189 he talks about the possibility of getting negative variances - this is impossible. On page 190 he talks about the variance being bounded by 1 as a maximum. This is nonsense even with normalised data the variance = 1 V is not <1 as="" he="" nbsp="" p="" states.=""></1>Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-28353547385017422282017-09-27T09:16:00.000-07:002017-09-27T13:34:30.077-07:00How not to design a questionnaire. Lord Ashcroft's dangerous political polls. Lord Ashcroft has had a big impact on election polling in the UK. He has even had favourable mentions with Nate Silver on his blogs. But I have been taking a deeper look into his polls.<br />
<br />
I have to admit to some political activism and I was previously a Liberal Democrat Councillor. I collected canvassing data and fed it into the party's own analysis program and it makes predictions about the state of your campaign. Most of the time it got it pretty close to right and I won by the amount I expected. That was small local scale analysis.<br />
<br />
Lord Ashcroft is well known and a Tory donor and he has been running polls in both the UK and more recently in the US. He conducted a lot of focus groups around the Trump election and also the Brexit vote. What concerns me is not the polls and the data, but the way the polls are carried out. Most specifically the questions that are used.<br />
<br />
I was reading a story on <a href="https://capx.co/can-the-tories-save-themselves-from-demographic-disaster/" target="_blank">CapX by Robert Colville about the demographic disaster awaiting the Conservative Party</a> and he used some very particular phrasing.<br />
<br />
<blockquote class="tr_bq">
<span style="background-color: white; color: #181c1e; font-family: "merriweather" , "georgia" , serif; font-size: 16px;">If people think that multiculturalism, immigration, the internet, the green revolution and feminism are forces for good, they will vote Labour/Democrat. If they think they are bad, they will vote Tory/Republican.</span></blockquote>
<br />
Now who exactly thinks in those terms? Oh yes, there is a force for good and I am behind it 100%. People just never say that. Oh that is a force for evil/bad, I am really against that. These phrases are straight from Lord Ashcroft's poll published in his book Hopes and Fears. Participants had to chose on a scale whether they thought that:<br />
<br />
<ul>
<li>Feminism</li>
<li>The green movement</li>
<li>The internet</li>
<li>Multiculturalism</li>
<li>Immigration</li>
</ul>
have made America better or worse.<br />
<br />
I use these questions for my second year statistics class as examples of non-scientific questions. These are in fact sound-bites and propaganda disguised as poll questions. They provide a frame of reference to lead participants towards where the person asking the questions wants to take them. The questions are based on invoking feelings and reactions and not actually obtaining rational responses.<br />
<br />
Take for example this more detailed question.<br />
<blockquote class="tr_bq">
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<br />
<div class="p1">
<span style="font-size: small;">Thinking about the following changes in America over recent years, do you think they have made America better or worse?</span></div>
<div class="p1">
<span style="font-size: small;">More lesbian and gay couples raising children</span></div>
</blockquote>
How can lesbian women and gay men raising children have ANY effect WHATSOEVER on whether a country is better or worse? What does it mean for a country to be better or worse? If it means economically less successful then how do lesbian and gay couples raising children affect the economy? If it means the country has gotten worse because of a rise in crime then again how is this caused by lesbian and gay couples raising children? The responses to this question will be pure framing based on current personal experience. If your standard of living has declined recently then you will respond that America has become worse, but the relationship to lesbian and gay couples is forgotten in the question. I could have asked the same question about America getting better or worse and used "More Bush family members raising children" and I would get the same response.<br />
<br />
This sort of question is nonsense. It is intended to bias and put words into the participant's mouths by limiting the spectrum of possible causes. The motivation behind these polls is generating easily digestible journalistic content. They can then summarise the poll by saying a majority of participants think that feminism or multiculturalism has made America/UK worse. These are leading questions and the poll is at best meaningless and at worst pure propaganda. Polls like this are designed to influence the opinions of participants and not to actually discover what their opinions are.<br />
<br />
We need to think seriously about the impacts of polling carried out in this way, as for me it raises ethical concerns about how they are being carried out and how they are being used.<br />
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</style>Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-38503421454789809482017-07-20T23:58:00.002-07:002017-07-20T23:58:47.245-07:00Bill Gates, VR and Influenza Vaccines<a href="https://www.gatesnotes.com/Health/How-Virtual-Reality-Can-Help-Us-Fight-Viruses" target="_blank">Bill Gates was shown around the NIH</a> where they wanted to show him how VR helps to create better vaccines.<br />
<br />
