Piled assumptions indicate that the ice ages of 80 and 50 million years ago — were caused by tectonic plates collision — and the associated push up of marine rock into tropical conditions — that exposed this rock to warm-wet weathering — a process that chemically sopped carbon dioxide up — thereby causing both climatic coolings

© 2016 Peter Free

Citation — to study

Oliver Jagoutz, Francis A. Macdonald, and Leigh Royden, Low-latitude arc–continent collision as a driver for global cooling, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1523667113 (early edition, 18 April 2016)

Citation — to press release

Jennifer Chu, Study: Ancient tectonic activity was trigger for ice ages, MIT News (18 April 2016)

Do tell

From Jennifer Chu’s well-constructed press release:

[The research team] found that 90 million years ago, the northeastern edge of the African plate collided and slid under an oceanic plate in the Neo-Tethys Ocean [see here], creating a chain of volcanoes.

At 80 million years ago, as Africa continued advancing north, the oceanic plate was pushed further up and over the continent, exposing ocean rock to the atmosphere, while simultaneously terminating the volcanoes.

Then, 50 million years ago, India merged with Eurasia in a second collision in which a different region of the oceanic plate was pushed up onto that continent.

Both collisions took place in the Intertropical Convergence Zone (ITCZ) [see here], an atmospheric region hovering over the Earth’s equator, in which trade winds come together to generate a region of intense temperatures and rainfall.

Certain types of rock, if exposed to high heat and heavy rain, undergo chemical reactions and effectively absorb carbon dioxide, a process known as silicate weathering. These rocks include basalts and “ultramafic” rocks, which are often found within oceanic plates. If these rocks are exposed to the atmosphere in a tropical region, they can act as very efficient carbon sinks.

The team hypothesized that the two collisions, involving Africa and then India, brought basaltic and ultramafic rocks up from the oceans and onto land, creating carbon sinks 80 and 50 million years ago.

Both collisions also effectively turned off carbon sources by burying volcanoes that had been emitting carbon dioxide and other gases into the atmosphere.

To know whether such a sequence of events directly reduced carbon dioxide in the atmosphere, the researchers looked to weathering rates of different rock types, including granites, basalts, and ultramafics. These rates, which have been calculated by other researchers, describe the way rocks erode and take up carbon dioxide, given exposure to a certain amount of rainfall.

They then applied these weathering rates to their model’s estimates of the amount of oceanic plate that was pushed up onto Africa and India, at 80 and 50 million years ago, respectively. After determining the amount of carbon dioxide sequestered by these rocks, they calculated the total amount of atmospheric carbon dioxide through time, from 100 million years ago to around 40 million years ago.

The team found that carbon dioxide dipped dramatically at precisely the time the two collisions occurred. The levels of carbon dioxide also mirrored the temperature of the oceans during this interval.

© 2016 Jennifer Chu, Study: Ancient tectonic activity was trigger for ice ages, MIT News (18 April 2016) (extracts)

OMG

How conveniently all these assumptions meshed:

our pretended ability to estimate the type and quantity of the tectonically surfaced ocean rock,

its chemical composition(s),

the rate and degree at and to which these chemically pertinent portions weathered,

to take up and sequester an allegedly quantifiable mass of carbon dioxide,

80 and 50 million years ago,

in a material, weather and climate world that we mostly cannot even crudely yet know.

I especially liked the fact that the volcano chain(s) simultaneously got (totally enough) squished, so as to turn off the problematic greenhouse gas faucet. And the Intertropical Convergence Zone apparently worked similarly to today, despite the distant past’s different distribution of land masses and (presumably) ocean and wind currents.

Now that’s some construct!

The moral? — There is no BS too large to be crammed into eagerly receptive models

I can imagine the mathematical computations (read “fudging”) that was necessary to make this hypothesis come out right.

