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Research Is Art and Other Science Outreach - Don't Panic Geocast

Featured News - Fri, 03/04/2016 - 12:00
Lamont graduate student Hannah Rabinowitz talks in a podcast about Lamont's Research Is Art project, Girls' Science Day and other science outreach.

Correctly evaluating metabolic inference methods

Chasing Microbes in Antarctica - Fri, 03/04/2016 - 11:47

Last week I gave a talk at the biennial Ocean Sciences Meeting that included some results from analysis with paprica.  Since paprica is a relatively new method I showed the below figure which is intended to validate the method.  The figure shows a strong correlation for four metagenomes between observed enzyme abundance and enzyme abundance predicted with paprica (from 16S rRNA gene reads extracted from the metagenome).  This is similar to the approach used to validate PICRUSt and Tax4Fun.

Spearman's correlation between predicted and observed enzyme abundance in four marine metagenomes.

Spearman’s correlation between predicted and observed enzyme abundance in four marine metagenomes.

The correlation looks decent, right?  It’s not perfect, but most enzymes are being predicted at close to their observed abundance (excepting the green points where enzyme abundance is over-predicted because metagenome coverage is lower).

After the talk I was approached by a well known microbial ecologist who suggested that I compare these correlations to correlations with a random collection of enzymes.  His concern was that because many enzymes (or genes, or metabolic pathways) are widely shared across genomes any random collection of genomes looks sort of like a metagenome.  I gave this a shot and here are the results for one of the metagenomes used in the figure above.

Correlation between predicted and observed (red) and random and observed (black) enzyme abundances.

Correlation between predicted and observed (red) and random and observed (black) enzyme abundances.

Uh oh.  The correlation is better for predicted than random enzyme abundance, but rho = 0.7 is a really good correlation for the random dataset!  If you think about it however, this makes sense.  For this test I generated the random dataset by randomly selecting genomes from the paprica database until the total number of enzymes equaled the number predicted for the metagenome.  Because there are only 2,468 genomes in the current paprica database (fewer than the total number of completed genomes because only one genome is used for each unique 16S rRNA gene sequence) the database gets pretty well sampled during random selection.  As a result rare enzymes (which are also usually rare in the metagenome) are rare in the random sample, and common enzymes (also typically common in the metagenome) are common.  So random ends up looking a lot like observed.

It was further suggested that I try and remove core enzymes for this kind of test.  Here are the results for different definitions of “core”, ranging from enzymes that appear in less than 100 % of genomes (i.e. all enzymes, since no EC numbers appeared in all genomes) to those that appear in less than 1 % of genomes.

The difference between the random and predicted correlations does change as the definition of the core group of enzymes changes.  Here’s the data aggregated for all four metagenomes in the form of a sad little Excel plot (error bars give standard deviation).

delta_correlationThis suggests to me a couple of things.  First, although I was initially surprised at the high correlation between a random and observed set of enzymes, I’m heartened that paprica consistently does better.  There’s plenty of room for improvement (and each new build of the database does improve as additional genomes are completed – the last build added 78 new genomes, see the current development version) but the method does work.  Second, that we obtain maximum “sensitivity”, defined as improvement over the random correlation, for enzymes that are present in fewer than 10 % of the genomes in that database.  Above that and the correlation is inflated (but not invalidated) by common enzymes, below that we start to lose predictive power.  This can be seen in the sharp drop in the predicted-random rho (Δrho: is it bad form to mix greek letters with the English version of same?) for enzymes present in less than 1 % of genomes.  Because lots of interesting enzymes are not very common this is where we have to focus our future efforts.  As I mentioned earlier some improvement in this area is automatic; each newly completed genome improves our resolution.