As I said in another Blogpost. I began my research career in structure based drug design. Then I learned that you models are only as good as the data you feed in and so I moved down the pipeline, first to crystallography and now to sequence data analysis. I know the limitations but the NIH wants money and they are less likely to talk about them.<br />
<br />
The limitation in influenza research is sampling. We simply do not collect the data properly. We have lots of data from China because that is where we think future outbreaks might come from, but the last Swine Flu pandemic originated in Mexico. There is not enough systematic global collection of data. This means that unexpected changes catch us unaware. Most of the times we do pick the right vaccine candidates but sometimes we get it wrong. VR will not help this.<br />
<br />
What will help is the IOT. That provides an opportunity for massive data collection. The Cloud allows us to share data globally. If we can stop the national laboratories from hoarding data this would also be a big step forward. The WHO also needs to be reformed to remove some of the political players who are a barrier to sharing. Scientists are bad politicians. My dad worked on a funding committee and they had to move meetings to secret locations because the scientists were always trying to lobby then and bully them into decisions. In influenza research there is a ruling clique that wishes to restrict research participation. When you mention citizen science or data sharing they have a fit.<br />
<br />
So what should we be looking at today?<br />
<br />
1) Why is there a <a href="http://www.independent.co.uk/environment/ospar-report-seabirds-plastic-pollution-fulmars-terns-wwf-marine-environment-a7813216.html" target="_blank">wide-spread breeding failure</a> in the Celtic seas? Is this related to the death of <a href="http://www.express.co.uk/news/nature/770582/dolphins-dying-british-waters-dead-decaying-shore-fisherman" target="_blank">marine mammals?</a> Both of these sets of species are possible influenza sources/sinks and it might be a good idea to do some influenza viral screens to see if a new more pathogenic strain has evolved. If it is an influenza it is probably H7 or H3 and that it can affect mammals would be a concern.<br />
<br />
2) H5N8 from Viet Nam is a new emerging highly pathogenic H5 containing lineage. We had an outbreak in Korea that spread to North America and also Europe but it does not seem to be able to persist in either Europe or North America (although for North America that is disputed). However the most recent European cases are not related to the Gochang and Buan Korean lineages, but to a Viet Nam sequence that again spread via Korea.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<a href="https://2.bp.blogspot.com/-2gblh9fOLi0/WXGl1lmvi1I/AAAAAAAAD-I/AEH8o5SlbY0limkrzEviDumkNjj5IerDwCLcBGAs/s1600/2017_7_13_H5N8_M2_beast_annotated1.tree.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="591" data-original-width="783" height="241" src="https://2.bp.blogspot.com/-2gblh9fOLi0/WXGl1lmvi1I/AAAAAAAAD-I/AEH8o5SlbY0limkrzEviDumkNjj5IerDwCLcBGAs/s320/2017_7_13_H5N8_M2_beast_annotated1.tree.png" width="320" /></a></div>
<br />
<br />
The key is vigilance, wider participation and thinking outside the box. The bird breeding might be nothing and unrelated but lets do a quick check. Improved data collection and screening is where we will make the break-throughs not in the VR lab.<br />
<br />Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-34078671055080186712017-07-19T02:35:00.002-07:002017-07-19T02:35:38.333-07:00My F1000 paper on reassortment in H5N8 - even open peer review has flawsThis is really irritating me as this is version 3 of the same story. It is not even a particularly interesting story except it is if you think deeply about it.<br />
<br />
What I want to show is that H5N8 in the US is a subtype that has been produced by multiple events where an H5 containing virus reassorts with an N8 containing virus. To do this I constructed a tree for ALL the H5 sequences in the database and ALL the N8 sequences in the database.<br />
<br />
If I am wrong then the H5N8 sequences from the US would cluster in one group and not be spread across the tree in many distinct clades. They would at least be close neighbours. Am I wrong? Nope they are spread all over both trees. In the H5 tree there are lots of neighbouring H5 sequences that have been sampled but they are from other subtypes. In the N8 tree they are also widely spread with sequences from many other subtypes in between.<br />
<br />
So here is the referees comment <a class="new-orange" href="https://f1000research.com/articles/5-2463/v1#referee-response-18901" style="background-color: white; color: #f2673c; font-family: RobotoMedium, sans-serif; font-size: 12px; outline: dotted thin; text-decoration-line: none;" target="_blank">https://f1000research.com/articles/5-2463/v1#referee-response-18901</a><br />
<br />
I am completely incredulous about how this is a possible argument for rejection.<br />
<br />
If the referees are right int their arguments then you CAN have clades in a tree that are polyphyletic for subtype <b><u>without reassortment being the cause</u></b>. I can simply get from H5N2 to H5N8 by spontaneous mutation of the N2 to the N8 form. I can make hundreds of base changes and insertions and deletions and this is more likely than a simple reassortment event.<br />
<br />