OSMR cytokine receptor appears to play a critical role — in promoting gliobastoma multiforme brain cancer — in a mouse model

© 2016 Peter Free

Citation — to study

Arezu Jahani-Asl, Hang Yin, Vahab D Soleimani, Takrima Haque, H Artee Luchman, Natasha C Chang, Marie-Claude Sincennes, Sidharth V Puram, Andrew M Scott, Ian A J Lorimer, Theodore J Perkins, Keith L Ligon, Samuel Weiss, Michael A Rudnicki, and Azad Bonni, Control of glioblastoma tumorigenesis by feed-forward cytokine signaling, Nature Neuroscience, DOI: 10.1038/nn.4295 (advance online publication, 25 April 2016)

Citation — to press release

McGill University, Key mechanism identified in brain tumor growth, McGill.ca (25 April 2016)

Regarding the brain cancer known as glioblastoma multiforme (grade IV astrocytoma) . . .

Will interrupting the cytokine signaling chain medically help?

From the press release:

The research team then studied human brain tumor stem cells taken from glioblastoma patients. These cells are normally able to proliferate and form new tumors when injected into laboratory mice.

To the researchers’ surprise, however, they found that when they knock down the gene for OSMR [oncostatin-M specific receptor] in glioblastoma cells and inject these cells in mice they lose their ability to form tumors.

“It means that this protein is a key piece of the puzzle,” says Rudnicki, senior co-corresponding author of the study.

The researchers concluded that these two genes, OSMR and EGFRvIII [epidermal growth factor receptor variant III], conspire to promote tumor growth by making what’s known as a “feed forward” mechanism: when OSMR produces its protein, that signals EGFRvIII to rev up and produce its tumor-forming protein.

[Lead author] Jahani-Asl is now developing antibodies and small molecules designed to inhibit the OSMR protein or its interaction with EGFRvIII – a step toward the ultimate goal of finding ways to treat these tumors.

“If we find that they can reverse tumor formation in rodent models,” she says, “we will be equipped to adapt those techniques for testing in patients.”

© 2016 McGill University, Key mechanism identified in brain tumor growth, McGill.ca (25 April 2016) (extracts)

Notice that — with regard to properly communicating science

The university press release left out another important constituent of the signaling and activation chain — STAT3 [signal transducer and activator of transcription 3]. Demonstrating (again) that you cannot trust the media to get anything right. Even when the facts have already been written down for them:

EGFRvIII-STAT3 signaling is important in glioblastoma pathogenesis.

Here, we identified the cytokine receptor OSMR as a direct target gene of the transcription factor STAT3 in mouse astrocytes and human brain tumor stem cells (BTSCs).

We found that OSMR functioned as an essential co-receptor for EGFRvIII. OSMR formed a physical complex with EGFRvIII, and depletion of OSMR impaired EGFRvIII-STAT3 signaling.

Conversely, pharmacological inhibition of EGFRvIII phosphorylation inhibited the EGFRvIII-OSMR interaction and activation of STAT3.

[K]nockdown of OSMR strongly suppressed cell proliferation and tumor growth of mouse glioblastoma cells and human BTSC xenografts in mice, and prolonged the lifespan of these mice.

Our findings identify OSMR as a critical regulator of glioblastoma tumor growth that orchestrates a feed-forward signaling mechanism with EGFRvIII and STAT3 to drive tumorigenesis.

© 2016 Arezu Jahani-Asl, Hang Yin, Vahab D Soleimani, Takrima Haque, H Artee Luchman, Natasha C Chang, Marie-Claude Sincennes, Sidharth V Puram, Andrew M Scott, Ian A J Lorimer, Theodore J Perkins, Keith L Ligon, Samuel Weiss, Michael A Rudnicki, and Azad Bonni, Control of glioblastoma tumorigenesis by feed-forward cytokine signaling, Nature Neuroscience, DOI: 10.1038/nn.4295 (advance online publication, 25 April 2016) (at Abstract) (paragraph split, one sentence omitted)

The moral? — Excellent work that provides a ray of hope

Salute and appreciation to the research team.

