👓 What really happened when two mathematicians tried to publish a paper on gender differences? The tale of the emails | Retraction Watch

Read What really happened when two mathematicians tried to publish a paper on gender differences? The tale of the emails (Retraction Watch)
Retraction Watch readers may be familiar with the story of a paper about gender differences by two mathematicians. Last month, in Weekend Reads, we highlighted an account of that story, which appea…

This article and the related links cover a lot of the questions I had when I read the original in Quillette the other day and only wish I’d had the time to follow up on as a result. Now to go on and read all the associated links and emails….

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👓 Using Medieval DNA to track the barbarian spread into Italy | Ars Technica

Read Using Medieval DNA to track the barbarian spread into Italy (Ars Technica)
Cemeteries from the Longobard spread into Italy tell tales of migration and mixing.
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👓 Adaptable lizards illustrate key evolutionary process proposed a century ago | Science Daily

Read Adaptable lizards illustrate key evolutionary process proposed a century ago (ScienceDaily)
The 'Baldwin effect' has now been demonstrated at the genetic level in a population of dark-colored lizards adapted to live on a lava flow in the desert.

Highlights, Quotes, Annotations, & Marginalia

One explanation has been that many of an animal’s traits are not fixed, but can change during its lifetime. This “phenotypic plasticity” enables individual animals to alter their appearance or behavior enough to survive in a new environment. Eventually, new adaptations promoting survival arise in the population through genetic changes and natural selection, which acts on the population over generations. This is known as the “Baldwin effect” after the psychologist James Mark Baldwin, who presented the idea in a landmark paper published in 1896.  

September 11, 2018 at 08:57AM

Journal article available at: https://www.cell.com/current-biology/pdfExtended/S0960-9822(18)30899-6

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👓 Academic Activists Send a Published Paper Down the Memory Hole | Quillette

Read Academic Activists Send a Published Paper Down the Memory Hole by Theodore P. Hill (Quillette)
In the highly controversial area of human intelligence, the ‘Greater Male Variability Hypothesis’ (GMVH) asserts that there are more idiots and more geniuses among men than among women. Darwin’s research on evolution in the nineteenth century found that, although there are many exceptions for ...

I understand the potential political implications of such research, but blocking publication like this seems a tad underhanded. I’ve not yet read the paper, but want to take a look at it at least from an evolutionary theoretic standpoint. Admittedly on its face it sounds a bit more like pure theory rather than anything supported by actual evidence and underlying research in reality, but there’s no reason to stop the idea if it could potentially be a fruitful area.

If a formally refereed and published paper can later be erased from the scientific record and replaced by a completely different article, without any discussion with the author or any announcement in the journal, what will this mean for the future of electronic journals?

This is a very concerning issue and a good reason why people should also practice samizdat and place multiple copies online in various repositories.

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👓 Caught mid-flow: the “Baldwin effect” | The Economist

Read Caught mid-flow: the “Baldwin effect” (Economist Espresso)
While most side-blotched lizards living in the Mojave desert match the colour of its sand, those
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👓 Mutating DNA caught on film | Science | AAAS

Read Mutating DNA caught on film by Elizabeth Pennisi (Science | AAAS)
Study in bacteria shows how regularly DNA changes and how few of those changes are deadly

This is a rather cool little experiment.

h/t to @moorejh via Twitter:

Bookmarked on March 16, 2018 at 12:15PM

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👓 Living Bits: Information and the Origin of Life | PBS

Highlights, Quotes, & Marginalia

our existence can succinctly be described as “information that can replicate itself,” the immediate follow-up question is, “Where did this information come from?”

from an information perspective, only the first step in life is difficult. The rest is just a matter of time.

Through decades of work by legions of scientists, we now know that the process of Darwinian evolution tends to lead to an increase in the information coded in genes. That this must happen on average is not difficult to see. Imagine I start out with a genome encoding n bits of information. In an evolutionary process, mutations occur on the many representatives of this information in a population. The mutations can change the amount of information, or they can leave the information unchanged. If the information changes, it can increase or decrease. But very different fates befall those two different changes. The mutation that caused a decrease in information will generally lead to lower fitness, as the information stored in our genes is used to build the organism and survive. If you know less than your competitors about how to do this, you are unlikely to thrive as well as they do. If, on the other hand, you mutate towards more information—meaning better prediction—you are likely to use that information to have an edge in survival.

There are some plants with huge amounts of DNA compared to their “peers”–perhaps these would be interesting test cases for potential experimentation of this?

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The Physics of Life: Summer School | Center for the Physics of Biological Function

Bookmarked The Physics of Life: Summer School | Center for the Physics of Biological Function (biophysics.princeton.edu)
A summer school for advanced undergraduates June 11-22, 2018 @ Princeton University What would it mean to have a physicist’s understanding of life? How do DYNAMICS and the EMERGENCE of ORDER affect biological function? How do organisms process INFORMATION, LEARN, ADAPT, and EVOLVE? See how physics problems emerge from thinking about developing embryos, communicating bacteria, dynamic neural networks, animal behaviors, evolution, and more. Learn how ideas and methods from statistical physics, simulation and data analysis, optics and microscopy connect to diverse biological phenomena. Explore these questions, tools, and concepts in an intense two weeks of lectures, seminars, hands-on exercises, and projects.
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📖 Read pages 19-52 of The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

📖 Read Chapter 1: What is Life? pages 19-52 in The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane (W.W. Norton,
, ISBN: 978-0393088816)

Lane lays out a “brief” history of the 4 billion years of life on Earth. Discusses isotopic fractionation and other evidence that essentially shows a bottleneck between bacteria and archaea (procaryotes) on the one hand and eucaryotes on the other, the latter of which all must have had a single common ancestor based on the genetic profiles we currently see. He suggest that while we should see even more diversity of complex life, we do not, and he hints at the end of the chapter that the reason is energy.

