{"id":159,"date":"2013-08-18T00:05:14","date_gmt":"2013-08-18T00:05:14","guid":{"rendered":"http:\/\/thetravellerslastjourney.com\/shai\/science-090813-ii-pubpeer-social-influence-bias-transcription-factories-microbiome-speciation-and-neuronal-methylation"},"modified":"2019-07-15T13:21:29","modified_gmt":"2019-07-15T13:21:29","slug":"science-090813-ii-pubpeer-social-influence-bias-transcription-factories-microbiome-speciation-and-neuronal-methylation","status":"publish","type":"post","link":"https:\/\/thetravellerslastjourney.com\/shai\/2013\/08\/18\/science-090813-ii-pubpeer-social-influence-bias-transcription-factories-microbiome-speciation-and-neuronal-methylation\/","title":{"rendered":"Science 090813 II: PubPeer, social influence bias, transcription factories, microbiome speciation, and neuronal methylation"},"content":{"rendered":"

This is a continuation of an effort to review\u00a0Science 9 August 2013 Vol. 341 no. 6416.<\/p>\n

V. PubPeer<\/a> is a nice, interesting, and new website, designed to allow readers to critique papers<\/strong> they’ve read.<\/p>\n

VI. P647, I read the full research paper, entitled Social Influence Bias: A Randomized Experiment<\/em>\u00a0– basically about how knowing about aggregated opinions affects our own<\/strong>, albeit in different ways depending on the data available and our relations to it. The first and unsurprising conclusion that is drawn from this study is that knowledge of general opinions affects one’s own opinions. Although specific conclusions may be applied to the study’s model\/methodology, there’s not all that much more that can be generalised further. Nonetheless, the study did demonstrate positive herding, and neutralization of negative social influences.<\/p>\n

It’s worth noting also, that this paper provides great direction if I’m ever to research not merely rating systems, but also the negative effect so-called\u00a0collective intelligence<\/em> can have on society (references #1 through to #14).<\/p>\n

VII. There was a Perspective piece (P621) along with an original research article (P664), about the “nuclear transcription factories” that form around RNA polymerase II<\/strong> and their activity. I found these to be of interest in the first place because they characterise a mode of complexity within molecular biology: The central dogma of molecular biology is an incredible simplification which hides not only the control of gene activation, but as studied here, also the Spatio-temporal framework within which transcription occurs.<\/p>\n

I should probably note that part of what makes this a high impact paper is the methodology – details for which read again – by which the authors adroitly combine existing technologies to answer an old question. The authors show that the “transcription factories” are transiently generated in response to demand, and that in response to increased demand they form more often and last longer.<\/p>\n

Part of what makes this paper interesting to\u00a0me<\/em>, is the perspective it offers on transcription, and that once I’m in that frame of mind I’m likely to wander in wonder about all sorts of things. It seems as if the nucleus (which is of-course, not<\/em> a homogenous locality) can localize demand for transcription, and that this demand is satisfied by bursts of protein quaternary-structural assemblage and transcription initiation. Amongst the tantalising questions unanswered is whether these “factories” are specific in any way to gene (sets), and whether and how initiation dynamics affect total transcription dynamics.<\/p>\n

VIII. There’s another fascinating original research article (P667), entitled\u00a0The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus<\/em>\u00a0Nasonia. By “hologenome” the authors refer to the functional unity of gut microbiome plus host genome, as they show that the microbiome can contribute to speciation by causing lethality in certain hybrids<\/strong>.\u00a0<\/em>This was demonstrated in wasp species, and lethality could be abrogated by raising antibiotic-cured hybrids. This study is fascinating for the light it shines on the role of the microbiome, and for blurring the lines that demarcate the species that are the carrier vehicles for genes in evolution.<\/p>\n

IX. The last paper (P629) I liked in this journal – Global epigenomic reconfiguration during mammalian brain development<\/em>\u00a0– \u00a0was about the growing understanding of the role of methylation in the central nervous system. Methylation<\/strong> (including hydroxymethylation) in neuronal genomes specifically, continues post-natal, strikingly overlapping with the period of synaptogenesis and synapse pruning<\/strong> (weeks to years in mice to humans respectively).<\/p>\n

Hypothetically, since this is a post-natal process, it may be dependent on sensory-input dependent neuronal activities, and in doing so, might contribute to another level of neuronal heterogeneity. What is more likely (though without excluding these hypotheses) is that the methylation contributes to “normal” neuronal sub-type formation – this idea was encouraged by the data, namely the types of genes that were found to be methylated.<\/p>\n","protected":false},"excerpt":{"rendered":"

