User:Gbaor/Thoughts

Things I should not forget, and recall them in the right time.

Innovation Africa

 * Building institutions for endogenous development - "...paper that Jean Gradé and her colleagues contributed to the Innovation Africa symposium in Uganda; it will appear in the upcoming book entitled Innovation Africa, due to appear this (2008) autumn." The book will be probably freely available via FAOs website (this is just a guess from me).

 Highlights


 * "When assessing the current situation of natural resources in their area, elders cited several problems that were not present, or were less severe, when they were young. These include: less rain, fewer water-catchment ponds and more contamination of the limited available water; diminished plant life, including fewer savannah trees; dramatically fewer wild animals; erosion; and lower soil fertility. They felt that the traditional indigenous knowledge system and communal efforts to manage resources had weakened."


 * "In an effort to help ‘modernise’ the culture, outsiders did not recognise traditional leadership structures and did not deal with Karamojong leaders directly."


 * "Elderly pastoralists recalled a clan of women, the Ngiyepan, who protected trees in various ways,... they were persuasive verbally and sometimes even physically. It is unclear why they are no longer active,... "


 * "They perceived two more recent external innovations – automatic weapons and forced schooling ... The school system also led people to look outside of their own ‘culture-box’ for new answers to the same problems. Elders saw tradition and schooling as mutually exclusive options. In endogenous development, people seek a balance between modern and traditional practices.(e.g. ‘modern’ schooling with the traditional system)"


 * "One potential bridge to this process is the institution of traditional healers.Because the Karamojong depend on cattle for both subsistence and cultural pride, one of the most important forms of indigenous knowle is ethnoveterinary knowledge ... This includes various different treatments: store-bought, homemade, prescribed and/or prepared by traditional healers, mainly from plant extracts."


 * "participatory action research (PAR) approach and an ethnographic framework were used. PAR is ‘research which involves all relevant parties in actively examining together current action (which they experience as problematic) in order to change and improve it. PAR is not just research which is hoped will be followed by action. It is action which is researched, changed and re-researched, within the research process by participants’ (Wadsworth, 1998)"


 * "A natural extension of ethnoveterinary knowledge in a damaged environment is medicinal plant agroforestry. ... high priority to multipurpose plants."


 * "One component of ethnoveterinary knowledge preservation is documentation and conservation of the medicinal plants. ... Tree planting is not otherwise a part of Karamojong culture. The healers’ associations, however, now promote agroforestry and protection of medicinal plant species. Their agroforestry scheme has focused on domestication of 32 tree species, 24 of which are indigenous."


 * "Many make thick fences from thornbush branches to protect crops from wild animals and raiders. ... These fencing plants are medicinal, fruit-producing and/or protective."


 * "Dengel Lino, a livestock healer from Bokora: ‘We used to share food and knowledge only with our family, but now I feel comfortable sharing with other healers from Pian and Kenya. It has helped me with my cattle’. ... Peace has been an unintended consequence of these meetings, but is a critical component of development."


 * "In the Karamoja culture, after two people have shared a meal, they are like kin and cannot harm one another. ... More peace leads to more sharing, and the virtuous cycle continues."


 * "The healers’ associations decided to focus on agroforestry schemes and the prevention of endemic diseases (internal and external parasites), mainly of cattle."


 * "The success may be due partly to the fact that it has been an endogenous movement (from within) rather than exogenous (initiated or led from outside). Since indigenous people have led the processes from day one, they have developed the skills and local capacity to continue without help from outside."

Good old friends
Commeniusgasse-team, Vienna, 2007
 * Rafel from Barcelona
 * Zhonggui from Hangzhou
 * Milán from Budapest
 * me

Genome analysis
Reading lecture notes for E250-220 from Johan van Arendonk and Henk Bovenhuis (November 2000) - printed version

