{"id":11865,"date":"2017-03-31T07:32:06","date_gmt":"2017-03-31T07:32:06","guid":{"rendered":"http:\/\/revoscience.com\/en\/?p=11865"},"modified":"2017-03-31T07:32:06","modified_gmt":"2017-03-31T07:32:06","slug":"massive-computer-analyzed-geological-database-reveals-chemistry-ancient-ocean","status":"publish","type":"post","link":"https:\/\/www.revoscience.com\/en\/massive-computer-analyzed-geological-database-reveals-chemistry-ancient-ocean\/","title":{"rendered":"Massive, computer-analyzed geological database reveals chemistry of ancient ocean"},"content":{"rendered":"<figure id=\"attachment_11866\" aria-describedby=\"caption-attachment-11866\" style=\"width: 300px\" class=\"wp-caption alignright\"><img loading=\"lazy\" decoding=\"async\" class=\"wp-image-11866 size-medium\" src=\"http:\/\/revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385-300x231.jpg\" alt=\"\" width=\"300\" height=\"231\" title=\"\" srcset=\"https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385-300x231.jpg 300w, https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg 500w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><figcaption id=\"caption-attachment-11866\" class=\"wp-caption-text\">A stromatolite from Northern Wisconsin in the courtyard of Weeks Hall on the UW\u2013Madison campus. DAVID TENENBAUM<\/figcaption><\/figure>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">A study that used a new digital library and machine reading system to suck the factual marrow from millions of geologic publications dating back decades has unraveled a longstanding mystery of ancient life: Why did easy-to-see and once-common structures called stromatolites essentially cease forming over the long arc of earth history?<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">Stromatolites are contorted layers of sediment formed by microbes, and they are often found in limestone and other ancient sedimentary rocks deposited beneath oceans.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">\u201cGeologists have known for a long time that stromatolites were abundant in shallow marine environments during the Precambrian, before the emergence of multi-cellular life\u201d more than 560 million years ago, says Jon Husson, a post-doctoral researcher and co-author of a study now online in the journal Geology. \u201cBut, stromatolites are rare in the ocean today.\u201d<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">The new study measures the slide in stromatolite prevalence based on descriptions of rocks sifted from more than 3 million scientific publications.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">\u201cPaleontologists have largely attributed the decline in stromatolites to the evolution of animals, starting some 560 million years ago,\u201d says Shanan Peters, a professor of geoscience at University of Wisconsin\u2013Madison and study first author. \u201cMany multi-cellular animals, like snails, eat microbes. The evolution of these big microbe-grazing animals hit \u2018reset\u2019 on the stromatolite\u2019s world. Or so the story has gone.\u201d<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">The new study found a weak correlation between stromatolite occurrence and the diversity of animals, but a stronger link to seawater chemistry.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">\u201cThe best predictor of stromatolite prevalence, both before and after the evolution of animals, is the abundance of dolomite in shallow marine sediments,\u201d says Husson. Dolomite is a high-magnesium variety of carbonate, the type of sediment that forms limestone. Dolomite is harder to make than low-magnesium carbonate and it forms today in only a narrow range of marine environments.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">When the ocean water is super-saturated with carbonate, \u201cthat can make it easier for things like stromatolites to form,\u201d says Husson. \u201cIn Lake Tanganyika [Africa], there are stromatolites forming today, even though there are animals everywhere, snails and fish. The lake is super-saturated with carbonate, and it\u2019s begging to be precipitated. The microbes come along and help it to precipitate, and the result is an abundance of stromatolites.\u201d Elevated carbonate saturation can also help the formation of dolomite, thereby driving the correlation with stromatolites found in this study.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">Measuring the prevalence of stromatolites through all Earth history is difficult because counting the number of stromatolites alone is not sufficient. You must also know how many rocks could potentially have stromatolites, but do not.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">The big innovation of this study is the interplay of a new type of digital library and machine reading system called GeoDeepDive with a geological database called Macrostrat. Both were spearheaded by Peters at UW\u2013Madison.<\/span><\/p>\n<ul style=\"text-align: justify;\">\n<li><span style=\"color: #000000;\"><a style=\"color: #000000;\" href=\"https:\/\/geodeepdive.org\/\" target=\"_blank\" rel=\"noopener\">GeoDeepDive<\/a> is a digital library built on high throughput computing technology that can \u201cread\u201d millions of papers and siphon off specific information. To date, the GeoDeepDive library contains more than 3 million scientific publications from all scientific disciplines; some 10,000 new published papers are added daily.<\/span><\/li>\n<li><span style=\"color: #000000;\"><a style=\"color: #000000;\" href=\"https:\/\/macrostrat.org\/\" target=\"_blank\" rel=\"noopener\">Macrostrat<\/a> is a database describing the known geological properties of North America\u2019s upper crust, at different times and depths.<\/span><\/li>\n<\/ul>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">The massive computing capacity at UW\u2013Madison\u2019s Center for High Throughput Computing and HTCondor system, the brainchild of UW\u2013Madison computer scientist Miron Livny, powers GeoDeepDive. Combining the digital library with the geological database allowed the researchers to estimate, at different time periods, the percentage of shallow marine rocks that actually have stromatolites.