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France's Top Wines Face Climate Tipping Point - AFP

Featured News - Mon, 03/21/2016 - 12:00
Climate change has pushed French wines into uncharted territory, and could force producers to relocate or abandon the grapes that helped to make their vineyards famous, according to a study from Lamont's Ben Cook.

Warming Pushes Wine Harvests Earlier – Not Necessarily for the Better - The Conversation

Featured News - Mon, 03/21/2016 - 12:00
"Our analysis showed that wine harvests are happening earlier, which has historically been a harbinger of high-quality wines. But we also found that changing local weather conditions could make it harder to determine when to expect high-quality wines, and that higher temperatures could force wine growers to use different grape varieties," writes Lamont's Ben Cook.

Carbon Emissions Top Even Those of 56 Million Years Ago - Christian Science Monitor

Featured News - Mon, 03/21/2016 - 12:00
Carbon emissions hit a dramatic high nearly 10 million years after the demise of the dinosaurs some 66 million years ago. But emissions now far surpass that. "What we're doing today is much more extreme than what happened in Earth's history," says Lamont's Bärbel Hönisch.

Will Our Trees Survive the Warming Temps? - Public News Service

Featured News - Mon, 03/21/2016 - 09:37
A crew of scientists led by Lamont's Park Williams has been making its way through the Ozark Mountains, dodging snakes and poison ivy to study tree rings, to see how they're reacting to climate change.

Finding Microfossils Off Southern Africa

When Oceans Leak - Sat, 03/19/2016 - 19:13
 Dick Norris and Jason Coenen. Illustration by Deborah Tangunan

Expedition 361 micropaleontologists with their nannofossil specialties (not quite to scale …): Top, left to right: Margit Simon, Thiago Pereira dos Santos, Luna Brentegani and Deborah Tangunan. Bottom: Dick Norris and Jason Coenen. Illustration by Deborah Tangunan

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

Limpopo was awesome! We ended up with close to 4 million years of sediment from our latest coring site, off Mozambique near the Limpopo River. The accumulation rate for the last 2 million years is close to 10 cm per thousand years, so there is potential for highly resolved records in that interval. The accumulation rate between about 2 million and 4 million years is much lower, probably about a quarter, but that is also good news because we only had permission to go 250 meters, and if there had been more sediment we wouldn’t have covered nearly as much time.

The foraminifera are spectacular – translucent, glassy and “very pretty” throughout the whole sedimentary section. We do have a gap or two, as hard as we tried to avoid it, but we have overlap among holes for most of the site, and a continuous record back to close to 2 million years.

During coring at the Zambezi site earlier this week, the micropaleontologists had less to do since there were only two biostratigraphic datums (one foraminifera and one nannofossil), so nannofossil specialist Debs Tangunan made some cute art (above) with each of the biostratigraphers upon a fossil type of his or her specialty. Debs and Luna are the nannofossil specialists; Dick and Thiago are the planktonic (shallow floating) foraminifera specialists; Margit is the benthic (from the bottom) foraminifera specialist; and Jason is the diatom specialist. Jason’s pouting because most of our sites have not been good for diatom biostratigraphy, except the Agulhas Plateau. He has been a great sport though and has been helping with sample preparation and picking benthic foraminifera for a preliminary stable isotope record to help refine the age models for our sampling party.

The Agulhas Current. Image courtesy of Arnold Gordon.

The Agulhas Current. Image courtesy of Arnold Gordon.

We finished up at Limpopo this afternoon and now we are heading south to our final site, which is in the Cape Basin, and only eight hours from the harbor at Cape Town, South Africa. The catering staff put on a fantastic show for the 5-7 p.m. meal – it was sushi!  And what a beautiful layout, with butter carved into the shapes of fish and various melons and other food. It was delicious and amazing!

During the transit to the Cape Basin, which will take a little over four days, we will have a busy time finishing the cores from Limpopo and the Mozambique Channel. We had to put ~1/2 of a hole’s worth of cores to the side to get the shallow sites completed, and we will finish up those cores as we transit to the CAPE site. We must have all the data collected and reports finished before we arrive at CAPE because we are going to have to devote our full attention to the CAPE site in order to get the report finished on that site before we get to port.