This is a continuation of an effort to review\u00a0Science 9 August 2013 Vol. 341 no. 6416. V. PubPeer is a nice, interesting, and new website, designed to allow readers to critique papers they’ve read. VI. P647, I read the full research paper, entitled Social Influence Bias: A Randomized Experiment\u00a0– basically about how knowing about aggregated […]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[159,90,128,279,75,281,16,17],"tags":[],"metadata":[],"class_list":["post-159","post","type-post","status-publish","format-standard","hentry","category-all-posts","category-blog-posts","category-journal","category-journal-review","category-meanwhileii","category-reviews","category-science","category-science-news"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack-related-posts":[{"id":2499,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2013\/08\/17\/saturday-august-17-2013-2\/","url_meta":{"origin":159,"position":0},"title":"Saturday August 17, 2013","author":"Pala","date":"August 17, 2013","format":false,"excerpt":"Journal: Reading science literature: I did a once-over browse of the TRENDS journals that have been published so far in this month, and have selected a few that I thought could be interesting. In TRENDS IMMUNOL I found an article that claims to review what's known about the genetic implications\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2475,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2013\/04\/18\/science-review-keystone-species-population-cycle-dampening\/","url_meta":{"origin":159,"position":1},"title":"Science Review: Keystone species population cycle dampening","author":"Pala","date":"April 18, 2013","format":false,"excerpt":"Concepts:\u00a0Keystone species, and population cycle dampening. Source: Science\u00a0original research Report\u00a0(April 5, 2013). Background: A keystone species is one that disproportionally affects its ecosystem*. Relationships between predator-prey are generally assumed to be cyclic insofar as their amounts reflect each other in a cyclic manner (e.g. many plants feed many herbivores that\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":1759,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2011\/01\/08\/the-seven-beauties-of-science-fiction-br-2\/","url_meta":{"origin":159,"position":2},"title":"The Seven Beauties of Science Fiction (BR)","author":"Pala","date":"January 8, 2011","format":false,"excerpt":"The Seven Beauties of\u00a0Science Fiction\u00a0is a book written by\u00a0Istvan Csicsery-Ronay Jr, a professor of English at\u00a0DePauw University\u00a0and published in 2008. I wanted to have a bird's eye view; I ended up in outer space.\u00a0(Preface) There's something\u00a0inexpressible\u00a0about\u00a0SF[1]. This\u00a0inexpressible something, the author suggests, reflects the role of SF in helping us parse\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2515,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2013\/04\/07\/science-review-neural-decoding-of-dreams\/","url_meta":{"origin":159,"position":3},"title":"Science Review: Neural decoding of dreams","author":"Pala","date":"April 7, 2013","format":false,"excerpt":"Editorial notes: This is the first\u00a0in a\u00a0series of 30 Science News, documented mostly in Evernote between April 2013 and October 2014. Concepts: Neural decoding of dreams. Also: hypnagogic hallucinations. Source: A News and Analysis\u00a0and an (original research)\u00a0Report, both in Science\u00a0(April 5, 2013). History: A 2005 study developed an algorithm that\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2482,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2013\/04\/25\/science-review-animal-self-medication-2\/","url_meta":{"origin":159,"position":4},"title":"Science Review: Animal self-medication","author":"Pala","date":"April 25, 2013","format":false,"excerpt":"Concept: Animal self-medication. Source: Perspective\u00a0in Science\u00a0(April 12, 2013). Background: Self-medication (incl. prophylactic) can be administered to self, inter-generational (e.g. fruit flies lay preferentially in high ethanol foods following detection of parasitoid* wasps), social (e.g. anti-microbial resin incorporated by wood ants into nest). Criteria include that it must be costly (thus\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":2519,"url":"https:\/\/thetravellerslastjourney.com\/shai\/2013\/04\/07\/science-review-geoneutrinos\/","url_meta":{"origin":159,"position":5},"title":"Science Review: Geoneutrinos","author":"Pala","date":"April 7, 2013","format":false,"excerpt":"Concepts: Geoneutrinos Source: A News\u00a0piece in Nature\u00a0(April 3, 2013). History: The 2011 Fukushima disaster, and the consequent closure of Japanese nuclear reactors, silenced the barrage of particles to which the Japanese underground particle detector KamLAND was normally exposed. Thus KamLAND could clearly read the trickle of neutrinos that originate within\u2026","rel":"","context":"In "All Posts"","block_context":{"text":"All Posts","link":"https:\/\/thetravellerslastjourney.com\/shai\/all-posts\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]}],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/padotI-2z","_links":{"self":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/posts\/159","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/comments?post=159"}],"version-history":[{"count":0,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/posts\/159\/revisions"}],"wp:attachment":[{"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/media?parent=159"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/categories?post=159"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/tags?post=159"},{"taxonomy":"metadata","embeddable":true,"href":"https:\/\/thetravellerslastjourney.com\/shai\/wp-json\/wp\/v2\/metadata?post=159"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}