Now let me imagine this is not their argument and that they will admit that reassortment does exist in the clades but that they are not convinced about the specific H5N8 reassortment events. They are suggesting that these occur in both the N8 and H5 tree which are two independent samples in the same pattern <b><u>by chance </u></b>and that there is a need for the internal gene trees to corroborate these events. I say in the paper very clearly that I cannot KNOW what the origins of the H5 and N8 are and I can just make suppositions about them, but I know that a reassortment event has definitely occurred. Otherwise what are the chances that the H5 and N8 genes both undergo substantial mutational changes between samplings of H5N8 and that the neighbours include large numbers of sequences from many other subtypes? If this is true then H5N8 sampling must have been carried out appallingly or in a very biased manner while we detect all the other subtypes with ease.<br />
<br />
To be honest I have the internal gene trees as I just finished them for another paper about a different subject and oddly enough they show exactly what I said in the paper. I was 100% right. These two referees are 100% WRONG. In fact their arguments are so illogical and unsupported by evidence that I was surprised that they were brave enough to put their names to them.<br />
<br />
So let me ignore the sneering way the review is written, because everyone has a time in their life when they thing they know it all and recent graduates tend to fall into this trap more often than not. I know that I was the same 20 years ago when I started my career.<br />
<br />
Let me consider how they use rhetoric in order to create a straw-man to knock down by suggesting that the paper is about discovering reassortment - it is not. The title is very clear it says reassortment in H5N8 and then only part of the H5N8 tree - the US part is actually the main focus of the study. It is a paper about a specific example and the dangers of collecting data by subtype as this gives an incomplete picture of sequence evolution in a segmented virus that can undergo reassortment.<br />
<b><br /></b>
<b>This is the point. If the segments can reassort then they can pass between multiple subtypes in their evolutionary pathway. This is not rocket science this is just suggesting it is better to consider this possibility in trees and sampling and not just carry out phylogenetic analysis by subtype.</b><br />
<br />
This gives me with two options:<br />
1) The referees are idiots.<br />
2) The referees forgot to declare the conflict of interest in that they have a skewed view-point in order to protect their existing work. This paper starts to undermine the idea of monophyletic clades for subtype which underpins the WHO nomenclature system for H5 which Justin Bahl helps to manage.<br />
<br />
I do not think the referees are idiots, but I do think the second point is true and that there are good reasons why Dr Bahl should have declared a real and prejudicial interest and NOT taken up the review. Nobody is objective about seeing their work undermined, ever. I also think this is a good reason for me to ban Dr Bahl and Joseph Hicks from EVER reviewing any of my papers and for editors to consider any review that they provide with suspicion.<br />
<br />Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-46663788428474580872017-04-29T10:19:00.000-07:002017-07-19T03:01:13.846-07:00Let's go back to the beginning.I need to tell a long story and so I need to go back to the beginning. Part of this story I have already told but not very well and so this is an attempt to put everything into context.<br />
<br />
I did a degree in Chemistry and Law at the University of Exeter. When it came to choosing what to do next I wanted to stay in research. I had met some lawyers at the recruitment fairs and they had convinced me that I did not want to be a lawyer. My drive was wanting to change the world, their motivations were purely financial. I was not going to be Perry Mason and I was not going to write environmental protection legislation and so I turned back to science which had been my dream since my teens.<br />
<br />
What caught my eye was protein molecular modelling. I had not done much biological chemistry or biochemistry as an under-graduate but the beauty of the computer models captivated me. It was like the best video game I had ever seen (at that time they used the best graphics computers you could buy and they cost tens of thousands). I had applied for PhDs elsewhere in physical chemistry including with P.W. Atkins (his response was he didn't supervise students, then why was he is the graduate prospectus?). But nothing compared to those ribbon images of proteins.<br />
<br />
I received the Norman Rydon scholarship from the Chemistry Department at Exeter. This allowed me to pick my supervisor and the money would come with me. It was an incredible stroke of luck and so I got to follow my dream and study molecular modelling of proteins. My PhD was in homology modelling of FBP aldolase and also including using molecular dynamics to study the conformations of peptide inhibitors. Unfortunately about the time I finished Swiss-Model appeared and what had taken me 3 years to do now could be done in 10 minutes on a server ... That was the end of homology modelling research for me. What I also learned was that modellers depend on the quality of the data they are given. The FBP structure that I used had some limitations and so my models shared those limitations and so I went back a step to become a protein crystallographer.<br />
<br />
While I was doing my PhD and protein crystallography post-doc I was the general computational biologist or bioinformatician on call for the research group. This was the mid-1990s and so bioinformatics did not really exist as a subject. I did sequence alignment, BLAST searches and phylogenetic analysis for projects where we tried to understand the evolution of protein structure and function.<br />
