A newly discovered immunological twist — the innate immune system’s tissue resident natural killer cells — cops on specific organ beats — and apparently specifically evolved to perform that function

© 2014 Peter Free

Citation — to study

Dorothy K Sojka, Beatrice Plougastel-Douglas, Liping Yang, Melissa A Pak-Wittel, Maxim N Artyomov, Yulia Ivanova, Chao Zhong, Julie M Chase, Paul B Rothman, Jenny Yu, Joan K Riley, Jinfang Zhu, Zhigang Tian, and Wayne M Yokoyama, Tissue-resident natural killer (NK) cells are cell lineages distinct from thymic and conventional splenic NK cells, eLife 3:e01659, DOI10.7554/eLife.01659 (08 Aril 2014)

Citation — to press release

Michael C. Purdy, Some immune cells defend only one organ, Washington University (16 April 2014)

Background — what are natural killer cells?

From the paper:

Natural killer (NK) cells are components of the innate immune system.

Initially described on the basis of their inherent capacity to kill tumor cells without prior sensitization, NK cells are now known to participate in a wide variety of immune responses, such as early control of viral infections.

In addition, they can respond to pro-inflammatory cytokines by producing yet other inflammatory cytokines, such as interferon-γ (IFNγ), their signature cytokine that can influence adaptive immune cells.

© 2014 Dorothy K Sojka, Beatrice Plougastel-Douglas, Liping Yang, Melissa A Pak-Wittel, Maxim N Artyomov, Yulia Ivanova, Chao Zhong, Julie M Chase, Paul B Rothman, Jenny Yu, Joan K Riley, Jinfang Zhu, Zhigang Tian, and Wayne M Yokoyama, Tissue-resident natural killer (NK) cells are cell lineages distinct from thymic and conventional splenic NK cells, eLife 3:e01659, DOI10.7554/eLife.01659 (08 Aril 2014) (at Introduction) (paragraph split)

And from Michael Purdy’s excellent press release:

Scientists have thought that mature natural killer cells circulate through the body looking for viruses and cancers. When these immune cells identify a threat, they attack.

Scientists also thought that natural killer cells that stayed in the liver instead of circulating were immature or inactive and eventually would become like other natural killer cells, leaving the liver and moving through the body.

© 2014 Michael C. Purdy, Some immune cells defend only one organ, Washington University (16 April 2014) (paragraph split)

Method and findings

The point here was to figure out whether tissue-resident natural killer cells are generated by the same immunological (genetic and developmental) pathways that wide-ranging killer cells are.

From the abstract:

Herein we used detailed transcriptomic, flow cytometric, and functional analysis and transcription factor-deficient mice to determine that liver trNK cells form a distinct lineage from cNK and thymic NK cells.

Taken together with analysis of trNK cells in other tissues, there are at least four distinct lineages of NK cells: cNK, thymic, liver (and skin) trNK, and uterine trNK cells.

© 2014 Dorothy K Sojka, Beatrice Plougastel-Douglas, Liping Yang, Melissa A Pak-Wittel, Maxim N Artyomov, Yulia Ivanova, Chao Zhong, Julie M Chase, Paul B Rothman, Jenny Yu, Joan K Riley, Jinfang Zhu, Zhigang Tian, and Wayne M Yokoyama, Tissue-resident natural killer (NK) cells are cell lineages distinct from thymic and conventional splenic NK cells, eLife 3:e01659, DOI10.7554/eLife.01659 (08 Aril 2014) (at Abstract) (paragraph split)

As Michal Purdy explained in more detail:

In the new study, lead author Dorothy K. Sojka, PhD, a postdoctoral research fellow in Yokoyama’s laboratory, showed that some natural killer cells never leave the liver. She identified additional tissue-resident natural killer cells in the skin and uterus.

Sojka also experimented with transcription factors — molecular switches that turn a number of genes on and off.

Among other results, she found that disabling one of these switches could prevent circulating natural killer cells from developing without affecting tissue-resident natural killer cells in the liver, skin and uterus.

Disabling another transcription factor wiped out the liver and skin tissue-resident natural killer cells while having little effect on the circulating and uterus tissue-resident natural killer cells.

“If one group of cells absolutely needs a specific transcription factor to exist, while another group of cells doesn’t care if that factor is gone, that strongly suggests the two groups of cells use distinct developmental pathways and are therefore different,” Sojka said.

Her results point to at least four types of natural killer cells rather than just the one major type long recognized by immunologists.

She is looking for groups of resident natural killer cells in other organs and investigating the origins and functions of those she already has identified.

© 2014 Michael C. Purdy, Some immune cells defend only one organ, Washington University (16 April 2014) (paragraph split)

The moral? — Outstanding and potentially medically useful immunological research

A pains-taking application of scientific brain power and biological lab technique.

An Australian study of 453 pertussis isolates — shows that a part of whooping cough resurgence may be due to the bacterium’s evolved loss of the antigen — called pertactin — which the acellular vaccine prompts the immune system to react to

© 2014 Peter Free

Citation — to study

Connie Lam, Sophie Octavia, Lawrence Ricafort, Vitali Sintchenko, Gwendolyn L. Gilbert, Nicholas Wood, Peter McIntyre, Helen Marshall, Nicole Guiso, Anthony D. Keil, Andrew Lawrence, Jenny Robson, Geoff Hogg, and Ruiting Lan, Rapid Increase in Pertactin-deficient Bordetella pertussis Isolates, Australia, Emerging Infectious Diseases 20(4): 626-633, DOI: 10.3201/eid2004.131478 (April 2014)

The problem — apparently waning acellular pertussis vaccine efficacy

From the abstract:

Multiple factors probably contributed to the resurgence of pertussis in high-income countries that had long-standing pertussis immunization programs.

These factors include waning immunity (exacerbated by the change from WCVs [whole cell vaccines] to ACVs [acellular vaccines] and, in Australia, cessation of the booster vaccination at 18 months of age) and increased use of more sensitive diagnostic tests, such PCR.

An additional possible contributing factor is evolution of B. pertussis through vaccine-driven adaptation.

© 2014 Connie Lam, Sophie Octavia, Lawrence Ricafort, Vitali Sintchenko, Gwendolyn L. Gilbert, Nicholas Wood, Peter McIntyre, Helen Marshall, Nicole Guiso, Anthony D. Keil, Andrew Lawrence, Jenny Robson, Geoff Hogg, and Ruiting Lan, Rapid Increase in Pertactin-deficient Bordetella pertussis Isolates, Australia, Emerging Infectious Diseases 20(4): 626-633, DOI: 10.3201/eid2004.131478 (April 2014) (paragraph split)

For example, in more detail from a 2013 pediatrics study:

During the 1990s, the U.S. switched from whole-cell pertussis vaccine (in the diphtheria, tetanus, and whole-cell pertussis combination vaccine DTwP) to combined acelluar pertussis (DTaP) vaccines.