CAPE is located right were the eddies that constitute the “leakage” from the Agulhas Current enters the Cape Basin. So this site is going to be very important for tying together the story of how the Agulhas Current system is connected to global ocean circulation. The water depth of CAPE (as well as the other three of our deeper sites from this cruise: Natal Valley, Agulhas Plateau and Mozambique Channel) is in North Atlantic Deep Water (NADW). So we should be able to obtain some great co-registered records of how the shallow and deep ocean circulation are changing through time, as well as how the productivity and temperature and salinity have varied and how these are related in time to southern African climates.

//">Cardiff Half Marathon</a> to raise money for a charity by running the distance aboard ship. Photo: Tim Fulton/IODP

Stephen Barker (left) and Ian Hall prepare to participate in the March 26 Cardiff Half Marathon. They’ll be raising money for a South African education charity by running the 13.1 miles in laps around the ship’s helideck. Photo: Tim Fulton/IODP

Another exciting thing that is going to happen while we are at CAPE on March 26, is that Co-Chief Scientist Ian Hall and Stratigraphic Correlator Steve Barker, both from Cardiff University, are going to be running a half marathon around the deck of the JOIDES Resolution at the same time the Cardiff Half Marathon is underway in the UK. Steve is a former Lamont postdoc and an adjunct associate research scientist at Lamont.

Their goal is to raise funds for a charity that supports children in South Africa. The small South African charity, located in the Western Cape, is called the Goedgedacht Trust, and it promotes education to help poor rural African children escape grinding poverty.  We are also planning to provide some of the Trust’s children with a tour of the ship during our visit in Cape Town. Ian and Steve will appreciate any support you (or your colleagues) can give!  Donations can be made online. I’m planning to contribute, and I hope you will too.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

China's Forest Conservation Program Shows Proof of Success - Christian Science Monitor

Featured News - Sat, 03/19/2016 - 12:00
"When it comes down to climate and carbon sequestration, these are global problems," says Lamont's Kevin Griffin.

California City Worries About Expansion and Future Water Supply - The Tribune

Featured News - Sat, 03/19/2016 - 12:00
Worried about how climate change will affect rainfall in the coming decades, some San Luis Obispo residents are calling on the city to stop allowing developers to build new homes — at least until the city recalculates its future water supply.

How Israel Survived the Levant's Worst Drought in 900 Years - JNS

Featured News - Fri, 03/18/2016 - 15:53
A combination of water from rainfall, recycling of wastewater, desalination of seawater, and a large-scare water conservation campaign helped Israel get through what research from Lamont's Ben Cook shows is the region's worst drought in more than 900 years.

So, Was That Climate Change? - CNN

Featured News - Thu, 03/17/2016 - 17:17
Scientists are increasingly able to attribute aspects of extreme weather to the overall change in the climate, as John Sutter discusses with Lamont's Park Williams.

A Surprise from the Zambezi River

When Oceans Leak - Wed, 03/16/2016 - 20:05
//">JOIDES Resolution</a>. Photo: Tim Fulton/IODP

Alexis Armstrong and Beth Novak of the International Ocean Discovery Program (IODP) prepare a core for laser engraving aboard the JOIDES Resolution. Photo: Tim Fulton/IODP

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

We have finished coring the Zambezi site and are on our way to the Limpopo site. Both are just off shore from major rivers that flow through Mozambique and should provide a record of the terrestrial climate variability in southeastern Africa through time, but we discovered a surprise. Based on short cores from nearby, as well as seismic surveys, we were expecting that the sediment accumulation would be 10 cm per thousand years. We were wrong by almost 10 times. The accumulation rate is approximately 1 meter per thousand years. Luckily, one of the scientists has been studying records from short cores, and the correlations to them is very clear even though the accumulation rates are so much greater, and we have two biostratigraphic datums that are further consistent.