<br />
What I realised from building these alignments and trees was that if your data is very partial and contains mostly sequences from related species and only a few sequences from more distant species, then this will bias the tree towards your data and possibly away from a better representation of reality. The problem is how do you select sequences to include and exclude? An even bigger issue is the irregularity of the sampling across the "tree of life" (we also did not call it that then either we just called it across the kingdoms). We worked with the recently discovered Archaea and they are dramatically different to the bacteria and the eukaryotes and putting the Archaeal sequences into trees was difficult.<br />
<br />
From alignments I also learned that making secondary structure predictions on all the sequences in the alignment is better than just making predictions on a single instance. They should all have the same structure and so this sequence level variation should disappear in predictions. This turned out the be a major discovery (made by someone else) and that ended investigation in secondary structure prediction (OK I have missed out neural nets etc. but I have serious doubts that they contribute anything more than the use of multiple alignment and using GOR or even Chou and Fasman).<br />
<br />
I continued as a post-doc in protein crystallography but also dabbled in bioinformatics until in 1999 Exeter set-up an MSc in Bioinformatics. As one of the local experts I helped to set up the course and I taught the sequence and structure modules. I was made a lecturer in 2000 and I remained at Exeter for five years until I got caught up in the departmental politics of the closing of the Chemistry Department (I was a lecturer in Biological Sciences and Engineering and Computer Science at the time). Exeter made me redundant but the atmosphere had soured for me there anyway, because they disapproved of me trying to have a work life balance and putting my wife and newly born children first. They also did not like my involvement in politics. I was a city councillor in Exeter for five years.<br />
<br />
One of my students had said did you see this advert for a bioinformatics lecturer at Oxford. I hadn't but the closing date hadn't passed and so I applied. My curriculum was okay. I was much better at teaching than research. Setting myself up as an independent researcher had also been made difficult by having to separate my research from my PhD and post-doctoral supervisor. Luckily I had the support of Dr Ron Yang and we had worked together on some projects. He did the computing (most of it) and I gave the biological input (a bit at the end to make sure that it actually worked). This meant that I had my four publications and that is what matters in UK academia.<br />
<br />
I went to the interview at Oxford. I thought it went well. The head of the course was young, bright and very unexpected. Dr (now Prof.) Charlotte Dean would go on to be head of the department of statistics. What was unexpected was how relaxed and casual she was. She was not the serious unapproachable Oxford don. They offered me the job on the same day and I started a few months later. We moved from Devon to Oxfordshire. I lead the teaching in the modules Charlotte was not leading. In Oxford the Bioinformatics MSc was in the Department of Statistics and I became a Departmental Lecturer in Statistics. This also meant I taught statistics, Perl programming and he biology courses. I had gone from being a lecturer in Biological Sciences and Engineering and Computer Science to a lecturer in Statistics. I had degrees in none of these subjects but I am 100% a computational biologist. This is the curse of being inter-disciplinary. I did start to think about systems biology at Exeter and we had a meeting there where I met Kitano and his work was a major influence on my thinking.<br />
<br />
This is when I became an accidental statistician and I am glad that it happened, because apart from the stunning molecular images I found that data is what fascinates me. I just can never get enough data. I think that if I had been introduced to statistics earlier on then I might have been a statistician from the start but at school it is never taught well and people fear statistics. At Oxford I learnt to love it. When the lecturer who taught statistical data mining left I took over his module. Now I was teaching masters level statistics to people who had degrees in maths and some of them from Oxford. It was an amazing experience, although I have to admit to spending the entire summer reading the textbooks from cover to cover (thanks to Hastie, Tibshirani and Friedman and also to Brian Ripley).<br />
<br />
Charlotte went on to other things and I became acting head of the MSc teaching more and more. My interests now were systems biology and trying to put together data from different experiments and perspectives. What really troubled me and what still sits in the back of my mind is entropy and how it works in living systems. I was a book worm for systems biology.<br />
<br />Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-21540099191832509072016-09-24T01:45:00.002-07:002017-04-29T11:34:00.728-07:00Dawkins' and Pinker's geneThe two biggest problems for Dawkins' and Pinker's interpretation of what the gene means as a heritable "element" that affects phenotype. Is that first it is most often not an element but a system of non-local and interacting elements and secondly and most importantly it will not follow Mendelian genetics. It will not be segregating and discrete. There will be a myriad of variations depending on how the system responds to the environment it finds itself.<br />