The study, “Comparative Effectiveness of Acellular Versus Whole-Cell Pertussis Vaccines in Teenagers,” in the June 2013 issue of Pediatrics (published online May 20) looked at individuals born between 1994 and 1999 who received four pertussis-containing vaccines in the first two years of life.

Some individuals received DTwP, and others received DTaP.

The authors found that during a 2009 and 2010 pertussis outbreak, those teenagers who received DTaP had a six times higher risk of contracting pertussis due to waning immunity compared to those who received DTwP.

Among teenagers who received DTaP, receipt of the Tdap booster did not overcome the advantage in protection from pertussis associated with previously receiving DTwP vaccines.

The authors conclude that that research into developing new pertussis vaccines with improved safety and long-lasting immunity is warranted.

© 2013 American Academy of Pediatrics, Whole Cell vs. Acellular Pertussis Vaccine Affects Disease Risk, AAP.org (20 May 2013) (paragraph split)

Background — whole cell versus acellular pertussis vaccines — what’s the difference?

From the World Health Organization:

Two forms of [pertussis] vaccine are in use, the whole-cell vaccine (wP), and the acellular vaccine (aP).

Whole-cell pertussis vaccines were developed first and are suspensions of the entire B. pertussis organism that has been inactivated, usually with formalin.

Most wP vaccines are available in combination with diphtheria (D) and tetanus (T) vaccines, contain aluminum salts as an adjuvant and, thiomersal as a preservative. Immunization with wP vaccines is effective and the vaccine is relatively inexpensive, but immunization has been frequently associated with minor adverse reactions such as redness and swelling at the site of injection, along with fever and agitation.

Local reactions tend to increase with age and the number of injections; wP vaccines are therefore not recommended for immunization of adolescents and adults.

To address the adverse reactions observed with the whole-cell vaccines, aP vaccines were developed that contain purified components of B. pertussis such as inactivated pertussis toxin either alone or in combination with other B. pertussis components such as filamentous haemagglutinin, fimbrial antigens and pertactin.

As with the whole-cell vaccines, a wide variation exists between the bacterial clones used, the number and quantity of components, the methods of purification and inactivation, and the formulation, making direct clinical comparisons between vaccines difficult.

For the primary series of immunization, aP vaccines have no greater frequency of adverse events than controls, although in subsequent doses a higher rate of swelling has been observed leading to the use of vaccines with reduced antigen content for adolescents and adults.

Although aP vaccines have gradually supplanted the use of wP vaccines in industrialized countries, the significantly higher development and production costs of aP vaccines result in prices that are much higher than that of a dose of wP vaccine.

Given that the relative protective efficacy of the best wP and aP vaccines are comparable and the adverse events of both vaccines are relatively minor, wP vaccines remain the vaccine of choice in many developing countries.

© 2013 World Health Organization, Pertussis, WHO.int (25 October 2013) (paragraphs split, italics added)

Method — of the Australian study

The team examined the genetics of 453 Australian pertussis isolates, including:

133 from 1997-2008,

194 from 2008-2010,

and

126 more from 2011-2012.

Findings

From the abstract:

Acellular vaccines against Bordetella pertussis were introduced in Australia in 1997. By 2000, these vaccines had replaced whole-cell vaccines.

During 2008–2012, a large outbreak of pertussis occurred. During this period, 30% (96/320) of B. pertussis isolates did not express the vaccine antigen [see definition here] pertactin (prn) [see explanation here].

Multiple mechanisms of prn inactivation were documented . . . .

The mechanism of lack of expression of prn in 16 (17%) isolates could not be determined at the sequence level.

These findings suggest that B. pertussis not expressing prn arose independently multiple times since 2008, rather than by expansion of a single prn-negative clone.

This pattern is consistent with continuing evolution of B. pertussis in response to vaccine selection pressure.

© 2014 Connie Lam, Sophie Octavia, Lawrence Ricafort, Vitali Sintchenko, Gwendolyn L. Gilbert, Nicholas Wood, Peter McIntyre, Helen Marshall, Nicole Guiso, Anthony D. Keil, Andrew Lawrence, Jenny Robson, Geoff Hogg, and Ruiting Lan, Rapid Increase in Pertactin-deficient Bordetella pertussis Isolates, Australia, Emerging Infectious Diseases 20(4): 626-633, DOI: 10.3201/eid2004.131478 (April 2014) (at Abstract) (extracts)

The moral? — Acellular pertussis vaccine is not very effective, and perhaps this study partially shows why

Of interest:

In comparison, until 2001 and 2009, respectively, Russia and Senegal, which currently use only WCVs, have not reported prn-negative isolates.

However, it is difficult to draw a definitive conclusion on the correlation of timing of emergence of prn-negative strains with timing of introduction of ACVs.

Extensive analysis of isolates from earlier years from different countries would be required.

© 2014 Connie Lam, Sophie Octavia, Lawrence Ricafort, Vitali Sintchenko, Gwendolyn L. Gilbert, Nicholas Wood, Peter McIntyre, Helen Marshall, Nicole Guiso, Anthony D. Keil, Andrew Lawrence, Jenny Robson, Geoff Hogg, and Ruiting Lan, Rapid Increase in Pertactin-deficient Bordetella pertussis Isolates, Australia, Emerging Infectious Diseases 20(4): 626-633, DOI: 10.3201/eid2004.131478 (April 2014) (at Discussion) (extracts)

As a practical matter, I wonder whether it is true that whole cell and acellular pertussis vaccines are equally bad in conferring protection over time.  My guess is that the acellular pertussis vaccine’s protection may wane more rapidly, hence the reemergence of pertussis epidemics in developed countries.

Questionable methodology and reasoning — characterize an industry-sponsored report — which states that American nutritional supplement use is higher than previously estimated

© 2014 Peter Free

Citation — to study

Annette Dickinson, Judy Blatman, Neale El-Dash, and Julio C. Franco, Consumer Usage and Reasons for Using Dietary Supplements: Report of a Series of Surveys, Journal of the American College of Nutrition 33 (2): 176-182, DOI:10.1080/07315724.2013.875423 (14 April 2014)

This is one of those abstracts that irritated me (scientifically speaking) right off the bat

Rather than save my caveats for a subsequent paragraph, as I usually do, read with me — in the stream of scientific consciousness that one might employ while perusing an abstract.