Is Amazonian biodiversity loss being underestimated? — a before and after dung beetle study suggests so — but its reasoning is quantitatively questionable

© 2016 Peter Free

Citation — to study

Filipe França, Julio Louzada, Vanesca Korasaki, Hannah Griffiths, Juliana M. Silveira, and Jos Barlow, Do space-for-time assessments underestimate the impacts of logging on tropical biodiversity? An Amazonian case study using dung beetles, Journal of Applied Ecology, DOI: 10.1111/1365-2664.12657 (early view, 22 April 2016)

Citation — to press release

Lancaster University, Rainforest study shows biodiversity loss worse than anticipated, lancaster.ac.uk (22 April 2016)

The gist — measuring biodiversity before and after disturbance is more accurate

From the press release:

Lancaster University researchers and Brazilian colleagues went to the Amazon forest to measure dung beetle species diversity before and after logging exploration to contrast two different experimental methods.

The results are striking. When they compared the data from the different techniques, they discovered the most commonly used scientific method (space-for-time substitution) underestimated species loss by up to half.

Most ecological impact studies are conducted when the disturbance events (such as fires or logging) have already taken place and, as result, researchers are forced to use undisturbed sites in nearby regions to provide a picture of what the disturbed site may have looked like before the disturbance. This approach is known as space-for-time substitution and dominates literature on land-use change and disturbance.

In an ideal world, when researchers are able to sample prior to the disturbance event, they can use a before–after control–impact technique. This technique enables them to compare biodiversity before and after the disturbance event.

Researchers . . . used pitfall traps to sample 4,846 dung beetles dung beetles across 34 different plots in the state of Pará in the Brazilian Amazon.  The before–after control–impact approach was the only one to show significant negative effects of logging intensification; it also showed stronger negative effects on dung beetle species richness than the space-for-time approach.

© 2016 Lancaster University, Rainforest study shows biodiversity loss worse than anticipated, lancaster.ac.uk (22 April 2016) (extracts)

From the abstract:

We compare the SFT [space-for-time] substitution with a before–after control–impact (BACI) approach by assessing dung beetles before and after a logging exploration in the Brazilian Amazon.

We sampled 34 logging management units, of which 29 were selectively logged with different intensities after our first collection. We used dung beetle species richness, species composition and biomass as our biodiversity response metrics and the gradient of selective logging intensity as our explanatory metric.

Only the BACI approach consistently demonstrated the negative impacts of logging intensification on all dung beetle community metrics. Moreover, the BACI approach explained significantly more of the variance in all the relationships and it doubled the estimates of species loss along the gradient of logging intensity when compared to SFT.

Our results suggest that space-for-time (SFT) substitution may greatly underestimate the consequences on local species diversity and community turnover.

These results have important implications for researchers investigating human impacts on biodiversity. Incentivizing before–after control–impact (BACI) approaches will require longer-term funding to gather the data and stronger links between researchers and landowners. However, BACI approaches are accompanied by many logistical constraints, making the continued use of SFT studies inevitable in many cases.

We highlight that non-significant results and weak effects should be viewed with caution.

© 2016 Filipe França, Julio Louzada, Vanesca Korasaki, Hannah Griffiths, Juliana M. Silveira, and Jos Barlow, Do space-for-time assessments underestimate the impacts of logging on tropical biodiversity? An Amazonian case study using dung beetles, Journal of Applied Ecology, DOI: 10.1111/1365-2664.12657 (early view, 22 April 2016)

Caveats

It makes sense that a before and after method of measuring biodiversity totals would be preferable to one that approximates such a check by using purportedly equivalent and supposedly undisturbed sites as proxies.

On the other hand, is the research team correct in hypothesizing that the (idiotically named) space-for-time approach will, on average, underestimate biodiversity losses? Presumably some allegedly equivalent sites will have more biodiversity than the one originally affected and others less. On average, these differences should even out.

I am also not convinced that a dung beetle study can be extrapolated to have meaning for all manner of other species’ diversity. Surely some critters and plants are easier to find and count than others.

The biggest flaw in the space-for-time approach, it seems to me, is the difficulty of obtaining equivalency between sites. I suppose it is possible that researchers would be most interested in computing losses in the most species-favorable regions and, therefore, proxy undistrubed sites would be less rich — which would indeed underestimate the loss at the originally richer target site.

The moral? — Perhaps we are underestimating biodiversity losses, but maybe not

This study represents an important alert from the dung beetle team. But it is one that will take rigorous checking to prove at other locations and for a wider breadth of species.