Some additional thoughts on this.  There are parameters in paprica that might improve Δrho.  The contents of closest estimated genomes are determined by a cutoff value – the fraction of descendant genomes a pathway or enzyme appears in.  I redid the Δrho calculations for different cutoff values, ranging from 0.9 to 0.1.  Surprisingly this had only a minor impact on Δrho.  The reason for this is that most of the 16S reads extracted from the metagenomes placed to closest completed genomes (for which cutoff is meaningless) rather than closest estimated genomes.  An additional consideration is that I did all of these calculations for enzyme predictions/observations instead of metabolic pathways.  The reason for this is that predicting metabolic pathways on metagenomes is rather complicated (but doable).  Pathways have the advantage of being more conserved than enzymes however, so I expect to see an improved Δrho when I get around to redoing these calculations with pathways.

Something else that’s bugging me a bit… metagenomes aren’t sets of randomly distributed genomes.  Bacterial community structure is usually logarithmic, with a few dominant taxa and a long tail of rare taxa.  The metabolic inference methods by their nature capture this distribution.  A more interesting test might be to create a logarithmically distributed random population of genomes, but this adds all kinds of additional complexities.  Chief among them being the need to create many random datasets with different (randomly selected) dominant taxa.  That seems entirely too cumbersome for this purpose…

So to summarize…

  1.  Metabolic inference definitively outperforms random selection.  This is good, but I’d like the difference (Δrho) to be larger than it is.
  2. It is not adequate to validate a metabolic inference technique using correlation with a metagenome alone.  The improvement over a randomly generated dataset should be used instead.
  3. paprica, and probably other metabolic inference techniques, have poor predictive power for rare (i.e. very taxonomically constrained) enzymes/pathways.  This shouldn’t surprise anyone.
  4. Alternate validation techniques might be more useful than correlating with the abundance of enzymes/pathways in metagenomes.  Alternatives include correlating the distance in metabolic structure between samples with distance in community structure, as we did in this paper, or correlating predictions for draft genomes.  In that case it would be necessary to generate a distribution of correlation values for the draft genome against the paprica (or other method’s) database, and see where the correlation for the inferred metabolism falls in that distribution.  Because the contents of a draft genome are a little more constrained than the contents of a metagenome I think I’m going to spend some time working on this approach…

Scientists Just Found a Surprising Factor Speeding Greenland's Melting - Washington Post

Featured News - Thu, 03/03/2016 - 15:49
A new study from Lamont's Marco Tedesco shows that Greenland's ice sheet is “darkening,” or losing its ability to reflect both visible and invisible radiation, as it melts more and more, the research finds. That means it’s absorbing more of the sun’s energy — which then drives further melting.

Mideast Drought Worst in 900 Years - CNN

Featured News - Thu, 03/03/2016 - 12:00
A new study led by Lamont's Ben Cook finds that the drought that began in 1998 in the Levant is probably the region's worst in 900 years.

Greenland's Ice Melt Accelerating as Surface Darkens - The Guardian

Featured News - Thu, 03/03/2016 - 12:00
Greenland’s vast ice sheet is in the grip of a dramatic “feedback loop” where the surface has been getting darker and less reflective of the sun, helping accelerate the melting of ice and fuelling sea level rises, new research led by Lamont's Marco Tedesco has found.

The Worst Drought in 900 Years Helped Spark Syria's Civil War - Mashable

Featured News - Wed, 03/02/2016 - 13:28
The drought that played a role in triggering the catastrophic Syrian Civil War was the worst such climate event in at least the past 900 years, according to a new study published this week and led by Lamont's Ben Cook. Mashable also talks with Richard Seager.

Uptick in Small Earthquakes Raises Questions in New York Area - Wall Street Journal

Featured News - Wed, 03/02/2016 - 12:00
A cluster of low-magnitude earthquakes in the New York region has piqued the interest of residents, while some geologists predict the increase in temblors will continue and a large-scale one could be coming. Lamont's Won-Young Kim discusses the science.