Method

This study dives directly into its apparent “bogosity”.

As too vaguely laid out in the abstract:

Objective:

Consumer usage of dietary supplements is prevalent in the United States, and total usage is higher than reported in recent National Health and Nutrition Examination Surveys (NHANES) [see explanation here], because these surveys capture usage only in the 30 days prior to the respondent’s interview and do not capture occasional and seasonal use throughout the year.

We report data from a series of consumer surveys on the full extent of dietary supplement use, on the reasons for supplement use, and on the products most commonly taken, as well as other health habits of supplement users.

Methods:

The Council for Responsible Nutrition (CRN), a trade association of the dietary supplement industry, has contracted with Ipsos Public Affairs to conduct consumer surveys annually since 2000. The surveys have been administered online since 2007 to about 2000 subjects each year.

We report 5 years of data (2007 to 2011) on the prevalence of dietary supplement use, as well as more detailed data from the 2011 survey on the products used, the reasons for using supplements, and other health habits of supplement users.

© 2014 Annette Dickinson, Judy Blatman, Neale El-Dash, and Julio C. Franco, Consumer Usage and Reasons for Using Dietary Supplements: Report of a Series of Surveys, Journal of the American College of Nutrition 33 (2): 176-182, DOI:10.1080/07315724.2013.875423 (14 April 2014) (at Abstract) (paragraph split)

Curious reasoning

The authors’ “objective” starts off by implicitly slamming the accuracy of NHANES results.

The research team asserts that NHANES’ annual 30-day window into supplement-taking necessarily under-reports use.  As against what quantitative measure is left unsaid, until the concluding paragraph of the abstract:

Annual consumer surveys over a period of 5 years show that dietary supplement use is somewhat more prevalent in the United States than has been reported in the NHANES surveys, when occasional and seasonal use are taken into account, in addition to regular use.

© 2014 Annette Dickinson, Judy Blatman, Neale El-Dash, and Julio C. Franco, Consumer Usage and Reasons for Using Dietary Supplements: Report of a Series of Surveys, Journal of the American College of Nutrition 33 (2): 176-182, DOI:10.1080/07315724.2013.875423 (14 April 2014) (at Abstract) (paragraph split)

But of what argued significance is this distinction about occasional and seasonal use?

Does NHANES take place only at lows within the consumer cycle?  Why would not an annual 30-day window survey give a decent assessment of supplement use in quasi-averaged fashion?

The research team asserts, by implication, that the Ipsos surveys are more accurate than NHANES — but again without delineating Ipsos’ supposedly superior methodology and mathematical averaging.

Notice, too, that the 2011 Ipsos survey was apparently more detailed than its predecessors.  Which raises some obvious questions about Ipsos’ internal question and recall consistency across the five years.

Findings

The team’s vaguely explained methodology notwithstanding, the survey results sound interesting — my few comments in brackets:

The prevalence of supplement use fluctuated within the range of 64% to 69% from 2007 to 2011, and the prevalence of regular supplement use ranged from 48% to 53%, with no statistically significant differences from year to year.

Over the 5-year period, the percentage of respondents who said that they regularly used a variety of supplements increased from 28% to 36%, and the increase from 2010 to 2011 was statistically significant.

The percentage of respondents who said that they regularly used only a multivitamin, as opposed to a variety of supplements, declined from 24% to 17%, and the decrease from 2007 to 2008 was statistically significant.

[What happened to the other years?]

Detailed results from the 2011 survey confirm that supplement use increases with age and is higher in women than in men.

[How does 2011 detail statistically confirm something that this very sentence makes one doubt about the specificity of data from the previous surveys?]

Vitamin or mineral supplements were used by 67% of all respondents in 2011, specialty supplements by 35%, botanicals by 23%, and sports supplements by 17%.

[For how long?]

Among supplement users, multivitamins were the most commonly used supplement (71%), followed by omega-3 or fish oil (33%), calcium (32%), vitamin D (32%), and vitamin C (32%).

The reasons most often cited for supplement use were for overall health and wellness (58%) and to fill nutrient gaps in the diet (42%).

Supplement users were significantly more likely than nonusers to say that they try to eat a balanced diet, visit their doctor regularly, get a good night’s sleep, exercise regularly, and maintain a healthy weight.

[How much more likely?  One can have a difference of less than 1 percent be both statistically significant and completely meaningless in the practical realm.]

© 2014 Annette Dickinson, Judy Blatman, Neale El-Dash, and Julio C. Franco, Consumer Usage and Reasons for Using Dietary Supplements: Report of a Series of Surveys, Journal of the American College of Nutrition 33 (2): 176-182, DOI:10.1080/07315724.2013.875423 (14 April 2014) (at Abstract) (extracts, my comments in brackets)

Objections in general

It is communicatively a bad idea to slam something as reasonably done each year as NHANES is, without immediately setting down one’s supposedly superior methodology and/or reasoning.

Second, the assertion that the 2011 Ipsos survey was more detailed than its predecessors immediately sets out warning flags about whether it can be accurately integrated with, or compared to, previously collected data.

A detailed survey obviously provides a different recall context than a much more abbreviated one does.

One can reasonably surmise that the more detailed questions (presumably in 2011) might have prompted previously forgotten memories.  Thereby, dredging up a more detailed picture of dietary supplement use that year.  But, even if so, without actually saying anything reliable about differences in total consumption, or its distribution among supplement categories, from one year to another.

Then, the Bogosity Suspicion Meter

The authors’ affiliations:

Annette Dickinson — Dickinson Consulting, LLC

Judy Blatman — Council for Responsible Nutrition

Neale L. Dash — Ipsos Public Affairs

Julio C. Franco — Ipsos Public Affairs

All of these are presumably self-interested organizations and their representatives:

Dr. Dickinson is (one might infer) selling her consulting services.

Ms. Blatman represents the nutritional supplement trade group.

And Dr. Dash and Mr. Franco represent the polling business that the trade group hired to do its surveys.

Scientific caveats aside, the authors’ general conclusion sounds reasonable

The primary reasons given for supplement use are for overall health and wellness or to fill nutrient gaps.

Users of dietary supplements are more likely than nonusers to adopt a variety of healthy habits, indicating that supplement use is part of an overall approach to living healthy.

Annette Dickinson, Judy Blatman, Neale El-Dash, and Julio C. Franco, Consumer Usage and Reasons for Using Dietary Supplements: Report of a Series of Surveys, Journal of the American College of Nutrition 33 (2): 176-182, DOI:10.1080/07315724.2013.875423 (14 April 2014) (at Abstract) (paragraph split)

This, probably not coincidentally, might make a decent advertisement.   Which, one suspects, was the Council for Responsible Nutrition’s primary purpose in undertaking the surveys.