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">The study began in the summer of 2015, when the third author, Julia Wilcots, a Madison-native who was then an undergraduate at Princeton, asked Peters for a summer project. \u201cIn my typical fashion I gave Julia a few options,\u201d Peters says. \u201cShe picked stromatolites, so I said, \u2018Okay, go do it!\u2019 With minimal help from us, she developed a working application to discover and extract every mention of stromatolites from our library.\u201d<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">Among 10,200 papers that mentioned stromatolites, \u201cour program was able to extract 1,013 with a name of a rock unit, which enabled us to link stromatolite occurrences to Macrostrat,\u201d says Husson.<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">Wilcots did not have to travel to see stromatolites, Peters says. \u201cIn Madison, we are sitting on top of rocks recording one of the biggest rises in stromatolite abundance \u2013 at least during the age of animals.\u201d<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">Scientists long ago observed that stromatolites started a long decline just before the start of the Cambrian era, but that decline represented a \u201cfundamental question of paleobiology,\u201d Husson says. \u201cStromatolites are the oldest fossils that are visible to the naked eye. If you look at rock that is a billion years old, the chance for seeing evidence of life equals the chance of seeing stromatolites.\u201d<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">Beyond answering a fundamental question of Earth\u2019s history, the new study \u201callows us to do the kind of analyses that scientists used to only dream about, Peters says: \u2018If we could just compile all the published information on\u2026 anything!\u2019<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">\u201cDoing this study without GeoDeepDive would be all but impossible,\u201d Peters adds. \u201cReading thousands of papers to pick out references to stromatolites, and then linking them to a certain rock unit and geologic period, would take an entire career, even with Google Scholar. Here we got started with a talented undergrad working on a summer project. GeoDeepDive has greatly lowered the barrier to compiling literature data in order to answer many questions.\u201d<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">Another beauty of the big data, machine-reading approach is the baked-in capability for replication and improvement. \u201cNow that this study has been done, we can run the stromatolite application again and again. We can refine the searches, and they will evaluate the new data that is being published all the time,\u201d Peters says. \u201cSo a rerun could make a better study, with minimal effort.\u201d<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"color: #000000;\">For centuries, \u201cgeologists have transferred hard-to-get information from the field to hard-to-get information in the literature,\u201d Peters says. \u201cTo achieve a broad-scale synthesis, you have to survey all of the published knowledge. There are new discoveries waiting in the scientific literature, if you can see the big picture and get all the data into one place.\u201d<\/span><\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A study that used a new digital library and machine reading system to suck the factual marrow from millions of geologic publications dating back decades has unraveled a longstanding mystery of ancient life: Why did easy-to-see and once-common structures called stromatolites essentially cease forming over the long arc of earth history? Stromatolites are contorted layers [&hellip;]<\/p>\n","protected":false},"author":6,"featured_media":11866,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[17],"tags":[],"class_list":["post-11865","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-research"],"featured_image_urls":{"full":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"thumbnail":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385-150x150.jpg",150,150,true],"medium":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385-300x231.jpg",300,231,true],"medium_large":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"large":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"1536x1536":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"2048x2048":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"ultp_layout_landscape_large":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"ultp_layout_landscape":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"ultp_layout_portrait":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"ultp_layout_square":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"newspaper-x-single-post":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"newspaper-x-recent-post-big":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",468,360,false],"newspaper-x-recent-post-list-image":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",84,65,false],"web-stories-poster-portrait":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",500,385,false],"web-stories-publisher-logo":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",96,74,false],"web-stories-thumbnail":["https:\/\/www.revoscience.com\/en\/wp-content\/uploads\/2017\/03\/stromatolite-large-500x385.jpg",150,116,false]},"author_info":{"info":["Amrita Tuladhar"]},"category_info":"<a href=\"https:\/\/www.revoscience.com\/en\/category\/news\/research\/\" rel=\"category tag\">Research<\/a>","tag_info":"Research","comment_count":"0","_links":{"self":[{"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/posts\/11865","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/comments?post=11865"}],"version-history":[{"count":0,"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/posts\/11865\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/media\/11866"}],"wp:attachment":[{"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/media?parent=11865"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/categories?post=11865"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.revoscience.com\/en\/wp-json\/wp\/v2\/tags?post=11865"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}