Map of climate threats where you live

For NYT Opinion, Stuart A. Thompson and Yaryna Serkez mapped the most predominant “climate threat” in each county:

This picture of climate threats uses data from Four Twenty Seven, a company that assesses climate risk for financial markets. The index measures future risks based on climate models and historical data. We selected the highest risk for each county to build our map and combined it with separate data from Four Twenty Seven on wildfire risks.

Got me thinking about Tim Meko’s maps of natural disasters.

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Exclusive: University of Arizona says former researcher committed misconduct by plagiarizing figure

A former researcher in the University of Arizona’s optics school engaged in “a serious case of research misconduct,” Retraction Watch has learned. Palash Gangopadhyay, who until 2019 was a research scientist at Arizona, used a figure from a 2003 paper by other authors when he co-authored a 2018 paper in Optics Letters titled “High sensitivity … Continue reading Exclusive: University of Arizona says former researcher committed misconduct by plagiarizing figure

Herd immunity and the end of Covid-19


Following on from my previous posts about the SARS-CoV-2 virus, and Covid-19, the human disease that it causes, there are a number of miscellaneous topics that could also be discussed. Unfortunately, this is only a part of the post that I originally intended. I had written about some aspects of the pandemic that seem to be less well known. However, Blogger deleted the draft without warning, and this is the only part that I could recover.

Here, I talk about how the pandemic ends, as far as biology (rather than society) is concerned.
There is a lot of wishful thinking at the moment, that production of a vaccine will see the end of the pandemic, but the World Health Organization has warned that this may not be so. For example, they are apparently trying to develop a 5-year strategy for Europe, not a 5-month one. One of their officials, Hans Henri Kluge, has noted: "The end of the pandemic is the moment when we as a society learn how we can live with the pandemic."


Biologically, safety from pathogens involves what is called herd immunity. This refers to the proportion of the population who are not infectious, and thus are not spreading the pathogen (whether it is a virus, a bacterium, an apicomplexan, or a fungus). Lack of infectiousness can be achieved by:
  1. being resistant to the pathogen in the first place, perhaps due to past immunological events (eg. Coronavirus: How the common cold might protect you from COVID)
  2. becoming infected and then recovering, by producing antibodies or T-cells (eg. This trawler’s haul: Evidence that antibodies block the coronavirus)
  3. being vaccinated, which produces the same immune response as 2., by producing protective antibodies.

Note that 2. is not necessarily dangerous for most people, as reports show that anything up to half of the people who have antibodies to SARS-CoV-2 did not report clinical symptoms, or only mild symptoms. [Note also: lack of symptoms does not mean that you are not infectious.] However, the variation in human response has clearly been huge (see From ‘brain fog’ to heart damage, COVID-19’s lingering problems alarm scientists), in many cases resulting in cytokine storms, and death.

The main risk factors are also clear — age and gender (The coronavirus is most deadly if you are older and male — new data reveal the risks), and any pre-existing medical conditions, notably obesity (Individuals with obesity and COVID‐19: a global perspective on the epidemiology and biological relationships). Furthermore, we do not yet know how long any immune protection lasts — for example, we now have people who have been infected more than once (Researchers document first case of virus reinfection), although most have kept their antibodies for at least 4 months (Fyra av fem behåller antikroppar mot nya coronaviruset).

Nor do we yet know about the success or danger of 3., because it normally takes a couple of years of clinical trials before a vaccine is approved for use, and even then we can get it badly wrong (cf. the originally undetected side-effects of thalidomide). As far as health care is concerned, responsibility for treatment of any unfortunate outcomes from immunization is not at all clear. Furthermore, those nations that spend the most on healthcare per person may not be ranked highest for health outcomes and quality of care (see: What country spends the most on healthcare?). Therefore, it is hardly surprising that many people are concerned about taking any new vaccine (A Covid-19 vaccine problem: people who are afraid to get one), and that the World Health Organization is being much more cautious than many government leaders (Most people likely won't get a coronavirus vaccine until the middle of 2021).