The moral? — Non-science or questionable science arguably masquerading as something more objective

Notice, in passing, how useful a list of author affiliations is.

Exotic state, 4 quark hadron confirmed — does not conform to conventional quark theory

© 2014 Peter Free

Citations — to press releases

Cian O’Luanaigh, LHCb confirms existence of exotic hadrons, CERN (09 April 2014)

Syracuse University, New form of matter: Exotic hadron with two quarks, two anti-quarks confirmed, ScienceDaily (11 April 2014)

Method

From Syracuse University:

“We analyzed tens of thousands of meson decays, selected from trillions of collisions in the Large Hadron Collider [the world's largest, most powerful particle accelerator] at CERN,” [Professor Sheldon Stone] says.

“Because the data sample was so large, it forced us to use statistically powerful analysis that could, in turn, measure properties in an unambiguous manner. It’s great to finally prove the existence of something that we had long thought was out there.”

Syracuse University, New form of matter: Exotic hadron with two quarks, two anti-quarks confirmed, ScienceDaily (11 April 2014) (paragraph split)

Findings

From the same press release:

Physicists have confirmed the existence of exotic hadrons — a type of matter that cannot be classified within the traditional quark model.

“We’ve confirmed the unambiguous observation of a very exotic state — something that looks like a particle composed of two quarks and two anti-quarks,” said one of the scientists.

“The discovery certainly doesn’t fit the traditional quark model. It may give us a new way of looking at strong-interaction physics.”

Quarks are hard, point-like objects found within the nucleus of an atom. When quarks combine in threes, they form compound particles known as baryons. Protons are probably the best-known baryons.

Sometimes, quarks interact with corresponding anti-particles (i.e., anti-quarks), which have the same mass but opposite charges. When this happens, they form mesons. These compounds often turn up in the decay of heavy human-made particles, such as those in particle accelerators, nuclear reactors, and cosmic rays.

Mesons, baryons, and other kinds of particles that take part in strong interactions are called hadrons.

© 2014 Syracuse University, New form of matter: Exotic hadron with two quarks, two anti-quarks confirmed, ScienceDaily (11 April 2014) (extracts)

The moral? — Hmmm

Will this discovery rework existing thinking?

Farming oysters on the Potomac riverbed could substantially reduce the stream’s algal eutrophication — which presumably would also help Chesapeake Bay — says a modeling effort — described in an exceptionally well written abstract

© 2014 Peter Free

Citation — to study

Suzanne B. Bricker, Karen C. Rice, and Owen P. Bricker III, From Headwaters to Coast: Influence of Human Activities on Water Quality of the Potomac River Estuary, Aquatic Geochemistry 20 (2-3): 201-323, DOI: 10.1007/s10498-014-9226-y (May 2014)

Citation — to press release

Ben Sherman and Karen Rice, Oyster aquaculture could significantly improve Potomac River estuary water quality, National Oceanic and Atmospheric Administration [NOAA] (09 April 2014)

A problem looking for a solution

From the abstract:

The natural aging process of Chesapeake Bay and its tributary estuaries has been accelerated by human activities around the shoreline and within the watershed, increasing sediment and nutrient loads delivered to the bay.

Riverine nutrients cause algal growth in the bay leading to reductions in light penetration with consequent declines in sea grass growth, smothering of bottom-dwelling organisms, and decreases in bottom-water dissolved oxygen as algal blooms decay.

Historically, bay waters were filtered by oysters, but declines in oyster populations from overfishing and disease have led to higher concentrations of fine-sediment particles and phytoplankton in the water column.

Assessments of water and biological resource quality in Chesapeake Bay and tributaries, such as the Potomac River, show a continual degraded state.

© 2014 Suzanne B. Bricker, Karen C. Rice, and Owen P. Bricker III, From Headwaters to Coast: Influence of Human Activities on Water Quality of the Potomac River Estuary, Aquatic Geochemistry 20 (2-3): 201-323, DOI: 10.1007/s10498-014-9226-y (May 2014) (extracts)

Study method

Again, from the paper’s summary paragraph:

Data from headwaters, nontidal, and estuarine portions of the Potomac River watershed and estuary were analyzed to examine the contribution from different parts of the watershed to total nitrogen loads to the estuary.

An eutrophication model was applied to these data to evaluate eutrophication status and changes since the early 1990s and for comparison to regional and national conditions.

A farm-scale aquaculture model was applied and results scaled to the estuary to determine the potential for shellfish (oyster) aquaculture to mediate eutrophication impacts.

© 2014 Suzanne B. Bricker, Karen C. Rice, and Owen P. Bricker III, From Headwaters to Coast: Influence of Human Activities on Water Quality of the Potomac River Estuary, Aquatic Geochemistry 20 (2-3): 201-323, DOI: 10.1007/s10498-014-9226-y (May 2014) (extracts)

Findings

How’s the following for a brilliantly communicated synopsis?

Results showed that

(1) the contribution to nitrogen loads from headwater streams is small (about 2 %) of total inputs to the Potomac River Estuary;

(2) eutrophic conditions in the Potomac River Estuary have improved in the upper estuary since the early 1990s, but have worsened in the lower estuary.

The overall system-wide eutrophication impact is high, despite a decrease in nitrogen loads from the upper basin and declining surface water nitrate nitrogen concentrations over that period;

(3) eutrophic conditions in the Potomac River Estuary are representative of Chesapeake Bay region and other US estuaries; moderate to high levels of nutrient-related degradation occur in about 65 % of US estuaries, particularly river-dominated low-flow systems such as the Potomac River Estuary;

and

(4) shellfish (oyster) aquaculture could remove eutrophication impacts directly from the estuary through harvest but should be considered a complement—not a substitute—for land-based measures.

The total nitrogen load could be removed if 40 % of the Potomac River Estuary bottom was in shellfish cultivation;

a combination of aquaculture and restoration of oyster reefs may provide larger benefits.

© 2014 Suzanne B. Bricker, Karen C. Rice, and Owen P. Bricker III, From Headwaters to Coast: Influence of Human Activities on Water Quality of the Potomac River Estuary, Aquatic Geochemistry 20 (2-3): 201-323, DOI: 10.1007/s10498-014-9226-y (May 2014) (reformatted)

A caveat

From NOAA’s press release:

Although the estuary bottom area needed to grow oysters to remove the nutrients exists, it is unlikely that such a management measure would be implemented because of conflicting uses.