Illustrating the difficulties inherent in distinguishing between no longer existing species — supposedly separate mammoth species may have interbred — thereby indicating that they were not actually genetically separate

© 2016 Peter Free

Citation — to study

Hendrik Poinar,  Ross MacPhee, Jake Enk, Alison Devault,  Chris Widga, Jeff Saunders, Paul Szpak, John Southon, Jean-Marie Rouillard, Beth Shapiro, Brian Golding, Grant Zazula, Duane Froese, and Dan Fisher, Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography and Introgression, Frontiers in Ecology and Evolution, DOI: doi: 10.3389/fevo.2016.00042 (accepted 06 April and apparently published on 21 April 2016)

Citation — to press release

Frontiers in Ecology and Evolution, DNA proves mammoths mated beyond species boundaries, EurekAlert! (21 April 2016)

Accurately detecting evolutionary speciation is not as easy as Linnaean classicism might lead us to think

From the press release:

A species can be defined as a group of similar animals that can successfully breed and produce fertile offspring. By using differences in the size and shape of their fossilized teeth, a number of North American mammoth species have been identified.

But, some scientists are not confident this method of species categorization tells the whole story.

© 2016 Frontiers in Ecology and Evolution, DNA proves mammoths mated beyond species boundaries, EurekAlert! (21 April 2016) (paragraph split)

To wit — from the abstract:

[W]e sequenced 67 complete mitochondrial genomes from non-primigenius specimens representing M. columbi (Columbian mammoth), M. jeffersonii (Jeffersonian mammoth), and M. exilis (pygmy mammoth), including specimens from contexts not generally associated with good DNA preservation.

While we uncovered clear phylogeographic structure in mammoth matrilines, their phylogeny as recovered from mitochondrial DNA is not compatible with existing systematic interpretations of their paleontological record.

Instead, our results strongly suggest that various nominal mammoth species interbred, perhaps extensively.

We hypothesize that at least two distinct stages of interbreeding between conventional paleontological species are likely responsible for this pattern – one between Siberian woolly mammoths and resident American populations that introduced woolly mammoth phenotypes to the continent, and another between ecomorphologically distinct populations of woolly and Columbian mammoths in North America south of the ice.

© 2016 Hendrik Poinar,  Ross MacPhee, Jake Enk, Alison Devault,  Chris Widga, Jeff Saunders, Paul Szpak, John Southon, Jean-Marie Rouillard, Beth Shapiro, Brian Golding, Grant Zazula, Duane Froese, and Dan Fisher, Mammuthus Population Dynamics in Late Pleistocene North America: Divergence, Phylogeography and Introgression, Frontiers in Ecology and Evolution, DOI: doi: 10.3389/fevo.2016.00042 (accepted 06 April and apparently published on 21 April 2016) (at Abstract) (paragraph split)

In more detail

From the press release:

Professor Poinar and his co-authors used cutting-edge methods to distinguish species of North American mammoths. Tiny samples of fossilized mammoth bone, teeth and faeces, were generously donated by a number of museums across America and Canada.

DNA was extracted from these samples in a specialized laboratory of the Ancient DNA centre at the McMaster University, and used to create a family tree of their evolution. The results proved to be very interesting.

North American mammoths such as the Columbian and Woolly Mammoths were historically thought to originate from two separate primitive species. However, this latest DNA analysis agrees with a more recent idea that all North American mammoths originated from a single primitive species, the Steppe Mammoth.

“Individuals of the Woolly and Columbian mammoths look like they represent different species in terms of their molar teeth, but their genetics say that they were not completely separate in the evolutionary sense and could successfully interbreed,” says Professor MacPhee.

Professor Poinar continues, “Mammoths were much better at adapting to new habitats than we first thought — we suspect that subgroups of mammoths evolved to deal with local conditions, but maintained genetic continuity by encountering and potentially interbreeding with each other where their two different habitats met, such as at the edge of glaciers and ice sheets.”

So, while mammoths clearly evolved differences in their physical appearance to deal with different environments, it did not prohibit them from cross-breeding and producing healthy offspring.