<br />
Mendel was lucky with the characteristics he chose to examine and when you do have genes that segregate then you do have a gene as described by the molecular biologist and geneticist, of they type that Pinker riles against. They are just different alleles corresponding to an expressed region of DNA or possibly their cis regulatory regions. They are not the nefarious and indeterminate objects defined by Pinker and Dawkins. If we are to take their views seriously then we have to go back to before the modern synthesis and try again.<br />
<br />
Now that we know that most of the genome can be defined as loosely functional, even if just in terms of spacing between coding regions, then perhaps we do need to look at what the term gene means.Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-4905724817825012842016-09-22T13:59:00.000-07:002016-09-22T13:59:07.140-07:00I finally understand what Dawkins means by geneI was reading a short article by Steven Pinker in the book "<a href="https://www.amazon.co.uk/This-Idea-Must-Die-Scientific/dp/0062374346/ref=sr_1_1?ie=UTF8&qid=1474576459&sr=8-1&keywords=theory+must+die" target="_blank">This Idea Must Die</a>". There Pinker was saying about how molecular biologists have a different view, a very restrictive view of what a gene is. They only consider the protein encoding region of the DNA as the gene.<br />
<br />
That was a Eureka moment as I finally understand what Dawkins was trying to say. He shares exactly the same view as Pinker. To him a gene is a heritable element that produces a phenotype. This is a much older view of the gene than the view I was brought up with. It predates knowing anything about DNA at all.<br />
<br />
To the atomistic and DNA based molecular biologists and geneticists this means the sections of DNA that produce the protein that is responsible for the phenotype. That piece of DNA when expressed causes the phenotype. This is why the molecular biologists got such a shock when they found that there were only 20-30 thousand protein expressing segments, genes in their words, in the human genome. This looks the same as Dawkins' gene but it is completely different. Dawkins because he knows very little about genetics and molecular biology is living in the world view before the modern synthesis which linked DNA to genes. Pinker shares the same anti-reductionist perspective. Even though both would consider themselves materialist and reductionist scientists.<br />
<br />
Their view of the gene would include all of the regulatory elements, both local and non-local in the genome. It would also include all of the mechanisms for regulation and post-translational modification, for localisation and for every other modifier that affects the process of taking that section of DNA or those multiple sections of DNA to produce a phenotype. In Dawkins' view there are no multi-gene effects to produce a phenotype because the genetic atom is actually that complete system that relates DNA and phenotype.<br />
<br />
That is what makes me so strongly critical of Dawkins' work because he has no appreciation of the system at the molecular level. I work with proteins and how they fold and I even dislike DNA. I see the disconnect between the DNA code that can be mutated and the proteins that they produce. There is a huge non-linearity in their connection. The effects of mutations are almost impossible to predict. But if you take Dawkins' and Pinker's way of specifying a gene just as a heritable element then their writing makes a lot more sense.<br />
<br />
It makes more sense but they still ignore the fundamental problems with this view. That is that these "atomic entities" these genes are not atomic. They are overlapping, intertwined, non-local and non-linear systems that cannot be approximated by some atomic genetic theory. In each cell-type the networks of connections between regulatory elements and expressed regions is different and that is not even considering spatial effects. <br /><br />In their world each cell type would have its own set of genes, because each have their own phenotype and own system of expression. Even each of my tissues would become a collective organism and and animal would become a collective of collectives. It is this decision to ignore the relationships between the parts and to impose an artificial genetic atomism on these heritable elements that makes it unrealistic as a view. Playing with my sons' Lego makes it clear. I have all those bricks which are the genes of the model. But unless I put those bits together in the right way I never get my car or my space ship. If you don't think at the systems level you can never understand biology. Atomism and reductionism are doomed to failure.<br />
<br />Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-3327195838593857772016-09-03T03:42:00.001-07:002016-09-03T03:42:56.528-07:00Big Government should Amazon and Starbucks pay more tax?Yesterday I posted about beggar my neighbour and why the Ireland/Apple tax case matters for democracy and stability. Today Amazon and Starbucks are he focus of attention. These are two more in a very long list that will also include Google, Vodafone. Microsoft and many others who use their global clout to minimise regulation and taxation.<br />
<br />
What was amusing is the posts on social media by neo-cons about the companies being justified because the governments waste money and so they should keep avoiding the tax.<br />
<br />