Global Warming in New York - Le Figaro

Featured News - Tue, 03/01/2016 - 12:00
Since the ravages of Hurricane Sandy in 2012 and the massive floods in the U.S. East Coast, New York has focused on creating a new ecosystem to contain the risks of sea level rise. Le Figaro talks with Lamont's Klaus Jacob and Adam Sobel. (In French)

Arctic Sea Ice Growth Could Be Lowest on Record Again - ThinkProgress

Featured News - Tue, 03/01/2016 - 09:29
Arctic sea ice growth has been sluggish this winter. And that's a huge problem for the animals and communities that depend on it, says Lamont's Ray Sambrotto.

Preparing for the Inevitable Sea-Level Rise Caused by Climate Change - The Atlantic

Featured News - Mon, 02/29/2016 - 17:47
Scientists are struggling to figure out the timeline for how climate change will affect vulnerable waterfront communities. The Atlantic talks with Lamont's Maureen Raymo about the challenges.

Trials & Tribulations of Coring the Agulhas Plateau

When Oceans Leak - Sun, 02/28/2016 - 14:03
 Tim Fulton/IODP.

Sedimentologists Thibaut Caley of the University of Bordeaux and Andreas Koutsodendris of the University of Heidelberg and Deborah Tangunan, a paleontologist from the University of Bremen, work in the core lab 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.

A lot has happened since my last post. As we were heading south to the Agulhas Plateau, one of the scientists had to be evacuated by helicopter for medical treatment. We were within a day of the Agulhas Plateau site and had to go back to near Port Elizabeth for the handoff and then return to drill the plateau. The weather at the plateau was bad enough that we were probably going to have a delay anyway, so we didn’t lose too much time. Our colleague is fine now, and our drilling on the Agulhas Plateau has been a success.

We have had some trials and tribulations because of the large ocean swells and because the sediments do not have as strong of a physical property signal as the previous site. Both of these factors increased the challenge for the stratigraphic correlators, so it has been a real cliff-hanger to find out if we can splice together a continuous section. Because of the small signal-to-noise of the physical properties, the scanning took longer and the records for correlating are not quite as clear. This has created a backup in the work flow, and it means the descriptions and scanning (and some sampling) of the split cores will be continuing as we begin our transit. And it means that until all this is completed we will not know for sure how continuous of a record we have. We are reasonably sure we will have few or no gaps in the splice, but it will be nice to see it all completed.

 Tim Fulton/IODP

The end of a fresh core, just brought aboard the JOIDES Resolution. Photo: Tim Fulton/IODP

Meanwhile, we came here thinking that we would get a high accumulation rate record for the last million years, but the accumulation rates are modest between the surface and about 100 meters – approximately 2 cm per thousand years. Below that, they turned out to be really quite nice, approaching 7 cm per thousand years through much of the Pliocene. The low accumulation in the Pleistocene is a disappointment as there is a great interest in the mid-Pleistocene climate transition, but it does look like it is a continuous record. The higher accumulation in the older sediment is exciting because the early Pliocene is a warm time in Earth’s history and the most recent with global temperatures as warm as modern times. So we Earth scientists are quite eager to understand everything we can about this interval. The Agulhas Plateau site, near where the Agulhas Current swings back toward the east, is well situated to provide some important information about linkages of different factors in the climate system.

Again at this site, as with the previous site, the development of the time scale has been fun and exciting to watch. We have four groups of organisms that are aiding in our time scale – in addition to foraminifera and nannofossils, there are abundant diatoms and dinoflagellates here. This is great for the biostratigraphy and also great for our participants whose post cruise research will use diatoms for documenting paleo-environmental changes. The magnetic stratigraphy started out looking bleak because the weak signal was messed up by the coring process in the first hole, due to the ship’s heave in the waves.  They almost gave up, but the second core preserved a great record. So we are going to have an excellent time scale for this site as well.

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

Expedition 361’s coring sites. APT is the Agulhas Plateau. NV is the Natal Valley. Credit: IODP

Meanwhile the saga continues in our quest to get permission from Mozambique to drill in their waters. We have word from our contact in the American embassy that the form has been signed by the Foreign Ministry and is now with the ministry that deals with fisheries. While that process continues, we have to start toward our next site. Our decision is to head toward the Zambezi site, as it is going to take us six days to get there anyway. If we don’t get permission before we arrive, we’ll have to turn around and head for the Cape site.