 Highlights


 * Conservation of a breed is especially important for those breeds which are shown to have a large genetic distance to other breeds.
 * Molecular biology
 * Keywords: restriction enzymes, restriction map, DNA cloning, plasmid, genomic library, cDNA library, polymerase chain reaction, human genome project, microsatelite
 * In the future, it will be increasingly difficult to find areas of animal health and production that are not substantially affected by this technology
 * Also sequencing of the genomes of parasites and pathogens will be important, in order to control these organisms.
 * Molecular biology techniques are creating a revolution in veterinary diagnosis, ... the tests can identify the presence of particular species/strains/serogroups of viruses, retroviruses, bacteria, fungi roundworms or tapeworms. They can distinguish between meat from different species of animals.
 * Parentage testing and forensic research
 * Keywords: DNA typing, Hardy-Weinberg equilibrium, Linkage equilibrium
 * Population substructure
 * Keywords: genetic differentiation, Wright's F statistics, fixation index, Wahlund principle
 * Genetic differentiation may result from natural selection favoring different genotypes in different subpopulations, but it may also result from random processes in the transmission of alleles from one generation to the next of from chance differences in allele frequency among the initial founders of the subpopulations.
 * Fixation index ... equals the reduction in heterozygosity expected with random mating at any one level of population hierarchy relative to another ... it allows an objective comparison of the overall effect of population substructure.
 * In population genetics, a race is a group of organisms in a species that are generally more similar to each other than they are to the members of other such groups.
 * Isolate breaking (Wahlund principle)...(i.e. reduction of homozygosity) - Fusion of subpopulations with random mating and Hardy-Weinberg equilibrium decreases the average frequency of homozygous recessives by an amount equal to the variance in allele frequency among the original subpopulations.
 * Interval mapping of QTL
 * Keywords: genetic marker, quantitative trait loci, interval mapping,
 * Mapping of a QTL requires the usage of multiple marker genotypes in the analysis.
 * Interval mapping - term is used for estimating the position of a QTL within two markers (often indicated as "marker-bracket"). Interval mapping is originally based on the maximum likehood, but there are also good approximations with simple regression.
 * Regression on QTL probability - For a given haplotype that was inherited from the sire, we can calculate the probability for having inherited the Q or the q allele It seems therefore natural to regress phenotype on Q-probability. The model is (standard): y=μ+αx where y is the observed phenotype, x is the probability of having inherited a paternal Q, given the observed marker genotype

Stopped at 5-10 - put aside, more background knowledge needed

Genomic selection
''Off-topic note: This reminds me a (great) movie - Gattaca. Scary... Could this come true also in the human society? Well, if we take Verne as a reference, then the answer is "yes".''

Notes and exact citations from Journal of Animal Breeding and Genetics; December 2007 - Vol. 124 Issue 6 Page 321-390 ISSN 0931-2668 link, my notes are in square brackets

Keywords to be familiar with: genomic selection, linkage disequilibrium, BLUP, Bayesian statistics, estimated breeding value (GS-EBV), Bulmer effect, haplotype, prior distribution, Deterministic model, stochastic simulations

 Genomic selection (Editorial by Theo. Meuwissen)

Full title: Genomic selection : marker assisted selection on a genome wide scale (Editorial by Theo. Meuwissen)
 * Genomic selection (GS) may be deﬁned as the simultaneous selection for many (tens or hundreds of thousands of) markers, which cover the entire genome in a dense manner so that all genes are expected to be in linkage disequilibrium with at least some of the markers.
 * A variety of methods have been suggested for the calculation of GS-estimated breeding values (EBV), ranging from BLUP (Kolbehdari et al.), Bayesian methods such as BayesB (Meuwissen et al., Genetics 157:1819–1829), and machine learning techniques (Long et al.). These methods differ in their assumptions about the underlying genetic model. ... The method that reﬂects the biological nature of the gene effects closest is expected to yield the most accurate GS-EBV. Thus, more research into the distribution of gene effects is warranted.
 * Traditional selection is successfully improving a large number of traits in ongoing breeding schemes, but it requires widespread (all selection candidates), reasonably accurate and preferably early in life recording of the traits. Especially, functional traits only partially fulfill these requirements, and their rates of genetic gain are therefore much lower than that of production traits. As mentioned in several of the papers, GS may overcome these problems, although Calus and Veerkamp found substantially reduced accuracies of GS-EBV for lowly heritable traits.
 * As GS has the potential to achieve a more balanced selection response (balanced over production and functional traits), and substantially reduced inbreeding rates (Daetwyler et al.), its main effect on future breeding schemes may be an increased sustainability.

 Genomic selection (Review article by M.E. Goddard and B.J. Hayes)