What do governments spend their money on? A lot of it is social security and a lot of that is pensions (much more than unemployment in the UK). So shall we cut pensions because Amazon and Starbucks don't pay up? Should those Daily Mail reading baby boomers who support the neo-con illusion get shafted by their own stupidity? Should we allow them to poke themselves in the eye? Sounds good to me but maybe not.<br />
<br />
What else does the government pay for? Healthcare is a big spend as well. We could allow Amazon and Starbucks to use their tax avoided cash to invest in sponsored hospitals and to reproduce the philanthropy of Carnegie or Rockerfeller. Look at Oracle and the billions of Larry Ellison as an example he used all that cash to build - the most expensive racing yacht in history. So maybe expecting billionaires to give away their money is not such a good idea (I know Bill Gates has done amazing things and George Lucas and Warren Buffett as well but they do not run countries).<br />
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The government also spends money on defence. From an evidence based view this is often a waste of money and the social media post is correct. Britain is building two stupid carriers to fight the types of war that no longer exist against enemies that are no longer there. We are about the renew nuclear weapons that nobody will ever use and that are also a waste of time. Oddly enough I suspect that the person who made the media post would say that this is NOT a waste of government money as the neo-cons are easily deceived by Eisenhower's military industrial complex that sells what nobody needs at an extortionate price.<br />
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Then there is education. We could all do with a lot less of that so that we can all be as stupid as the Daily Mail readers and the neo-con social media enthusiasts. That keeps people from questioning. Yes you need to train an elite to run your business and keep globalisation going but an ignorant population is good for business.<br />
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What about the infrastructure paid for by taxes? The roads etc. Well there is lots of mis-mangement of funds there, but is is caused by the neo-con push to privatise all services and to have the market find the best price. Just ask Halliburton how this works for them in the US and ask any local government how it has worked out in the UK. Higher price poorer service and don't mention PPI.<br />
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So yes Amazon, Starbucks etc. should be paying taxes and while sometimes government does waste money it is a lot better than the alternative.Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-70977286459319912402016-09-02T09:20:00.001-07:002016-09-02T09:20:39.838-07:00Beggar my neighbour: Apple's Tax Problem in IrelandThere is well known economic rule called "beggar your neighbour". It is important in behavioural economics when you consider the model of the repeated Prisoner's dilemma. In that case beggar my neighbour represents the defection strategy. There is also a connection to companies seeking countries with the minimum regulation/taxation. This is when the companies are defecting.<br />
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Companies have a duty to shareholders which in the short term and when you do not expect there to be a repeat of the circumstances means that defection is the preferred strategy and politicians often think the same way. This is sib-optimal capitalism. It is sub-optimal because in reality we have longer term interactions and repeat business which are undermined by defection. Axelrod has shown that the best strategy as proposed by Rappaport is Tit-for-tat. You respond to defection by defecting and then you go back to a position of trust. Trust is the essential feature that makes the system optimal. You have to maximise the trust to reduce the costs of regulation and defection.<br />
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At a national level a defecting country is one that offers a lower level of regulation and taxation compared to all the other countries as business will move to that country and not pay taxes where they actually are active. This is how the Swiss canton of Zugg has become the European HQ of many multi-nationals. Zugg has a tax rate of 5% which is very attractive to global business. Given the size of the canton this minimal amount of tax from a large number of corporations raises more than enough for the infra-structure and services that the canton has to pay for. In fact they should be making a considerable profit. Levels of taxation elsewhere have to be larger because nations are expensive and levels of tax are set to avoid a deficit. This is why Zugg is beggaring its neighbours and why Ireland with its Apple tax deal was also beggaring its neighbours by removing tax revenues from other countries where Apple was doing business. Apple was unlucky enough to be the first company that was brought to court but it will not be the last and Google and Amazon are two more big names that stand out.<br />
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Ireland with a much smaller economy can survive without all the tax that is owed but this deficit is pushed onto all the other EU nations. That is why this sort of tax deal is illegal and why the UK deal with Vodafone also needs to be investigated. Governments do this because they want to keep the jobs in their countries but if I did this as a small business or as an individual even if I did not do my duty well enough only in the expectation of a future benefit I would be in jail for up to 12 years and face an unlimited fine under UK law. In fact the recent report about the possible dropping of the investigation of BHS in return for Sir Philip Green paying a large sum to the pension fund is also bordering on illegal under the Bribery Act 2010. I begin to see why an Italian mafia judge called the UK the most corrupt country in Europe.<br />