The Zambezi and Limpopo sites are near major rivers. We hope they 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. The hope is that we will get a continuous record with a variety of proxy data for factors such as precipitation, runoff, distribution of vegetation on the landscape, and surface ocean temperatures. The coring is going to be fast at these sites because they are much shallower. In the happy case that we get to drill there, we will then have another long transit to finish off the analyses.

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.

Snowpacks Relied on for Water are Declining - WAMC Academic Minute

Featured News - Sun, 02/28/2016 - 12:00
Justin Mankin, a postdoctoral fellow at Lamont, describes how a changing climate may change the way cultures get their water in the spring and summer.

7 Years of Earthquakes in Japan in 52 Seconds - TimeOut

Featured News - Thu, 02/25/2016 - 12:00
We know an earthquake involves movement, but what if you could capture these seismic tremors in sounds too? This thought experiment proved to be the catalyst for the Seismic Sound Lab, a project by Lamont geophysicist Ben Holtzman.

The Science Behind Ethiopia’s Hunger Crisis - Mother Jones

Featured News - Thu, 02/25/2016 - 12:00
Ethiopia's last mega-droughts killed hundreds of thousands. Could the same thing happen again? Lamont's Park Williams and Richard Seager weigh in on why the drought is not a surprise.

An Airborne Look Through the Ice - The Antarctic Sun

Featured News - Wed, 02/24/2016 - 13:00
Scientists are working to fill in one of the largest remaining blank spots on ocean charts: the sea floor beneath Antarctica's Ross Ice Shelf. Lamont-Doherty's Kirsty Tinto discusses the IcePod and how it's mapping that area.

Changing Faces on the Ice - Nature

Featured News - Wed, 02/24/2016 - 12:00
Diverse faces are coming to work in the polar regions, Lamont's Robin Bell tells Nature.

Coral Reef Growth Is Declining. Is There Hope? - Christian Science Monitor

Featured News - Wed, 02/24/2016 - 12:00
Scientists find more evidence that coral reefs are suffering from environmental changes. But, they say it's not too late. Lamont's Bärbel Hönisch discusses the possibilities.

Sailing into a Storm as We Head for the Agulhas Plateau

When Oceans Leak - Fri, 02/19/2016 - 16:49
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The team aboard the JOIDES Resolution collected the first four cores of Expedition 361 from the Natal Valley site. Here, scientists prepare to open the first. (Tim Fulton/IODP) To drill down into the sea floor, the ship uses a large rig and a professional drilling crew. ( Jens Gruetzner, Alfred-Wegener-Institut for Polar and Marine Research) Professional rig personnel bring the first core aboard. Each segment is 9.5 meters long and is sectioned into smaller pieces for analysis and storage. (Tim Fulton) Scientists work the core catcher, which holds each segment of core in as it lifted from the sea floor. (Tim Fulton) Once the cores are split, they are photographed in shipboard imaging equipment called a Section Half Image Logger. (Tim Fulton) The shipboard labs are ready for scientists to go to work. Kaoru Kubota of the University of Tokyo and Xibin Han of China work on reports in the core lab. (Tim Fulton) Sedimentologists Julien Crespin of the University of Bordeaux and Alejandra Cartagena-Sierra of Notre Dame take down descriptions of the core. (Tim Fulton) Nambiyathodi Lathika, a physical properties specialist from India's National Centre for Antarctic and Ocean Research, enters core data at the sample table. (Jens Gruetzner) Jeroen van der Lubbe of the University of Amsterdam works with a cyrogenic magnetometer to analyze the magnetic properties of a sample. (Jens Gruetzner) A map of the Agulhas Current, which the scientists of Expedition 361 are studying along with southern Africa's climate history. (Courtesy of Arnold Gordon)
The team aboard the JOIDES Resolution collected the first four cores of Expedition 361 from the Natal Valley site. Here, scientists prepare to open the first. (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 finished up at our first core site yesterday, and now we are steaming south toward the Agulhas Plateau. The groups presented their summaries this morning, and the results from this site are awesome.