Nevertheless, once herd immunity is achieved in my local population, I am relatively safe, irrespective of whether I have been vaccinated or not — there will be few infectious people around me, and so I am not very likely to catch the pathogen. Personally, I could wait a while to see how the myriad new vaccines affect people, as they have been rush-produced in a way that would not normally be accepted as safe for public use (what is called the Phase 3 trial takes time). After all, there seems to be an awful lot of politics involved, especially in the USA (The 943-dimensional chess of a trustworthy Covid-19 vaccine).


Some calculations

The point here is that the development of any epidemic is an interaction between infectivity, herd immunity and infection control. Let's consider some explicit numbers to make this clear (based on: Flockimmunitet på lägre nivå kan hejda smittan).

Infectivity refers to how the pathogen spreads among the at-risk population, usually described as the basal reproductive rate (R0). If each infected individual infects 2-3 others, then the R0 value is c. 2.5 (each person infects 2.5 other people, on average). This means that the epidemic must spread — if R = 1 then there is no spread; and if R < 1 then the infection slowly dies out (it stops instantly if R = 0).

Clearly, infectivity can be reduced by any infection control measure that reduces R. Some of these were listed in the previous section. These measures can easily reduce the initial R0 by one half, meaning that the epidemic spreads much more slowly, if R = 1.25.

Herd immunity comes into this by also reducing R. For example, if herd immunity reaches 60%, then only the remaining 40% of the people are susceptible to the infection. If we combine this 40% with the initial R0 = 2.5, then R = 1, and the epidemic no longer increases. That is, we now have it under control. Moreover, if we have managed to get to R = 1.25, then a herd immunity of even 20% will cause the epidemic to decrease.

Bhoj Raj Singh has a good slide presentation elaborating on this topic.

These calculations interact with the concept of relative risk, of course. The calculations so far assume that infection exposure is random in society, which is obviously too simple an idea. Some people are more socially active than others, are thus likely to be more exposed, and they will then quickly achieve significant herd immunity. Others find it difficult to self-isolate because of their work or social conditions, which also increases the development of herd immunity. All of this also helps more isolated people, of course, because they are not at risk of infection from those active groups with herd immunity.

We would thus expect herd immunity to develop first in cities (eg. Experts say Stockholm is close to achieving herd immunity ; A third of people tested in Bronx have coronavirus antibodies) and in poor communities (Herd immunity may be developing in Mumbai’s poorest areas), both of which seem to be the case for SARS-CoV-2.

Equally importantly, herd immunity cannot develop if we all hide from the virus. This has happened in New Zealand, for example, which has so far successfully quarantined itself from the rest of the world — they have not successfully fought the virus, they have instead successfully hidden from it. The issue is that the populace can never come out of hiding, and can thus never let anyone come into the country, not even returning New Zealanders. As an example, Hawaii had the same isolation advantage, and they lost it, just as expected (Hawaii is no longer safe from Covid-19), as also did Australia (Coronavirus (COVID-19) current situation and case numbers).

It is a classic question: which is better, fight or flight? In a pandemic, flight cannot lead to herd immunity, which is what we need in order to "learn how we can live with the pandemic".

So, where are we now? Well, a recent poll in the USA suggests that it is an even split about whether people will actually take a vaccine if offered soon (U.S. public now divided over whether to get Covid-19 vaccine). Will 50% be enough to ensure herd immunity in that country?

Weekend reads: Retracting racist and sexist work; The Lancet learns from a retraction; Trump administration interferes with publications

Before we present this week’s Weekend Reads, a question: Do you enjoy our weekly roundup? If so, we could really use your help. Would you consider a tax-deductible donation to support Weekend Reads, and our daily work? Thanks in advance. The week at Retraction Watch featured: The retraction of 23 papers, and block of 35 more, … Continue reading Weekend reads: Retracting racist and sexist work; The Lancet learns from a retraction; Trump administration interferes with publications

John Ray on species fixity and race

For since in nature the number of species is fixed and determined, since ‘God on the sixth day rested from all his labour’, that is,…

Smoke from the U.S. West Coast travels east and overseas

Smoke from the wildfires made its way to the other side of the country and over the ocean. Using data from NOAA, Reuters animated the smoke clouds over time:

With climate change expected to exacerbate fires in the future, by worsening droughts and warming surface ocean temperatures, wildfire research is becoming especially important. Over the last year, the world has seen record fires in Australia, Brazil, Argentina, Siberia and now the U.S. West.