However, a smaller area could still provide great benefits if aquaculture leases were approved. According to the study, if only 15 to 20 percent of the bottom was cultivated it could remove almost half of the incoming nutrients.

© 2014 Ben Sherman and Karen Rice, Oyster aquaculture could significantly improve Potomac River estuary water quality, National Oceanic and Atmospheric Administration [NOAA] (09 April 2014)

And another consideration not mentioned

Would even only 15 to 20 percent river bottom oyster coverage still fall within the limits of (previously) natural conditions?  If not, would the oysters alter ecological conditions in a potentially harmful way?

It doesn’t take much of a historian to recognize that humanity’s previous attempts at one-shot solutions to complex problems have frequently exacerbated troubles in unforeseen ways.

The moral? — Maybe and maybe not

Whether oyster aquaculture to clean up the Potomac would work, or even be ecologically advisable and saleable, remains to be seen.  But it seems an excellent idea.

Notice, too, that this team’s writing and synopsized scientific communication ability is absolutely superior to virtually everything one sees in the majority of science journals.  A+, indeed.

A paper on uncertainty in regard to climate change — claims that greater uncertainty requires more action today — (basically the potential catastrophe and Precautionary Principles combined) — when one could just as well argue that more uncertainty means that inaction may be a wiser course, for at least some people and regions

© 2014 Peter Free

Citation — to studies

Stephan Lewandowsky, James S. Risbey, Michael Smithson, Ben R. Newell, and John Hunter, Scientific uncertainty and climate change: Part I. Uncertainty and unabated emissions, Climate Change, DOI:10.1007/s10584-014-1082-7 (online publication, 04 April 2014)

Stephan Lewandowsky, James S. Risbey, Michael Smithson, and Ben R. Newell, Scientific uncertainty and climate change: Part II. Uncertainty and mitigation, Climate Change, DOI:10.1007/s10584-014-1083-6 (online publication, 04 April 2014)

Citation — to press release

University of Bristol, Scientists unmask the climate uncertainty monster, Bristol.ac.uk (04 April 2014)

Some people on both sides of the climate debate claim to know more and less than we actually do

Usually these folk are the climate warming denialists, who seem to think that the evidence for climate change, mainly in the form of the planet’s increasing heat content, doesn’t exist.

But every once in while, a scientist will pretend that more evidence exists for forecasting the probable future than actually does.

An example of a statistical argument, which actually says almost nothing useful

From the abstract for Part I:

Uncertainty forms an integral part of climate science, and it is often used to argue against mitigative action.

We show that increasing uncertainty is necessarily associated with greater expected damages from warming, provided the function relating warming to damages is convex.

This constraint is unaffected by subjective or cultural risk-perception factors, it is unlikely to be overcome by the discount rate, and it is independent of the presumed magnitude of climate sensitivity.

The analysis also extends to “second-order” uncertainty; that is, situations in which experts disagree.

Greater disagreement among experts increases the likelihood that the risk of exceeding a global temperature threshold is greater. Likewise, increasing uncertainty requires increasingly greater protective measures against sea level rise.

This constraint derives directly from the statistical properties of extreme values.

We conclude that any appeal to uncertainty compels a stronger, rather than weaker, concern about unabated warming than in the absence of uncertainty.

© 2014 Stephan Lewandowsky, James S. Risbey, Michael Smithson, Ben R. Newell, and John Hunter, Scientific uncertainty and climate change: Part I. Uncertainty and unabated emissions, Climate Change, DOI:10.1007/s10584-014-1082-7 (online publication, 04 April 2014)

This is essentially the old common sense formulation that indicates that — the more catastrophic a future phenomenon might be — the more and earlier we should attempt to mitigate it

From the press release:

The scientists used an ordinal approach – a range of mathematical methods that address the question: ‘What would the consequences be if uncertainty is even greater than we think it is?’

They show that as uncertainty in the temperature increase expected with a doubling of CO2 from pre-industrial levels rises, so do the economic damages of increased climate change.

Greater uncertainty also increases the likelihood of exceeding ‘safe’ temperature limits and the probability of failing to reach mitigation targets.  The authors highlight this with the case of future sea level, as larger uncertainty in sea level rise requires greater precautionary action to manage flood risk.

© 2014 University of Bristol, Scientists unmask the climate uncertainty monster, Bristol.ac.uk (04 April 2014)

In basic form

This is the argument that we are uncertain.  And our uncertainty potentially extends out beyond what we think are its limits.  In other words, Donald Rumsfeld’s famous “we don’t know what we don’t know” aphorism.

Notice the authors’ core and not necessarily accurate assumption

The abstract for Part I says that:

We show that increasing uncertainty is necessarily associated with greater expected damages from warming, provided the function relating warming to damages is convex.

But what if the warmth does not increase economic and life quality damage in all geographic regions?

What if warming brings positives in some places, as well as the anticipated negatives in others?

How does one net those (as yet unknown) pros and cons?

I get impatient with people who cannot accept that ambiguity is ambiguity — and that sometimes we don’t have a clue as how to proceed

It is fine to be deeply concerned about the effects of warming.  And it is fine to think that wise people might want to reduce it by beginning to limit the emission of the gases that cause it.  At least that way, we stay closer to the province of the known.  Such, incidentally, is the reasoning that underlies the Precautionary Principle.

But in fairness, one can argue the opposite way.  One could rationally think that warming might not work out to be a blanket evil.  Which means that the statistical outlier (meaning the catastrophic catastrophe that the research team warns us against) may not be as large as we envision.

And, if you think about it, why should it be?  How probablistically often does absolutely everything go to hell all at the same time?

If this less than sensational thinking is true (as some people think it is), then one can forgiven for wondering whether:

the economic harm that comes from taking measures today,

to ameliorate a possible future catastrophe,

might not outweigh that ultimate catastrophe’s net harm, when it does finally arrive in lesser form.

There is nothing in the research team’s reasoning that refutes this argument — for the simple reason that they had to make the convex function assumption (meaning that warmth increases damage without interruption) to get to where their reasoning wound up.

The moral? — Attaching numbers to unproven assumptions does not make the assumptions any more likely to be real

The fact is that we do not know what the net outcome of increasing planetary heat content is going to be.

That makes (a) self-interested people (who are content to benefit from the status quo) and (usually equally self-interested) policy-makers both unlikely to be persuaded to do anything about climate change.