Inevitably there is a gap between each sediment core because of how the cores have to be taken. The drilling crew drills down to the level of the previous core’s penetration and then sends the piston core down again. There are potential coring artifacts, such as “suck-in” of sediment at the bottom, “fall-in” of sediment at the top (these are descriptive terms), or loss of sediment because the core catcher didn’t catch. That is the reason for triple – and in this case quadruple – holes at each site. The stratigraphic correlators, Steve Barker and Chris Charles, take data from the physical properties measurement tracks and work fast to determine how the cores that are coming up can be correlated to previous cores. They find the gaps and work with the drillers to ensure that the gaps from all the holes do not overlap. With the help of the lithologic description team, they also avoid parts of the core that have been disturbed by the drilling.

At the Natal Valley site, the correlators were able to achieve a continuous splice going back more than 5 million years!  We obtained samples older than that, but they are “floating”. The splice, like it probably sounds, uses the overlapping physical features in the cores to identify a combination of cores that, when pieced together, yield a full continuous record. This splice is where most of the sampling and measurements will be conducted at the post-cruise sampling party. That will probably take place in September to give enough time for the cores to be shipped to Texas A&M and, we hope, scanned with an XRF scanner in order to construct the best sampling plan.

Women scientists and technicians of Expedition 361 on UN Women in Science Day. (Tim Fulton)

Women scientists and technicians aboard the JOIDES Resolution for IODP Expedition 361 on UN Women in Science Day. (Tim Fulton)

We still do not have permission to drill in Mozambique waters. This is causing considerable anxiety for the team, and by steaming south, we will definitely not be able to drill our northern-most planned site. However, if permission comes before we finish the Agulhas Plateau site, we could still meet our Zambezi and Limpopo objectives. The Zambezi and Limpopo are major rivers that drain from the African continent. We hope to capture sediment coming from those two rivers to answer questions about rainfall and runoff and weathering.

The Agulhas Plateau is also an exciting site. It is a little bit north of the sub-tropical front, which is the northern boundary of the Antarctic Circumpolar Current. Today, it is under the Agulhas retroflection, where the Agulhas Current swings back toward the east (see the map at the end of the slideshow). Our goal is to understand how the position of the sub-tropical front and the Agulhas retroflection have changed through the last 5 million years, and how those changes are related to climatic variability in southern Africa.

Allison Franzese’s Ph.D. research used a time-slice approach to compare the modern composition of sediments washed in from the continents with those deposited during the last glaciation about 20,000 years ago (ice at that time covered what today is New York City). She has suggested that the path of the Agulhas retroflection was very similar between modern and glacial times. Her results are enigmatic because they indicate both a weakening of the current and a similar path for the retroflection, and these observations are inconsistent with what is predicted from physical oceanographic modeling. The cores we collect here should allow her to extend her studies back to 5 million years and achieve a much greater understanding of how the system has worked under a range of climate conditions, particularly when combined with results from the Natal Valley site and the Cape site (the final site of the cruise).

As an aside, I am pretty pleased that even though we are sailing through a storm with about 30 knot winds right now and the ship is swaying, I’m still feeling pretty good. Apparently this could change – we are heading toward the “roaring 40s”.

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.

Sea Level Rise Could Put NYC's Proposed Transit System Under Water - Vice News

Featured News - Fri, 02/19/2016 - 09:31
Lamont geologist Klaus Jacob says that while the proposed Brooklyn-Queens Connector project solves desperate transportation needs, the problem is that it runs along current and future flood zones.

Can Germany's Renewable Energy Revolution Be Replicated in the US? - Bulletin of the Atomic Scientists

Featured News - Thu, 02/18/2016 - 12:00
As governments around the world invest in new energy policies and climate strategies, none has gone as far as Germany. Could the model be replicated? Lamont adjunct research scientist Beate Liepert explores the possibilities.



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