“I’m concerned that we are starting to see these phenomena more often … everywhere in the world,” Gassó said. “If it’s one year like this, it’s fine, as long as it doesn’t keep repeating itself like this.”

Uh oh.

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Improved chromosome searching in Genome Browsers

Are you interested in searching for a chromosomal region in a genome, but don’t know how to write the correct query?  The good news is that the NCBI Genome Data Viewer (GDV) now supports a much wider array of search options. Some examples are listed below: chr1:1,500,000-2,000,000 chr2: 1.5M – 2M chr2: 1.5M-2,540.2K 2:1,500,000-2,000,000 3: … Continue reading Improved chromosome searching in Genome Browsers

RefSeq Release 202 is public

RefSeq release 202 is accessible online, via FTP and through NCBI’s Entrez programming utilities, E-utilities. This full release incorporates genomic, transcript, and protein data available as of September 8, 2020, and contains 255,571,455 records, including 186,755,483 proteins, 33,077,068 RNAs, and sequences from 104,969  organisms. The release is provided in several directories as a complete dataset … Continue reading RefSeq Release 202 is public

Election night might take weeks

For The Washington Post, Ashlyn Still and Kevin Schaul charted how long it took for primary ballots to be counted in each state. The times might give a hint of what we’re in for on election night:

Before the pandemic struck, mail-in states like California were already counting slowly. Then the coronavirus forced dozens of states to quickly expand absentee voting, and the slowdowns got more dramatic. These two trends — more absentee voting, not much time to prepare for it — could lead to some snail’s-paced race calls in November.

There are some nice details to note in this piece.

The inverted vertical axis and area fills focus on ballots left to count over time instead of ballots already in. The limited contrast keeps attention away from the white space under the lines.

The states move up to the top, and as the lines roll out (in the scrollytelling format), the speed is fixed, so that states that took more time count finish moving later.

And finally, the scrollytelling format helps highlight individual states at a time, and the small multiples at the end probably help satiate those who want to just see it all at once.

It’s a relatively straightforward dataset with multiple time series lines, but the choices make the patterns obvious.

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9/10/20 Virtual Office Hours Recap – Systematics

The Division of Environmental Biology (DEB) held a special Virtual Office Hour on September 10th, 2020 focusing on opportunities for funding research in Systematics.

The presentation is available here:

              Slides (PDF)

If you were unable to attend, here are some of the questions asked during the Q & A session:

Considering the current uncertain situation related to COVID-19, is it possible to submit a proposal that has a substantial overseas travel component, including fieldwork?

At this time, we recommend that you incorporate into your proposal whatever travel and fieldwork is needed to complete your research aims. Since there is so much uncertainty, it is not possible to plan for the long term, and we do not know how long the current restrictions will remain in place. Ultimately, if one does receive funding, and travel to the particular regions still remains untenable, a no cost extension can be requested that will help extend the project until such travel may be possible.

Is specimen digitization of types in foreign countries acceptable in the budget?

Yes, it is, if the digitization activities are specifically connected to questions being addressed by the project. This type of activity may also help achieve goals related to open data, so it could be worthwhile to address in the Project Description and the Data Management Plan how collecting and sharing these data will be relevant for the proposed work.

Can a Small Grant (SG) be submitted as a subcategory of another grant program, like an Advancing Revisionary Taxonomy and Systematics (ARTS)?

Absolutely. Indeed, submitted grants can qualify for a number of such subcategories and thus can be submitted with multiple acronyms in the title.

If one is looking to create a reference genome to address ecological and ecophysiological questions using transcriptomics, is this the best program to target? 