Full title: Genomic selection
 * The ideal method to estimate the breeding value from genomic data is to calculate the conditional mean of the breeding value given the genotype of the animal at each QTL. This conditional mean can only be calculated by using a prior distribution of QTL effects so this should be part of the research carried out to implement genomic selection.
 * Meuwissen et al. (2001) proposed a variant of MAS that they called genomic selection. The key features of this method are that markers covering the whole genome are used so that potentially all the genetic variance is explained by the markers; and the markers are assumed to be in LD with the QTL so that the number of effects per QTL to be estimated is small. Using simulation, they showed that the breeding value could be predicted with an accuracy of 0.85 from marker data alone.
 * Statistical analysis to calculate EBV from genome-wide DNA markers It is convenient to think of the process in three steps: 1. Use the markers to deduce the genotype of each animal at each QTL. 2. Estimate the effects of each QTL genotype on the trait. 3. Sum all the QTL effects for selection candidates to obtain their genomic EBV (GEBV).
 * An advantage of using the correct prior is that the estimates of the biggest or most signiﬁcant QTL are not overestimated. This means that the effects can be estimated from all available data regardless of whether the data was part of that used to discover the QTL or not.
 * The requirements to implement genomic selection in breeding programmes are relatively simple. Generally there will be a discovery dataset where a large number of SNP have been assayed on a moderate number of animals who have phenotypes for all the relevant traits. A prediction equation that uses markers as input and predicts BV is derived from this data. There should then be a validation sample ... The prediction equation is tested to assess its accuracy on this independent sample.
 * ...the estimation of QTL effects can be carried out on animals that are completely separate from the selection candidates. In fact the selection candidates do not need to have phenotypes recorded at all.
 * Interbull provides EBV that compare bulls from around the world. This situation is favorable to livestock producers but is threatened by genomic selection. Unless all genomic EBV are calculated using the same prediction equation(s), they will no longer be comparable.
 * [Database held by organizations responsible for national genetic evaluation] ... this may inhibit commercialization of genomic selection because it makes it difficult for a company to recover the investment needed to develop and market a set of markers for genomic selection. The alternative would be for each company to have its own markers, database and EBV. How the future will unfold is not clear.
 * Genomic selection has the potential to radically alter the structure of livestock breeding programmes. ... formal progeny testing will disappear ... [it could] potentially cut the cost of operating dairy breeding companies by 92% (Schaeffer 2006). More generally, genomic selection will cause a tendency to shorten generation intervals because the markers can be genotyped at birth or even before.
 * Except for the cost of genotyping, "stud" animals could be produced as cheaply as commercial animals. Then traditional stud breeders who record their animals with a breed association would be unable to compete with breeders who relied entirely on marker data.
 * Genomic selection means that all selection candidates can be evaluated for any environment for which the prediction equation is known. Consequently, many divergent populations, each specialized to a particular environment, are likely to be replaced by one general purpose population with a decrease in the total effective population size. [Is this an advantage or disadvantage? Decreased effective population size should mean loss of genetic diversity...]

 Prediction of response to MAS and GS (Original article by J.C.M. Dekkers)

Full title: Prediction of response to marker-assisted and genomic selection using selection index theory

P = G + E = Q + R + E Path coefﬁcient diagram illustrating the relationships among components contributing to phenotype with marker-assisted selection for a single trait [changed a little due to technical difficulties] :


 * P ← G
 * ← E

$$\sqrt{1 - h^2}$$


 * G ← Q
 * ← R

$$\sqrt{1 - q^2}$$


 * Q ← Q^ (Q')
 * ← e

$$\sqrt{1 - r^2_Q}$$ ...... [Q^instead of Q]

Where: P, phenotype; G, total genetic value; E, environmental component of P; Q, component of G that is associated with markers; R, component of G that is independent of markers; Q^, estimated breeding value (EBV) for Q based on marker data; e, prediction error of Q^; $$h_2$$, heritability of P; $$q_2$$, proportion of genetic variance associated with markers; $$r_Q'$$, accuracy of Q^ as a predictor of Q;

Stopped at: p. 334 - Extension to multiple traits

Idea collection for "the" wiki

 * Start a Wikiversity Project
 * Template:Module Intro Page
 * Template:Make Navigator
 * Activity type icons
 * Educational technology - there is a lot here
 * Educational Technology Lesson Plans
 * Re-shape a part from here?
 * The layout of this guided tour could be good for the tutorials.

New colleagues

 * User:Anita op
 * User:Yvn
 * User:Syounis
 * User:Habibjan

Motivation for contributing to Wikipedia/Wikiversity (from Colloquium)
I was told this is the place to ask questions. This is to people who are contributing.

Needless to mention that I'm a newbie. I was really impressed by the contributions people had in WIKIPEDIA.

The question isn't a productive one for either of us or shall I say it is in a way. I could write for improvement on articles for no less than 16hrs/day.


 * Q: Do you get paid for this work? OR What are the benefits, monetary or otherwise, one could have by a great contribution like yours?


 * The answer can't be recognition as all this can and will be deleted or changed or updated, probably before I die. It is true that change is constant and inevitable but creation that lasts the longest is more powerful. Thinking of writing an article or contributing so much that lasts for 100 years after I die (like you did) but need more out of it for the time I live.