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Ireland has been caught cheating but both Ireland and Apple are going to seek to contest the judgement. The only way that you can prevent beggar my neighbour is if we go beyond short term interests or if we promote supra-national agreements. We call these trade deals and although TTIP is a dirty word at the minute there are many others that we rely on everyday. The WTO is the largest agreement to make sure that nations do not deliberately cause economic hardship for each other. But the most successful is the European Union and that is why Ireland and Apple in the end have to lose if we are to have any faith in nations and democracies and if we want to live in a world which has not been taken over by corporations.<br />
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So why does not being able to beggar your neighbour matter? History shows that wars are usually about resources and as a response to internal economic challenges. Harming another countries economy has political and social consequences and not just economic ones. If we want a more peaceful and equal world we have to get beyond Brexit and Beggar my Neighbour and start understanding the long term benefits of working together.Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-71311863102130195812016-06-20T05:55:00.002-07:002016-06-20T06:03:51.794-07:00BrexiteersI have just received the EU Myth Buster from the Brexiteers. Firstly it still has the already proven wrong 350 million a week claim, as well as the nonsense about expansion to new members including Turkey. This is all scare mongering and the gall of the Brexiteers to claim it is Remain that are using economic fear to win the argument is just nonsense.<br />
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On the back the great and the good making their arguments. I wanted to go through them one at a time.<br />
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1) Sir Richard Dearlove - former chief of MI6.<br />
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"Brexit would bring about two potentially important security gains: the ability to dump the European Convention on Human Rights ... and more importantly, greater control over immigration from the European Union."<br />
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Sorry but this makes me very worried when a former head of the security service thinks that not having human rights is a good thing. This is the person who was in charge during 9/11 and then the dodgy dossier fiasco. Regarding his second statement, is the EU a source of terror threats to the UK? The 7/7 attacks were home grown and we do control immigration from outside the EU. He is also on record as stating that the media have exaggerated the threat from Islamic terrorists. So maybe he thinks the French farmers have been radicalised and are a threat?<br />
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2) Tim Martin - chairman of Weatherspoons<br />
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"The EU places tariffs on goods from outside the EU, which is bad for British shoppers and the developing world. And the EU forces us to charge VAT on goods, pushing up bills for working families."<br />
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By his argument leaving the EU and becoming one of those countries outside this is going to be good because now we are subject to those tariffs he is talking about. The levels of taxation are set by governments and they are to make sure that the finances of the country are in good order. The UK sets its own levels of VAT. These had to be increased because of the banking crisis not the EU. When we face tariffs because we are outside of the EU tax levels are likely to rise even more.<br />
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3) Nigel Lawson - former Chancellor of the Exchequer.<br />
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"As Chancellor, I became increasingly aware that, in economic terms, membership of the EU did us more harm than good. Outside the EU, we would prosper, we would be free and we would stand tall."<br />
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Sorry Nigel but this is pure rhetoric without a single shred of evidence or valid argument. He was last Chancellor in 1989 before the Berlin wall had fallen. The world has changed a bit since then and certainly the economy has changed beyond all recognition. Free and tall are not economic arguments, they are useful for boxers and cage fighters but they do not secure wealth for nations.<br />
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4) John Longworth Director of the British Chambers of Commerce.<br />
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"The EU interferes with UK firms and stacks the rules in favour of a select number of big businesses. It we Vote Leave jobs will be safer. We can have faster growth and greater prosperity in the future."<br />