So with our 200 meters of core we were only able to get back to 200,000 years instead of the 2 million years we anticipated. This is happy news on one hand, as this will allow some extraordinarily highly resolved records of climate variability back to approximately 120,000 years, and maybe (with small gaps) back to 200,000 years. But it is also disappointing from the view of the goal to get a long record of climate variability in the Zambezi catchment. It allows different kinds of questions to be pursued, and they are also very valuable. We feared encountering a bunch of sand, and that did not happen, so all in all this was a successful site, and we are still absorbing the change of approach that would be required to get the most out of it.

Expedition 361's coring sites. APT is the Agulhas Plateau. NV is the Natal Valley.

Expedition 361’s coring sites.

We should get to the Limpopo site at about midnight ship time (Cape Town time) tonight, and expect the first core on deck early Thursday morning. It seems highly unlikely that our estimate of sediment accumulation will be much different, but we are eager to find out! The location of our site is on the outside of a terrace feature in the indentation feature on the African margin (both the Zambezi and Limpopo enter the Indian Ocean in distinctive indentations on the eastern margin of southern Africa). Based on the seismic cross sections, the deposit is what is called a “plastered drift,” it is a body of sediment that is built up by bottom currents flowing southward along the margin. So even though the site is in the Limpopo area, its location relative to the currents is such that we may expect to get a similar record here as well. We will need to make some careful comparisons using the many existing short cores to establish how to best apply and interpret our methods.

Meanwhile, things are very busy on the ship. We were not able to complete the measurements and description of the final hole from the highly successful first Mozambique site before arriving here, and we are still working on the Zambezi cores as we approach the Limpopo site. We hope to keep up the pace so we will be finished with both soon. We expect the coring at Limpopo to take approximately two full days. Then we have about four days transit to our final site, CAPE, off the tip of South Africa. We want to have all three site reports completed before we arrive at CAPE since we will have no scrap of extra time after that!

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

Some Trees Could Help Fight Climate Change - Science

Featured News - Wed, 03/16/2016 - 12:00
Compared with trees suddenly exposed to hot temperatures, acclimated trees may release far less CO2 at night, a new study suggests. Science talks with Lamont's Kevin Griffin.

Helping the Earth Store Carbon - Fusion

Featured News - Mon, 03/14/2016 - 09:11
Lamont's Peter Kelemen discusses ways of using mantle rocks as natural carbon capture and storage solutions.

Mozambique Core Brings Up 7 Million Years of Climate History

When Oceans Leak - Fri, 03/11/2016 - 17:00
 Tim Fulton/IODP

Scientists crowd around the stratigraphic correlators’ screens as new details come in. Co-chief scientists Sidney Hemming and Ian Hall are on the right, joined by Luna Brentegani, Christopher Charles and Stephen Barker. Photo: Tim Fulton/IODP

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

We just completed coring at our northernmost Mozambique site. The sea is still. The weather is hot and muggy, but so still. This is how sediment coring should be. The stratigraphic correlators think they are having a dream. We have no gaps, beyond the absolute minimum from the coring process, and the variability in the physical properties makes correlating among the holes dead easy.  And the variability looks like a fantastic, cyclic climate signal that is continuous back to 7 million years ago!

We are heading to the Zambezi site now. For our two river sites – offshore from the Zambezi and Limpopo Rivers – our big goal is making the most direct connection possible between what happened on land and in the oceans over the past ~2 million years. We’re only expecting about 2 million years because the accumulation rates are higher, but the nice thing about that is that we can get much more detail about the variability.

 Tim Fulton/IODP

The drilling crew works with equipment aboard the JOIDES Resolution. Photo: Tim Fulton/IODP

Among our science party, we have multiple tools to probe how the rainfall may have changed through time. We have organic biomarkers as well as several measures of terrigenous (land-derived) sediment sources, weathering intensity and fluxes. The Zambezi catchment is located at the very southern part of the annual shift in the Intertropical Convergence Zone (the so-called thermal equator), so there is a strong gradient to drier climate to the south.  And that is one of the reasons having both the Zambezi and Limpopo is so exciting to think about. The “great grey-green greasy“ Limpopo catchment is much drier than the Zambezi.