© 2016 Frontiers in Ecology and Evolution, DNA proves mammoths mated beyond species boundaries, EurekAlert! (21 April 2016) (extracts)

This harmonizes with one of my long-held questions regarding ice age mammoth speciation

It seemed to me that there may not have been enough time during the icy periods for those elephant-like animals (which did adapt to the cold) to have thoroughly segregated themselves from each other, so as to generate the firmly separate species that we thought they were. Habitats along the ice front might not have been dynamically different enough to “speed” the pace of evolutionary change, even among temporarily isolated groups. As the authors suggest, mammoths were a mobile group, probably likely to encounter one another.

The moral? — Erroneous hypotheses and conclusions are necessary to the scientific process

Science is ultimately aimed at winnowing truth from the conceptual and factual detritus. It is only after this process is complete that we recognize “bullshit” for what it was.

In a meaningful sense what distinguishes science from other forms of humor endeavor is not that we do not generate high volumes of probable BS. But that, rather than hold to it, we whack at it enough to prove or disprove it.

Types of gut microbiota in mice may negatively affect neuro myelination — as well induce depressive-like behaviors — this clever experiment might eventually lead to significant medical advances

© 2016 Peter Free

Citation — to study

Mar Gacias, Sevasti Gaspari, Patricia Mae-Santos, Sabrina Tamburini, Monica Andrade, Fan Zang, Nan Shen, Vladimir Tolstikov, Michael A Kiebish, Jeffrey L Dupree, Venetia Zachariou, Jose C Clemente, and Patrizia Casaccia, Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior, eLife, DOI: 10.7554/eLife.13442 (20 April 2016)

Citation — to press release

Icahn School of Medicine at Mount Sinai, Transfer of Gut Bacteria Affects Brain Function and Nerve Fiber Insulation, Mount Sinai Hospital (20 April 2016)

Not entirely surprising, but nevertheless — wow

From the press release:

Specific combinations of gut bacteria produce substances that affect myelin content and cause social avoidance behaviors in mice . . . . This research suggests that targeting intestinal bacteria, or their metabolites, could be one way to treat debilitating psychiatric disorders and demyelinating diseases, like multiple sclerosis.

Researchers transferred fecal bacteria from the gut of depressed mice to genetically distinct mice exhibiting non-depressed behavior.

The study showed that the transfer of microbiota was sufficient to induce social withdrawal behaviors and change the expression of myelin genes and myelin content in the brains of the recipient mice.

“Our findings will help in the understanding of microbiota in modulating multiple sclerosis,” says Dr. Casaccia. “The study provides a proof of principle that gut metabolites have the ability to affect myelin content irrespective of the genetic makeup of mice. We are hopeful these metabolites can be targeted for potential future therapies.”

In an effort to define the mechanism of gut-brain communication, researchers identified bacterial communities associated with increased levels of cresol, a substance that has the ability to pass the blood-brain barrier. When the precursors of myelin-forming cells were cultured in a dish and exposed to cresol, they lost their ability to form myelin, thereby suggesting that a gut-derived metabolite impacted myelin formation in the brain.

© 2016 Icahn School of Medicine at Mount Sinai, Transfer of Gut Bacteria Affects Brain Function and Nerve Fiber Insulation, Mount Sinai Hospital (20 April 2016) (extracts)

Most succinctly:

Here, we identify gut microbiota as sufficient to induce depressive-like behaviors in genetically distinct mouse strains.

Our results thus demonstrate that the gut microbiota modifies the synthesis of key metabolites affecting gene expression in the prefrontal cortex, thereby modulating social behavior.

© 2016 Mar Gacias, Sevasti Gaspari, Patricia Mae-Santos, Sabrina Tamburini, Monica Andrade, Fan Zang, Nan Shen, Vladimir Tolstikov, Michael A Kiebish, Jeffrey L Dupree, Venetia Zachariou, Jose C Clemente, and Patrizia Casaccia, Microbiota-driven transcriptional changes in prefrontal cortex override genetic differences in social behavior, eLife, DOI: 10.7554/eLife.13442 (20 April 2016) (at Abstract)

Caveat

Obviously in an experiment of this complexity, given the number of possibly pertinent variables, it would be easy to go astray.

The moral? — Impressive results, replication required

If verified, it would be difficult to overstate the medical potential of these findings.