I could do a lot of this if I get anything out of it, I think. Rather this is what I love to do. But I also love money. I don't want to do it as a selfless service as of now. I'd better have my own blog to document my thought process that no one could edit. I know wikipedia is an encyclopedia, needs existing knowledge and isn't a book about undocumented inventions, theories or simply ideas but I'm equally good at this. I've thoroughly studied all the articles from Getting started onwards (still a lot to learn on formatting). I was learning some Wikipedia's own rule for using bold and italic. I simply loved the fundas.

IF there is no answer then I probably have this feeling of 'giving back to the society and getting contentment by the selfless work' post 65yrs of age.

Hopefully I'll have an honest and helpful answer.

P.S: I do not want you to take this message de-motivating in anyway. If you have a slightest of that feeling in the corner of your heart please feel free to delete it and do not care to reply. You've done an amazing job buddy and I don't want you to rethink on your credits due to this scribble of mine.

--Amit Bhise 07:25, 1 February 2010 (UTC)


 * Welcome to Wikiversity, Amit. Wikiversity is a non-profit organization. I don't get paid for contributing to Wikiversity. There may be some people who are paid by their job to contribute to Wikiversity, but Wikiversity does not pay anyone, and I don't know of anyone who is paid by their job to contribute.


 * People have different motivations for contributing to Wikiversity (and for supporting Wikiversity with monetary donations for that matter). Some people may be motivated because they feel contributing will earn them recognition. Some people may be motivated by selflessness. Some people may feel that learning should be free, or that charging people for an education is wrong, and will be motivated by that to volunteer their time helping to make learning free. Some people may feel like they have an obligation to help others and be motivated by that.


 * What motivates a person can directly effect what benefit that person sees in contributing to Wikiversity. A person being paid by their job might see a limited monetary benefit to contributing to Wikiversity. Someone whose motivated by a feeling of obligation might see helping others as the benefit. Someone who feels that learning should be free might see contributing to a free resource for learning as a benefit. There is no one correct answer. The answer depends on the person and what you make of the answer. Giving back is also a possible answer.


 * All in all, people find Wikiversity a useful resource.


 * Wikiversity does welcome your ideas and theories as part of any learning you wish to do. Wikiversity is different from Wikipedia in that way. -- dark lama  12:35, 1 February 2010 (UTC)


 * First, do you realize that this is Wikiversity, not Wikipedia ? Here the rules are a bit different, and you can indeed have your own research or project area that nobody else can edit.


 * Now, as for the basic motivation, I recently watched a documentary, "The Human Spark", which studied differences between humans and other animals. One that's pertinent here is that humans seem to have an innate desire to teach.  Why should this be ?  Well, being that we are social animals and rely on one another for survival, helping out other humans is likely to help you and your family, say if they return the favor and help you out some day.  This was far more likely when we lived in small groups, but, thankfully, many people still feel the desire to help others who are very distant from them.


 * Another way to look at it is that it's essentially the same motivation as those who give to charity, such as donations to Haiti. Some give out of altruistic motivations, some so they will feel better about themselves, some so they will be recognized by others, etc.


 * Finally, I suggest you use better titles for any additional questions, as "A question" tells us nothing about what you are asking. "Motivation for contributing to Wikipedia/Wikiversity ?" would be a good title.  StuRat 14:54, 1 February 2010 (UTC)

Wikiversity talk: Original research
...About Wikiversity being a free subset of WP, I disagree and I think you got that part backwards. Universities usually have libraries with encyclopedias. I think Wikiversity has the potential to be much larger than Wikipedia. Wikipedia consists only of a subset of that which can go on at Wikiversity. -- darklama 20:33, 21 February 2010 (UTC) .....Are you saying that WP is a subset of wv? Don't you think that is a little grandiose?--JohnBessa66.pngBessatalk 14:01, 22 February 2010 (UTC) ...........I think thinking of the projects in terms of one being subset of another is a mistake. If you are to going to do that though than yes WP is a subset of WV. No I don't think that is a little grandiose. The extent and scope of Wikiversity is broader then Wikipedia. Wikipedia is limited in extent and scope to writing articles encyclopedic in nature and can be seen as a single work or collection. Wikipedia could amount to either a single book or a volume of books that sit on a bookshelf if it were in a library. This is true of Wiktionary, Wikiquotes, and Wikispecies as well. In ascents Wikibooks extends that practice from one book to many. If Wikibooks had existed first I don't think people would of seen a need to have separate projects for an encyclopedia, a dictionary, a quotes book, and a species book, because they are all books. If Wikiversity had existed first writing books could of happened on Wikiversity with a similar outcome. The same cannot be said for the reverse. I wouldn't expect to find lessons in an encyclopedia, or mathematic books, science books, etc. incorporated inside an encyclopedia. I would expect to find all those at a University though. I see nothing grandiose about that. -- darklama 14:49, 22 February 2010 (UTC)