We are going to be so busy. We have finished the coring and yet more than half the cores are waiting to be processed for the various observations and measurements we have been making. We will get to the Zambezi site in less than two days, and the water depth is much shallower there, meaning the cores are going to come up every 20 minutes or so rather than every 45 minutes, as at the northern site. And then we only have about one more day to get to the Limpopo where the same rate of coring is expected.  So we are going to be buried in cores by the time we finish at Limpopo, and we’ll have about four days to finalize the data collection and reports before arriving at our final site, CAPE, off the tip of South Africa. More about CAPE later.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.

Links Between Climate Change & Extreme Weather Increasingly Clear & Present - Washington Post

Featured News - Fri, 03/11/2016 - 12:00
Our science has reached the point where we can look for the human influence on climate in single weather events, and sometimes find it, writes Lamont's Adam Sobel.

Building the paprica database

Chasing Microbes in Antarctica - Fri, 03/11/2016 - 11:04

This tutorial is both a work in progress and a living document.  If you see an error, or want something added, please let me know by leaving a comment.

Build the paprica database provides maximum flexibility with paprica but involves more moving parts and resources than conducting analysis with paprica against the provided database.  Basic instructions for using the script are provided in the manual, this tutorial is intended to provide an even more detailed step-by-step guide.


While a laptop running Linux, VirtualBox, or OSX is perfectly adequate for analysis with paprica, you’ll need something a little beefier for building the database (unless you’re really patient).  A high performance cluster is overkill, I build the provided database on a basic 12 core Linux workstation with 32 Gb RAM (< $5k).  Something in this ballpark should work fine, of course more cores will get the job done faster (but keep an eye on memory useage).

Once you’ve got the hardware requirements sorted out you need to download the dependencies.  I recommend first following all the instructions for the script, then installing RAxML and pathway-tools.  The rest of this tutorial assumes you’ve done just that, including running the test file.

Install remaining dependencies

In addition to all the dependencies required by you need pathway-tools and RAxML.  These are very mainstream programs, but that doesn’t necessarily mean installation is easy.  In particular pathway-tools requires that you request a license (free for academic users).  This takes about 24 hours after which you’ll receive a link to download the installer.  Regardless of whether you’re sitting at the workstation or accessing via SSH a GUI will pop up and guide you through the installation.  In general you can accept the defaults, however, the GUI will ask you where pathway-tools short create to directory ptools-local.  This is where the program will create the pathway-genome databases that describe (among other things) the metabolic pathways in each genome.  By the time you are done creating the database this directory will be > 100 Gb, so pick a location with plenty of space!  This may not be your home directory (the default location).  For example on my system my home directory is housed on a small SSD.  To keep the home directory from becoming bloated I opted to locate ptools-local on a separate SATA drive.

You will receive a number of download options from the pathway-tools development team.  I recommend that you conduct only the basic installation of pathway-tools, and do not download and install additional PGDBs.  Nothing wrong with installing these additional, well-curated PGDBs other than increased space and time, but they become ponderous.  You can always add them later if you want to become a metabolic modeling rock star.

To be continued…

Melting of Greenland’s Ice Sheet Accelerating with Loss of Reflectivity - National Geographic

Featured News - Thu, 03/10/2016 - 12:00
A new study led by Lamont's Marco Tedesco finds that the reflectivity, or albedo, of Greenland’s ice sheet could decrease by as much as 10 percent by the end of the century, potentially leading to significant sea-level rise.

Winter Blooms May Be Disrupting the Marine Ecosystem - Science News

Featured News - Wed, 03/09/2016 - 12:00
The dinoflagellate Noctiluca scintillans is taking over in the Arabian Sea, posing a potential threat to its ecosystem. Science News talks with Lamont's Joaquim Goes.

New York's Big Green Clean - BBC

Featured News - Wed, 03/09/2016 - 12:00
The BBC talks with Lamont's Bob Newton about the Billion Oyster Project, an effort to bring oysters back to New York harbor.

Faster-Merging Snow Crystals Speed Greenland Ice Sheet Melting - Eos

Featured News - Wed, 03/09/2016 - 12:00
Satellite data and modeling reveal a trend toward coarser-grained, more-energy-absorbent snow on Greenland, as a new paper by Lamont's Marco Tedesco explains.

We’re Headed for Mozambique!

