Is perception of the whole based on perception of its parts? There is psychological and physiological evidence for parts-based representations in the brain, and certain computational theories of object recognition rely on such representations. But little is known about how brains or computers might learn the parts of objects. Here we demonstrate an algorithm for non-negative matrix factorization that is able to learn parts of faces and semantic features of text. This is in contrast to other methods, such as principal components analysis and vector quantization, that learn holistic, not parts-based, representations. Non-negative matrix factorization is distinguished from the other methods by its use of non-negativity constraints. These constraints lead to a parts-based representation because they allow only additive, not subtractive, combinations. When non-negative matrix factorization is implemented as a neural network, parts-based representations emerge by virtue of two properties: the firing rates of neurons are never negative and synaptic strengths do not change sign.

Learning parts of objects by non-negative matrix factorization

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

/pdf/the-genome-of-the-diatom-thalassiosira-pseudonana-ecology-2hwz6jrxaw.pdf

The Genome of the Diatom Thalassiosira Pseudonana: Ecology, Evolution, and Metabolism

The net inputs of silicic acid (dissolved silica) to the world ocean have been revised to 6.1 +/- 2.0 teramoles of silicon per year (1 teramole = 10(12) moles). The major contribution (about 80 percent) comes from rivers, whose world average silicic acid concentration is 150 micromolar. These inputs are reasonably balanced by the net ouputs of biogenic silica of 7.1 +/- 1.8 teramoles of silicon per year in modern marine sediments. The gross production of biogenic silica (the transformation of dissolved silicate to particulate skeletal material) in surface waters was estimated to be 240 +/- 40 teramoles of silicon per year, and the preservation ratio (opal accumulation in sediment/gross production in surface waters) averages 3 percent. In the world ocean the residence time of silicon, relative to total biological uptake in surface waters, is about 400 years.

https://science.sciencemag.org/content/sci/268/5209/375.full.pdf

The silica balance in the world ocean: a reestimate.

In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.

/pdf/scientists-warning-to-humanity-microorganisms-and-climate-4ypingcefs.pdf

Scientists' Warning to Humanity: Microorganisms and Climate Change

Marine phytoplankton blooms are annual spring events that are accompanied by a surge in heterotrophic bacteria, primarily roseobacters, flavobacteria and members of the Gammaproteobacteria, which recycle most of the carbon that is fixed by the primary producers. In this Review, Buchan et al. describe the emerging physiological features and functions of these bacterial communities and their interactions with phytoplankton.

Master recyclers: features and functions of bacteria associated with phytoplankton blooms

We estimate the global rate of biogenic silica production in the ocean to be between 200 and 280 × 1012 mol Si yr−1. The upper limit is derived from information on the primary productivity of the oceans, the relative contribution of diatoms to primary production and diatom Si/C ratios. The lower limit is derived independently using a multi-compartment model of nutrient transport and biogenic particle flux, and field data on the balance between silica production and dissolution in the upper ocean. Our upper limit is 30–50% lower than several previous estimates, due to new data indicating lower values for both the relative contribution of diatoms to primary productivity and their Si/C ratios. Globally, at least 50% of the silica produced by diatoms in the euphotic zone dissolves in the upper 100 m, resulting in an estimated export of 100–140 × 1012 mol Si yr−l to the deep ocean. Our estimates correspond to a global mean rate of biogenic silica production between 0.6 and 0.8 mol Si m−2 yr−1. Incubation experiments indicate that silica production rates exceed that mean by a factor of 3–12 in coastal areas and are 2–4 times less than the global average in the oligotrophic mid-ocean gyres. The mean silica production rate in waters overlying diatomaceous sediments (approximately 10–12% of the surface area of the oceans) is 0.7–1.2 mol Si m−2 yr−1. That rate is only slightly higher than the global average, indicating that the silica produced in those regions is only 10–25% of the global total. The estimated production of biogenic silica in surface waters of the mid-ocean gyres is approximately equal to that for all major areas of opal sediment accumulation combined. Regional comparison of silica production and accumulation rates suggests a strongly bimodal character in the efficiency of opal preservation in the sea. In waters overlying diatom-rich sediments 15–25% of the silica produced in the surface layer accumulates in the seabed, while virtually none of the silica produced in other areas is preserved. The global burial/production ratio of ˜ 3% is a composite of those two very different systems. The mechanisms leading to more efficient opal preservation in regions of silica accumulation are presently unknown, but they have no simple relationship to primary productivity. Regional differences in opal preservation appear to be controlled by factors such as low surface temperature, selective grazing and aggregate formation, which diminish the rate of silica dissolution in surface waters and/or accelerate its transport to the seafloor.

Production and dissolution of biogenic silica in the ocean: Revised global estimates, comparison with regional data and relationship to biogenic sedimentation

Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation

The distributions of biogenic and lithogenic silica concentrations and net silica production rates in the upper 120 m of the Eastern Equatorial Pacific (EEP) were examined in December 2004, on two transects situated at 110°W (4°N to 3°S) and along the equator (110°W to 140°W). Lithogenic silica (lSiO2) was generally <10 nmol Si l−1 with maximum concentrations reaching 25 nmol l−1 in surface waters. These low concentrations confirm low atmospheric inputs of particulate Si, consistent with reported low inputs of wind-borne material in the EEP. In spite of active upwelling of silicic acid-rich waters the biogenic silica (bSiO2) concentrations were generally low, falling between 100 and 180 nmol Si l−1 in the upper 50 m and decreasing to less than 50 nmol Si l−1 below ∼90 m. Estimates of net bSiO2 production rates revealed that the rate of production exceeded that of dissolution in the upper euphotic layer (0-40 m) along 110°W with net production extending somewhat deeper (60-100 m) to the west along the equator. Net production rates in the surface layer were low, ranging between 5 and 40 nmol Si l−1 d−1, consistent with previous observations that diatoms are small contributors to autotrophic biomass in the EEP. Net silica dissolution predominated in the lower euphotic layer (40-120 m), indicating active Si recycling which diminished the strength of the silica pump in this region.

David M Nelson

Papers

Production and dissolution of biogenic silica in the ocean: Revised global estimates, comparison with regional data and relationship to biogenic sedimentation

Production and dissolution of biogenic silica in the ocean: revised global estimates, comparison with regional data and relationship to biogenic sedimentation

Particulate silica and Si recycling in the surface waters of the Eastern Equatorial Pacific

A review of Si particle fluxes in the modern ocean