Weekend reads: Publication hijacking; questions about Sputnik vaccine; no more second round of review?

Would you consider a donation to support Weekend Reads, and our daily work? Thanks in advance. The week at Retraction Watch featured: NYU postdoc with federal research misconduct settlement awarded NIH grant An Elsevier journal said it would retract 10 papers two years ago. It still hasn’t. UPenn prof with four retractions “may no longer be affiliated” … Continue reading Weekend reads: Publication hijacking; questions about Sputnik vaccine; no more second round of review?

Increased distance to the nearest clinic

With Roe vs. Wade in place, there were areas in the United States where a woman had to travel farther than others to get to the nearest clinic. With Roe vs. Wade overturned, the geography will change as states enforce bans. For NYT’s The Upshot, Quoctrung Bui, Claire Cain Miller and Margot Sanger-Katz mapped what will likely happen.

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When Americans Had Intercourse with Opposite Sex for the First Time

The National Survey of Family Growth, run by the Centers for Disease Control and Prevention, asks participants about their birth and relationship history.

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NYU postdoc with federal research misconduct settlement awarded NIH grant

A postdoc at New York University’s Grossman School of Medicine who the U.S. Office of Research Integrity found engaged in research misconduct while a postdoc at another institution has been awarded an NIH grant just months after being sanctioned.  The postdoc, Shuo Chen, didn’t admit or deny the ORI’s findings, but agreed to one year … Continue reading NYU postdoc with federal research misconduct settlement awarded NIH grant

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AGBT 2022: Overhanging Questions

AGBT broke up a couple of weeks ago and I've failed to write anything here so far.  It was frustrating not attending, but not registering for a meeting in February seemed prudent given the pattern of COVID waves - I hadn't considered (nor would have wanted to bank on) AGBT organizers reacting so well and rescheduling the meeting.  It sounds like a number of attendees did catch the virus at the meeting -- though I'm presumably still quite protected by my infection a month earlier.  Anyways, I'm going to organize this around one to two questions that hover in my head for the different sequencing providers.  AGBT also had a strong spatial angle, but I feel ill-equipped to cover that in the absence of being on the scene -- I don't work with spatial data and so don't have a deep feel for it.  As always, please flag me here or on Twitter or by email for any errors I made -- or any juicy sequencing company gossip you wish to share!Read more »

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The Function Wars Part X: “Spam DNA”?

The authors of a recent paper think we need a new term "spam DNA" to describe some features of the human genome.

Fagundes, N.J., Bisso-Machado, R., Figueiredo, P.I., Varal, M. and Zani, A.L. (2022) What We Talk About When We Talk About “Junk DNA”. Genome Biology and Evolution 14:evac055. [doi: 10.1093/gbe/evac055]

“Junk DNA” is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as “Junk DNA”. These findings have been interpreted as fundamentally undermining the “Junk DNA” concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the “Junk DNA” concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that “Junk DNA” should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, “Spam DNA”, that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both “Spam DNA” and “Junk DNA”, and “Spam DNA” can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.

The authors are scientists at the Federal Univesity of Rio Grande do Sul in Brazil. They are concerened about the origins of junk DNA and whether true selected effect functions (strong selected effect = SSE) conflict with the definition of junk DNA. Here's how they put it,

Paradoxically as it may seem, under the SSE definition, elements that contribute positively to fitness and are maintained by purifying selection would still count as “junk” only because they did not originate as an adaptation.

This is essentially correct according to how many philosophers define selected effect functions but that issue was resolved by focusing on purifying selection as the important criterion and ignoring the history of the trait (= maintenance function, MF). There is only a 'paradox' if you stick to the philosophy definition of function (i.e. SSE) and even then, the paradox only exists if the SSE definition is the only way to identify junk DNA. [see: The Function Wars Part IX: Stefan Linquist on Causal Role vs Selected Effect] The authors recognize this since they include a good discussion of this other definition (MF) and its advantages. Nevertheless, they propose a new term called "spam DNA" to help clarify the problem.

"Spam DNA" represents every genomic element which has not been selected for during its origin in the genome, even if it currently participates in relevant biological functions.

All of the DNA in the light blue box is spam DNA. Note that it includes DNA that is currently functional as long as it originated from junk DNA as they define it. Also, some junk DNA isn't spam DNA as long as it arose from the inactivation of DNA that used to have a function. Thus, pseudogenes aren't junk and neither are bits and pieces of transposons.

This isn't helpful. The current debate is about how much of our genome is junk so who cares about the history of individual sequences? A significant amount of what we currently define as junk DNA may have come from once-active transposons but we may never be able to trace the history of each piece of junk DNA. Does it fall into the first category in the figure (functional to junk) or is it spam DNA? Is this really important? No,it is not.

Function Wars
(My personal view of the meaning of function is described at the end of Part V.)

Fungal species identification using DNA: a NCBI and USDA-APHIS collaboration with a focus on Colletotrichum

As reported in the journal Plant Disease,  a recent collaboration between National Library of Medicine’s NCBI and the U.S. Department of Agriculture’s Animal and Plant Health Inspection Service (APHIS) analyzed public sequence records for the fungal genus Colletotrichum, an important group of fungal plant pathogens that are a significant threat  to food production. Colletotrichum species … Continue reading Fungal species identification using DNA: a NCBI and USDA-APHIS collaboration with a focus on Colletotrichum

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✚ Visually Inefficient

Welcome to issue #194 of The Process, the newsletter for FlowingData members that looks closer at how the charts get made. I’m Nathan Yau, and this week I’m trading optimized visual efficiency for joy and interest.

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ASM Microbe 2022 was a success!

NCBI had the pleasure of attending and participating in this year’s American Society of Microbiology (ASM) Microbe conference, June 9-13 in Washington, D.C. NCBI staff participated in activities and events throughout the three-day conference. Over 4,500 attendees gathered in the exhibit hall and joined a variety of poster presentations and talks! Reflections from a few … Continue reading ASM Microbe 2022 was a success!

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