An unwarranted conclusion based on spears found in the same sedimentary layer as a fossil saber toothed cat

© 2014 Peter Free

Citation — to press release

Antje Karbe, Humans and saber toothed tiger met at Schöningen 300.000 years ago, Eberhard Karls Universität Tübingen  (01 April 2014)

The press release takes proximity to a surprising level of unwarranted inference

The story:

Scientists of the Lower Saxony Heritage Authority and of the University of Tübingen excavating at the Schöningen open-cast coal mine in north-central Germany have discovered the remains of a saber-toothed cat preserved in a layer some 300,000 years old – the same stratum in which wooden spears were found, indicating that early humans also inhabited the area, which at that time was the bank of a shallow lake.

It is highly likely that humans were confronted by saber-toothed cats at the Schöningen lakeside. In that case, all the human could do was grab his up to 2.3m long spear and defend himself.

In this context, the Schöningen spears must be regarded as weapons for defense as well as hunting – a vital tool for human survival in Europe 300,000 years ago.

Measuring more than a meter at the shoulder and weighing some 200kg [440 pounds], the saber-tooth was no pussycat. It had razor-sharp claws and deadly jaws with upper-jaw canines more than 10cm [4 inches] long.

The new finds demonstrate that a long time before anatomically modern humans . . . have reached Europe some 40,000 years ago, early man was able to defend himself against highly dangerous animals with his weapon technology.

© 2014 Antje Karbe, Humans and saber toothed tiger met at Schöningen 300.000 years ago, Eberhard Karls Universität Tübingen  (01 April 2014) (extracts)

Not even close

The purported finding does not at all indicate that “early man was able to defend himself against highly dangerous animals”.

All it does, if the dating has been correctly done, is show that 1 cat and some pre-humans lived in the same area at roughly the same time.

The inference that pre-humans had to defend themselves against, or evade predators seems fair enough, based on our knowledge of how tigers and lions sometimes like to eat people.

But the idea that the discovered spears were actually effective in defending against a 440 pound saber-tooth is unwarranted — unless spear head(s), or spearhead marks on bone, were found inside the fossilized animal.

These spears were probably primarily used for team hunting much smaller and far less dangerous animals.  Certainly, some spears may occasionally have been employed for self-defense.  But my somewhat educated guess would be that most of those who used them so, died.  It takes a lot to kill big cats.  And even a lucky strike to a vital organ would probably not incapacitate the animal quickly enough to prevent it from killing the spear wielder(s).

Consequently, I doubt that the people of the time would agree that “the Schöningen spears must be regarded as weapons for defense as well as hunting.”

That inference is approximately the same as saying that an 8 year old’s small pocketknife would be considered a purposefully carried weapon of defense to be used against large dogs that grossly outweigh him or her.

Proto-humans probably survived because they were good at staying out the cats’ ways, in large enough numbers to keep the human gene pool occupied.  Not that their spears were actually good at fending saber toothed cats off.

Therefore, I quarrel with the idea that the context in which these spears were found means that they were effective defense weapons.

The moral? — Overblown press release

The leap from proximity within a sedimentary layer to a further inference about predation — to yet another about the utility of defense weapons — is not science or even decently supported inferential logic.

Frequency of alcohol consumption is apparently noticeably and positively correlated to the relative risk of dying from stroke — but this finding also serves as a reminder that absolute numbers are often more important in assessing whether to pay clinical attention to the correlation

© 2014 Peter Free

Citation

S. H. Rantakömi, S. Kurl, J. Sivenius, J. Kauhanen,  and J. A. Laukkanen, The frequency of alcohol consumption is associated with the stroke mortality, Acta Neurologica Scandinavica, DOI: 10.1111/ane.12243 (early online publication, 08 March 2014)

Method and findings

Researchers wanted to see whether frequency of alcohol consumption had an effect on the rate of dying from stroke.

The study followed 2,609 men, who originally had suffered no strokes, in eastern Finland for an average of 20.2 years:

During the follow-up, 66 deaths from stroke occurred.

After adjustment for systolic blood pressure, smoking, BMI, diabetes, and socioeconomic status, the relative risk (RR) among men who consumed alcohol <0.5 times per week was 0.70 . . . compared with nondrinkers.

Respective RR was 1.08 . . . for men with alcohol consumption of 0.5–2.5 times per week

and

2.44 . . . for men who consumed alcohol >2.5 times per week after adjustment for risk factors.

When the total amount of alcohol consumption . . . was taken into account with other covariates, RR was 0.71 . . . for men with alcohol consumption <0.5 times per week

and

1.16 . . . among men who consumed alcohol 0.5–2.5 times per week.

Among men who consumed alcohol >2.5 times per week compared with nondrinkers, RR was 3.03 . . . .

This study shows a strong association between the frequency of alcohol consumption and stroke mortality, independent of total amount of alcohol consumption.

The risk of stroke death was the highest among men who consumed alcohol >2.5 times per week.

© 2014 S. H. Rantakömi, S. Kurl, J. Sivenius, J. Kauhanen,  and J. A. Laukkanen, The frequency of alcohol consumption is associated with the stroke mortality, Acta Neurologica Scandinavica, DOI: 10.1111/ane.12243 (early online publication, 08 March 2014) (extracts, reformatted)

The horror — or is it?

Most people would consider a two or threefold increased risk of dying to be a significant one — and maybe something one might go out of one’s way to avoid.

But if you look at the above numbers, you recognize that this finding constitutes a tempest in a teapot:

 Only 66 men among 2,609 died from stroke, total.  That’s 2.5 percent.

And that trivial percentage doesn’t even separate out those who died without drinking at all.  Which means that probably less than 66 deaths could be correlated to the frequency of imbibing.

Am I really going to worry about elevating my risk of stroke death from 2.5 to 5 percent?  Probably not. Especially, if I like my daily booze unwinder.

Caveats

Too small a study to reliably uncover relatively subtle effects.  Probably a limited genetic pool.  And possibly an unreliable recollection of drinking patterns.

The moral? — A sense of real world perspective matters, and absolute numbers often convey that more clearly than relative risks do

This is not to say that a medical provider would not want to warn someone who comes from a family with a history of stroke about these findings.

On the other hand, someone subject to the average risk of stroke might elect to ignore the correlation from this small and limited study.

A set of relaxed assumptions allowed a research team to conclude that an Archaea genus named Methanosarcina caused the Permian Extinction — by emitting loads of methane into the atmosphere — but is this science fiction masquerading as science?

© 2014 Peter Free

Citation — to purported study

Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014)

Citation — to press release

David L. Chandler, Ancient whodunit may be solved: The microbes did it!, MIT News – Massachusetts Institute of Technology (31 March 2014)

Introduction

What follows sounds more critical than I actually am of this team’s well executed work.  My quarrel with their paper has to do with its too certain tone.