Research using transcriptomics in this cluster is definitely supported, but the specific rationale for such approaches needs to be addressing questions relevant to systematics, for instance, reconstructing phylogenetic relationships. In this particular case, it does sounds like this work might be a better fit for another cluster in DEB, such as the Ecosystem Studies Program (ES), or perhaps even another Division within Biological Sciences, such as Integrative Organismal Systems (IOS). We encourage you to contact the Program Officers in either of these areas to receive additional information.

In a proposal, is it necessary for the Broader Impacts (BIs) to emphasize producing novel outreach or should they instead leverage existing outreach capacity?

Either approach is acceptable. If one can tap into an existing, successful program, then that can be one component of a set of BIs. Further, it may be easier to convince panelists and reviewers that such approaches will be successful. On the other hand, developing novel outreach activities tailored to your project can be exciting to reviewers, though It may be harder to convince panelists and reviewers that such approaches will be successful since they don’t have a pre-existing track record. When writing a proposal, you need to decide which approach fits better into the type of work you aim to do.

Are systematics proposals expected to include new or novel phylogenetic analysis methods?

New methods are always welcome, but they are not required or expected.

Is it possible to submit more than one proposal (with unrelated questions), as a PI?

Yes, currently there is not a limit on the number of proposals that an investigator can submit, as long as they focus on substantially different questions.

For ARTS proposals, should one aim to include questions/methods relevant to the evolution of the group of interest (e.g., biogeography, character evolution, etc.) in addition to the stated goals of revisionary taxonomy and systematics along with training?

A key aim of the ARTS category of proposals is to support revisionary taxonomy and systematics that leads to predictive classifications and includes training. Thus, this is not required. However, more significant ecological and evolutionary questions that can ultimately be addressed through such work may be more likely to resonate well with panelists and reviewers and thus are certainly encouraged.

What is the general distinction between a core SBS proposal and a Bridging Ecology & Evolution (BEE) proposal?

A BEE proposal needs to specifically connect core areas of theory between ecology and evolution or combine hypotheses between the two disciplines with a focus on mechanisms and processes. Such proposals are reviewed not solely within SBS but also by program officers from other clusters within DEB. It is very useful to have a specific statement in a BEE proposal that shows how the work integrates questions and mechanisms that span these different conceptual areas. Just as an example, mapping a set of ecological characteristics to a phylogeny could potentially be of interest as an SBS proposal, but it does not have enough focus on distinct ecological and/or evolutionary processes and mechanisms to make a compelling case for a BEE proposal. A connection across disciplines but also via mechanisms and processes is essential.

Would population/subspecies level proposals be appropriate for the Systematics and Biodiversity Science program?

It depends on your specific idea, but many proposals addressing only questions at the population level are best suited to the Evolutionary Processes cluster. However, many projects include components both above and below the species level, so we encourage you to contact a Program Officer to discuss your particular situation.

For proposals involving collecting taxa overseas, are there any specific requirements regarding the Nagoya protocol?

We expect adherence to the Nagoya protocol and any local regulations when conducting international field work.

I work primarily in developing countries and do a substantial amount of training of international students. Does training and capacity building of non-US students count?

When it comes to student training, the emphasis of NSF funding will be on students at US institutions. However, NSF recognizes the importance of true intellectual collaboration that provides a strong foundation for international work, which will frequently involve foreign researchers in training as well as the core research. Any training for non-US students should be described in terms of how it improves the efficiency of the activities of US researchers. We encourage you to speak with Program Officers if you have any specific questions about ways that this can be structured.

How essential is it to incorporate undergraduate or graduate student training into a proposal?

Such types of student training are an important type of Broader Impacts (BI), but they are not the only or even a required type, and indeed sometimes they may not even be feasible depending on the institution one comes from. Other BIs can be utilized instead. Pick the type of BIs that you think will fit best with your project, its aims, and the institution you are at.

Who do I need to contact if I would like to serve as a reviewer?

We are always looking for interested reviewers and panelists. If you would like to volunteer for panel service, please visit this site and let us know you are interested.

Please reach out to a Program Officer if you have any questions about the proposal submission and review process in DEB programs.