When Oceans Leak - Tue, 03/08/2016 - 00:15
 Tim Fulton, IODP

Sedimentologists Andreas Koutsodendris of University of Heidelberg, Masako Yamane of Japan Agency for Marine-Earth Science and Technology, and Thibaut Caley of University of Bordeaux study freshly split cores aboard the JOIDES Resolution. Photo: Tim Fulton, IODP

Read Sidney Hemming’s first post to learn more about the goals of her two-month research cruise off southern Africa and its focus on the Agulhas Current and collecting climate records for the past 5 million years.

At the time of the previous entry, we were heading toward the waters off Mozambique while hoping government permission would be in hand in time for coring. It was a month after we had left port in Mauritius, and we had a couple of firm deadlines – well, actually one that we later revised due to the delay because of the helicopter evacuation. We decided that if we did not have approval from Mozambique’s Fisheries office by Wednesday, we would give up hope and head to our CAPE site, off the tip of South Africa, with the prospect of another site that was not part of our original plan as a consolation prize.

We did not hear back on Wednesday, so we stopped and brought extra pipe up for the potential extra site. Thursday morning, with no word from Mozambique, we began to head south. Approximately 24 hours later WE GOT PERMISSION! I cannot tell you what an emotional roller coaster this has been for the entire party. Some of us had already started warming up to the alternative site, but everybody is ecstatic that we finally have verbal permission for the Mozambique sites. We hope cores from the Zambezi and Limpopo sites, near major rivers that run through Mozambique, will give us a record of the terrestrial climate variability in southeastern Africa through the last 5 million years that can be compared with the Agulhas Current and other oceanographic factors.

Expedition 361's coring sites.

Expedition 361’s coring sites.

We are approaching our northernmost site, which is a re-occupation of an old Deep Sea Drill Project (DSDP) site 242 on the Davie Ridge in the northern part of the Mozambique Channel. The site, MZC, which will be IODP 1476, in some ways, is more exploratory than the other five of our expedition although there are hints that this will be a good spot for paleoceanography. The original drilling was done in 1972 during the 25th leg of the DSDP – they sailed from Mauritius, too, on the Glomar Challenger, and ended in Durban, South Africa.

As an aside, this reminds me how the DSDP and its descendants – the Ocean Drilling Program, Integrated Ocean Drilling Program, and the current International Ocean Discovery Program (IODP) –  have made an incredible legacy of understanding the evolution of the ocean basins and the evolution of the oceans and climate system through the Cenozoic. We would know far less without these extraordinary programs. The DSDP site 242 was drilled to understand the history of separation between Africa and Madagascar, and to establish a mid-latitude faunal succession (the evolutionary change of marine creatures) for the western Indian Ocean. The hole was drilled and cored intermittently to 676 meters, and the bottom sediment recovered was from the Eocene (~50 million years old). The sediment was nannofossil ooze throughout. Nannofossil ooze is sediment that is made up of mostly calcareous nannofossils, which are single-celled organisms that have a calcium carbonate structure. This is also the composition of the first two sites we cored and a very common composition for tropical and subtropical sites without much terrigenous (land-derived) dust and debris. This location is upstream of the Agulhas Current, and it appears to have an important influence on Natal Pulses (turbulent pulses that are triggered by eddies originating in the Mozambique Channel) that pass down the Natal Valley and lead to the Agulhas Leakage.


Barbecue on the JOIDES Resolution‘s “steel beach.” Photo: IODP

We should get to our northernmost site, MCZ/1476, in the early morning on Tuesday March 8. By trimming our program of coring to only include the advanced piston coring and not go to greater depth than needed to capture the 5 million year interval, we think we can still get everything we need at all six sites. It is going to be a really busy final three weeks, but everybody is ready for the challenge.

Meanwhile, the reports are almost finished for site 1475, at the Agulhas Plateau. The correlators were able to put together a splice of cores that provides a continuous section, although there are intervals that will be further scrutinized back home. We had a barbecue on deck Saturday in the nice hot weather, and we are looking forward to the next site.

Sidney Hemming is a geochemist and professor of Earth and Environmental Sciences at Lamont-Doherty Earth Observatory. She uses the records in sediments and sedimentary rocks to document aspects of Earth’s history.



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