But let’s start with what the team wrote — rather than with what I think they actually meant.

Our era seems to persuade scientists that they must shout more sensationally than Sound Science with Integrity would allow.

Method and findings

From the abstract:

The end-Permian extinction is associated with a mysterious disruption to Earth’s carbon cycle. Here we identify causal mechanisms via three observations.

First, we show that geochemical signals indicate superexponential growth of the marine inorganic carbon reservoir, coincident with the extinction and consistent with the expansion of a new microbial metabolic pathway.

Second, we show that the efficient acetoclastic pathway in Methanosarcina emerged at a time statistically indistinguishable from the extinction.

Finally, we show that nickel concentrations in South China sediments increased sharply at the extinction, probably as a consequence of massive Siberian volcanism, enabling a methanogenic expansion by removal of nickel limitation.

Collectively, these results are consistent with the instigation of Earth’s greatest mass extinction by a specific microbial innovation.

© 2014 Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014) (at Abstract) (paragraph split)

Delving into the paper, we begin to see what a shaky chain of reasoning this is

The abstract end-runs the wild set of assumptions that the authors employed to come up with their sensation-making conclusion by using camouflaging terms like:

 “consistent with the expansion of a new microbial pathway”

“statistically indistinguishable”

and

“probably as a consequence of”.

These camouflaging terms translated

“Consistent with” — is a fudge phrase for — We didn’t check this against reality.

“Statistically indistinguishable” — is a meaningless claim — when one is talking:

(i) a half billion years

and

(ii) the narrow — arguably one to five thousand year window that would be required — if one wanted to pin down the allegedly causative event.

“Probably as a consequence of” — is a camouflaging phrase for — We know this is bullshit.

In the body of the paper — enormous assumptions out the wazoo

The first sign that the authors’ conclusions are most likely BS is their use of a mathematical formula that supposedly approximates the volume of the inorganic carbon reservoir at the time.  These mathematics are based on assumptions that cannot possibly be checked against geological reality.  In reality, we do not have much of a clue about what was actually going on at the time.

Hence, the authors’ initial formula is the equivalent of idle speculation.

The authors’ next imaginative leap drags in two more ideas.  First, that the inorganic carbon reservoir grew exponentially “or faster” (a curiously meaningless choice of language) toward the Permian Extinction.

And second, that:

Because such an upheaval of the carbon cycle implies substantial changes within the microbial biosphere, we hypothesize that the perturbation arises from the emergence of a new regime of microbial metabolic activity.

© 2014 Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014) (at The Carbon Source and Its Remobilization)

In other words — after indulging in our mathematical fantasy about the size of the inorganic carbon stockpile, “we” will slip in a couple of equally speculative assumptions, so as to give our hypothesis (about microbial responsibility for the Extinction) some legs.

The chain of speculation becomes even more involved

The authors, looking for a possible cause of their claimed (astonishingly increased) microbial methane production — the alleged smoking weapon that killed off most species — came up with the following chain of airy speculations:

Fournier and Gogarten (17) have recently shown that the high-efficiency pathway in Methanosarcina evolved via a single horizontal gene transfer event, probably from a clade of cellulolytic bacteria belonging to the class Clostridia, after the mid-Ordovician evolution of vascular land plants (450–500 Ma).

[Anybody who thinks that they can prove a single horizontal gene transfer event 450-500 million years ago — based on (a) geological evidence or (b) inferred molecular “clocks” — is of questionably sound brain.]

This is the only methanogenic pathway shown to have evolved via gene transfer.

It also appears to be a conspicuously recent event within the evolution of methanogenesis, as all other methanogenic pathways have a broader phylogenetic distribution implying much more ancient origins.

Methanosaeta may be more widespread in modern low-acetate marine environments (31).

[The terms — “implying” and “may be more widespread” — demonstrate that somebody knows that he and she is doing the metaphorical equivalent of creatively smoking dope.]

However, the dominance of the high-efficiency AckA-Pta pathway at high acetate concentrations (32) combined with the greater growth potential of Methanosarcina suggests that conditions for the emergence of acetoclastic Methanosarcina—specifically, a low-O2 marine environment (5, 12, 13) and the accumulation of sedimentary organic matter—would have been favorable in the Late Permian.

[“Would have been favorable” — meaning that, when we don’t have any evidence whatsoever for our inferences, we’ll just pretend that we do.]

Moreover, reports of significantly reduced marine sulfate concentrations (33–36) suggest that competition from sulfate-reducing bacteria would have been diminished, thereby amplifying the importance of methanogenesis in Late Permian marine sediments.

[“Suggests that” — perhaps so to minds that require little or no evidence for their presumptions.]

© 2014 Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014) (at The Carbon Source and Its Remobilization) (paragraph split)

Here’s the Clock Doozy

The following unconstrained, biological silliness should sound the alarm bells in any knowledgeable person’s brain:

The relevance of acetoclastic Methanosarcina to the end-Permian event depends crucially on the timing for the ancestor of this group.

To obtain an estimate for this date, we reconstructed archaeal phylogenies from 50 representative genomes and constructed relaxed molecular clock chronograms using PhyloBayes 2.3 (SI Text). Fig. 3A illustrates our results.

[“Constructed relaxed molecular clock chronograms” — in other words, we made stuff up.]

To estimate the time . . . of the last common ancestor of known acetoclastic representatives of Methanosarcina, we generated chronograms using four independent ribosome-based datasets, separately containing 29 concatenated universally conserved ribosomal proteins, 12 concatenated archaeal-specific ribosomal proteins, 16S ribosomal RNA, and 23S ribosomal RNA.

The phylogeny of these ribosomal components reflects the vertical cellular history of the Methanosarcinales, including Methanosarcina and its descendants, the recipient lineage of the ackA/pta transfer.

[“Reflects the vertical cellular history” is an unproven assumption.  Even if it is true — in general form — there is no reason to assume that the specific timing of its individual evolutionary elements can be reliably inferred.]

We further assume that ribosomal sequences evolve in a relatively clock-like manner, providing more reliable dates than most other genes in the absence of internal calibration.

[“We further assume” and “in a relatively clock-like manner” — defy (a) much of what we know about the specifics and timing of genetic mutation on the micro scale and (b) equally much of what we know about evolution on the macro scale.  In short, the authors’ assumptions are almost certainly nonsense or close to it.]

Our four independent age estimates, shown by the gray bars in Fig. 3A, are consistent with each other.