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The EU spends a very large amount of its business spending on what are called SMEs and not the very large firms. Big business and big interests are very effective at lobbying the EU. My dad was a lobbyist for the Cattle Breeders Association and the UK farming industry which is hardly a big business. He would have never dreamed of voting out. The EU actually is more effective than the UK in dealing with the excesses of global business such as Microsoft and Google. These are companies that individual nations do not take on. In fact the UK government is noticeable in its reticence to get involved in taxing many of these businesses (Vodaphone is a high profile example) which get special tax deals that are certainly not given to small UK firms. Exactly the opposite to his claims is closer to reality.<br />
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5) Gisela Stuart Labour MP<br />
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"The rights we have won for British workers came from our Parliament, not the EU. The EU is run in the interests of the big corporations who spend billions lobbying to make it work for them."<br />
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I think that billions is an exaggeration. Even big business cannot spend that much on a Parliament that has so little legislative authority. I seem to remember the Conservatives opposing EU legislation precisely because it did protect worker's rights and asking for opt-out clauses. I seem to remember the social charter causing uproar from Mrs Thatcher, which does not agree with the MP's claims. It was only finally accepted in 1998 by a Labour government. I was also discussing this issue and where Deutsche Bank would move to if there was Brexit and the wife of one of their employees said not back to Frankfurt because they are only allowed to work a 37 hour week in Germany because of the EU legislation (that has not bee adopted by the UK) whereas her husband has a 67 hour week here.<br />
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It is amazing that in 5 quotes there is not a single good reason to Brexit. There is nothing there that is not fabricated, untrue or not pure fallacy. If that is the best they have got in their arguments then the Remain camp have very little to worry about.Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0tag:blogger.com,1999:blog-974646706961868356.post-40154536166344367712016-04-13T00:04:00.000-07:002016-04-13T00:04:46.693-07:00Thoughts on Heritability<div style="border: 0px; color: #383838; font-family: gotham, helvetica, arial, sans-serif; font-size: 14px; line-height: 1.57143em; margin: 0px; padding: 0px;">
Using Waddington's idea of canalisation. This is the related to the width of the canalisation - this is the maximum variation between a pure in bred low phenotype and a pure in bred high phenotype. This is the variance in that characteristic which is attributable to the genes.</div>
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This is going to be very hard to measure unless you do it for a genuine population. If you have a non representative sample then that will have its own variability and the variation in that characteristic will depend on the state of all the different end points you are starting from in a normal mating population carrying all of its history and variation. Think of dogs the dog population includes all the breeds but the variation within breeds is very low, the same with horses but with humans you have Usain Bolt and me to compare for our 100 metres performance.</div>
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The width of the canals is important as it shows the plasticity in response to environment. How far does it need to be pushed to get someone outside the normal bounds. The genes make the landscape and they do not determine the outcome except in pure bred lines where the canals are very narrow. </div>
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High heritability could actually signify large canals and low determinism because we are very far from a pure bred line and everyone is close to the middle of a large canal. But it could also indicate low variation and a multi-modal population - mixing of species, comparing apples and oranges. Conversely low heritability measures would mean that there is low variation with very narrow canals and it is very strongly inherited.</div>
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The concept of heritability implies that you can have a pure bred line for a specific phenotypic characteristic and so that characteristic must be inheritable. So my reason for questioning the paper rejecting Haidt and heritability is that why would his classifications be capable of being bred for? Can I breed someone who believes in justice over everything? Can I breed someone who finds disgust in the unclean their biggest driving force? Can any of these higher human constructs be embedded into genes or are they more accurately modelled at the meme/cultural evolutionary level? This is what I meant by there being strong determinism - that you could breed for it and that the genes would determine the effect. </div>
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My opinion is that they are at the cultural evolutionary level and only the very simplest of behaviours is canalised at the genetic level. This would be probably things like higher level reasoning, personal identity, desire to reproduce, desire for satisfaction etc. The advantage of the cultural/meme level is that it is NOT Darwinian. It develops during lifetimes and is directly passed on to the next generation. It is Lamarckian and not wasteful random exploration. It builds on what we already have and is rapidly modified. It is much faster than genetic evolution. </div>
Andyhttp://www.blogger.com/profile/17784856869056663331noreply@blogger.com0