[Alternatively phrased — our “constructed” clocks and our sand-founded assumptions miraculously worked across all the lineages.  A claim that should lead careful thinkers to wonder what fudge factors had been applied and/or how “relaxed” the analyses had been.]

© 2014 Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014) (at Phylogenetic Analysis) (paragraph split)

Still more voluminously-indulged imagination

The authors then assume the following, so as to generate another “out of thin air” equation:

The resulting methane burst would have been oxidized to CO2, either by anaerobic methanotrophs at the expense of any remaining sulfate or aerobically.

O2 levels, which were likely already low (5, 12, 13), would have been depressed further.

Given the assumptions of an effectively unlimited substrate and a preexisting steady state, the size of the acetoclastic methanogenic niche . . . would therefore have increased, at a rate proportional to the rate at which nearby sulfate and O2 were depleted.

© 2014 Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014) (at Methanogenic Expansion) (paragraph split)

Last, the magical and magically appearing nickel supply

So close to the end of their imaginatively created construct, the authors could not let one final obstacle torpedo their string of piled high speculations:

Methanogens require nickel (18).

Nickel concentrations before the carbon isotopic spike are typically at least twice as high as after, and are up to seven times greater just before the abrupt downturn. With such elevated concentrations, nickel would no longer limit methanogenic activity.

All methanogens would have prospered, but the successful evolution and rapid expansion of acetoclastic Methanosarcina would have been especially favored in the substrate-rich end-Permian environment.

© 2014 Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014) (at Nickel Limitation and the Meishan Nickel Record) (paragraph split)

And — voila!

From the paper’s conclusion:

Our principal observations—a superexponential burst in the carbon cycle, the emergence of efficient acetoclastic methanogenesis, and a spike in the availability of nickel—appear straightforwardly related to several features of end-Permian environmental change:

Siberian volcanism (7, 8),

marine anoxia (5, 12, 13),

and

ocean acidification (14–16).

A single horizontal gene transfer (17) instigated biogeochemical change, massive volcanism acted as a catalyst, and the resulting expansion of acetoclastic Methanosarcina acted to perturb CO2 and O2 levels.

The ensuing biogeochemical disruption would likely have been widespread.

For example, anaerobic methane oxidation may have increased sulfide levels (47), possibly resulting in a toxic release of hydrogen sulfide to the atmosphere, causing extinctions on land (48).

Although such implications remain speculative, our work makes clear the exquisite sensitivity of the Earth system to the evolution of microbial life.

© 2014 Daniel H. Rothmana, Gregory P. Fournier, Katherine L. French, Eric J. Alm, Edward A. Boyle, Changqun Cao, and Roger E. Summons, Methanogenic burst in the end-Permian carbon cycle, Proceedings of the National Academy of Sciences [PNAS], DOI: 10.1073/pnas.1318106111 (published ahead of print, 31 March 2014) (at Conclusion) (paragraph split and reformatted)

The moral? — admirably creative Bogosity with a capital bee

The authors’ paper claims to demonstrate that:

[O]ur work makes clear the exquisite sensitivity of the Earth system to the evolution of microbial life.

In actuality, it does no such thing.  The paper merely demonstrates how easy it is to pile one speculation atop another, so as to make its massive methanogenesis claim appear to be justified.

Ergo, science fiction.

Here, I do not mean to demean either the authors or their investigation.  But I do criticize the too-certain tone with which they presented their methods and findings.  In my opinion, Science needs to be clear when “it” is doing mind experiments that are intended to guide future, more evidentiarily tied inquiries.

Poor sleep quality appears to be correlated with noticeably reduced cognitive ability in 70s-aged men

© 2014 Peter Free

Citation — to study

Terri Blackwell, Kristine Yaffe, Alison Laffan, Sonia Ancoli-Israel, Susan Redline, Kristine E. Ensrud, Yeonsu Song, and Katie L. Stone, Associations of Objectively and Subjectively Measured Sleep Quality with Subsequent Cognitive Decline in Older Community-Dwelling Men: The MrOS Sleep Study, Sleep 37 (4): 655-663, DOI: 10.5665/sleep.3562 (01 April 2014)

Citation — to press release

Lynn Celmer, Poor sleep quality linked to cognitive decline in older men, American Academy of Sleep Medicine (31 March 2014)

Method

The study followed 2,822 non-institutionalized men — aged 70 to 81 — for between 2.9 to 3.9 years.

Findings

From the abstract:

Among older community-dwelling men, reduced sleep efficiency, greater nighttime wakefulness, greater number of long wake episodes, and poor self-reported sleep quality were associated with subsequent cognitive decline.

© 2014 Terri Blackwell, Kristine Yaffe, Alison Laffan, Sonia Ancoli-Israel, Susan Redline, Kristine E. Ensrud, Yeonsu Song, and Katie L. Stone, Associations of Objectively and Subjectively Measured Sleep Quality with Subsequent Cognitive Decline in Older Community-Dwelling Men: The MrOS Sleep Study, Sleep 37 (4): 655-663, DOI: 10.5665/sleep.3562 (01 April 2014) (at Abstract)

A significant effect

From the press release:

Results show that higher levels of fragmented sleep and lower sleep efficiency were associated with a 40 to 50 percent increase in the odds of clinically significant decline in executive function, which was similar in magnitude to the effect of a five-year increase in age.

In contrast, sleep duration was not related to subsequent cognitive decline.

© 2014 Lynn Celmer, Poor sleep quality linked to cognitive decline in older men, American Academy of Sleep Medicine (31 March 2014)

Caveats

Sleep quality data were numerically sparse:

An average of five nights of objective sleep data were collected from each participant using a wrist actigraph [see definition, here].

Cognitive function assessment included evaluation of attention and executive function using the Trails B test.  According to the authors, executive function is the ability for planning or decision making, error correction or trouble shooting, and abstract thinking.

Results were adjusted for potential confounding factors such as depressive symptoms, comorbidities and medication use.

The underlying mechanisms relating disturbed sleep to cognitive decline remain unknown, the authors noted.

They added that additional research is needed to determine if these associations hold after a longer follow-up period.

© 2014 Lynn Celmer, Poor sleep quality linked to cognitive decline in older men, American Academy of Sleep Medicine (31 March 2014) (paragraphs split)

I am not persuaded that 5 nights of sleep data taken over 3 to 4 years is indicative of long-term sleep quality.  Particularly under circumstances in which one might be unconsciously tempted to presume that the presence of declined cognitive function confirmed the (methodologically questionable) extrapolation of those five sleep measurements to representatively characterize the subjects’ 3 to 4 years of sleep.

The moral? — Probably a legitimate finding, but needs methodologically stouter confirmation

A very valuable first effort.