In general, it’s much easier to follow than I anticipated it might be. His writing style is lucid and fluid and he has some lovely prose not often seen in books of this sort. It’s quite a pleasure to read. Additionally he’s doing a very solid job of building an argument in small steps.

I’m watching closely how he’s repeatedly using the word information in his descriptions, and it seems to be a much more universal and colloquial version than the more technical version, but something interesting may come out of it from my philosophical leanings. I can’t wait to get further into the book to see how things develop.

book cover of Nick Lane's The Vital Question
The Vital Question: Energy, Evolution and the Origins of Complex Life by Nick Lane
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Energy and Matter at the Origins of Life by Nick Lane | Santa Fe Institute

Bookmarked Energy and Matter at the Origin of Life by Nick Lane (Santa Fe Institute Community Event (YouTube))
All living things are made of cells, and all cells are powered by electrochemical charges across thin lipid membranes — the ‘proton motive force.’ We know how these electrical charges are generated by protein machines at virtually atomic resolution, but we know very little about how membrane bioenergetics first arose. By tracking back cellular evolution to the last universal common ancestor and beyond, scientist Nick Lane argues that geologically sustained electrochemical charges across semiconducting barriers were central to both energy flow and the formation of new organic matter — growth — at the very origin of life. Dr. Lane is a professor of evolutionary biochemistry in the Department of Genetics, Evolution and Environment at University College London. His research focuses on how energy flow constrains evolution from the origin of life to the traits of complex multicellular organisms. He is a co-director of the new Centre for Life’s Origins and Evolution (CLOE) at UCL, and author of four celebrated books on life’s origins and evolution. His work has been recognized by the Biochemical Society Award in 2015 and the Royal Society Michael Faraday Prize in 2016.

h/t Santa Fe Institute

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👓 The First Species to Have Every Individual’s Genome Sequenced | The Atlantic

Read The First Species to Have Every Individual’s Genome Sequenced by Ed Yong (The Atlantic)
It’s an endearing, giant, flightless, New Zealand parrot, and it’s a poster child for the quantified-self movement.


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Valerie Alexander on How Women Can Succeed in the Workplace (Despite Having “Female Brains”)

This morning, at the Friday morning coffee meetup of Innovate Pasadena held at Cross Campus, I saw one of the singularly best and most valuable talks I’ve heard in a long time. Many of these types of speakers, while engaging or even entertaining, are telling the same tired stories and at best you learn one sentence’s worth of value. Definitively not the case this morning!!!

How Women Can Succeed in the Workplace (Despite Having “Female Brains”) by Valerie Alexander

Entitled How Women Can Succeed in the Workplace (Despite Having “Female Brains”) writer and speaker Valerie Alexander presented a brief discussion of human evolutionary history (a topic I’ve studied closely for several decades) that featured the difference in development of male and female human brains. Based on this and with a clearer picture of what broadly differentiates the sexes, Valerie then gave a multitude of highly relate-able examples from her professional life highlighting how women can simply take back control in the workplace to not only better succeed for themselves, but to also help their companies see their true value and succeed simultaneously.

Further, she also included some simple and very actionable advice (for men and women) to be able to make a better space within corporations so that they’re able to extract more of the value women bring to the workplace. Hint: Women bring a HUGE amount of value, and a majority of companies are not only undervaluing it, but they are literally throwing it away.

Not only were the messages tremendously valuable and imminently actionable by both women AND men, but she delivered it with fantastic confidence, grace, wit, charm, and warmth. In fact, I’d say it was not only strikingly informative, but it was also very entertaining. If you’re in the corporate space and looking to turn around your antediluvian or even pre-historic work culture (I’m looking ominously at you Uber and similar Silicon Valley brogrammer cultures), then jump in line as quickly as you can to book up what I can only expect is the diminishing time in her speaking and travel schedule.

Innovate Pasadena recorded the talk and I’ll try to post it here as soon as it’s available. Until then I will highly recommend purchasing her book How Women Can Succeed in the Workplace (Despite Having “Female Brains”), which I’m sure has not only the content of her lecture, but assuredly includes a whole lot more detail and additional examples than one could fit into such a short time frame. I also suspect it’s the type of book one would want to refer back to frequently as well. I’ve already got a half a dozen copies of it on their way to me to share with friends and family. I’m willing to make a substantial bet that for uncovering inherent value, this book and her overall message will eventually stand in the pantheon of texts and work of those like those of Frederick Winslow Taylor, Lillian Gilbreth, Frank Gilbreth, Dale Carnegie, Napoleon Hill, J.M. Juran, and W. Edwards Deming.

Psst… If the good folks at TED need some fantastic content, I saw a shortened 25 minute version of her hour-long talk. It could be tightened a hair for content and length, but it’s got exactly the tone, tempo and has the high level of presentation skills for which you’re known. Most importantly, it’s definitively an “Idea worth spreading.”

Innovate Pasadena has finally uploaded a copy of the video of Valerie Alexander’s talk:

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📺 A Universal Theory of Life: Math, Art & Information by Sara Walker

Watched A Universal Theory of Life: Math, Art & Information from TEDxASU
Dr. Walker introduces the concept of information, then proposes that information may be a necessity for biological complexity in this thought-provoking talk on the origins of life. Sara is a theoretical physicist and astrobiologist, researching the origins and nature of life. She is particularly interested in addressing the question of whether or not “other laws of physics” might govern life, as first posed by Erwin Schrodinger in his famous book What is life?. She is currently an Assistant Professor in the School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science at Arizona State University. She is also Fellow of the ASU -Santa Fe Institute Center for Biosocial Complex Systems, Founder of the astrobiology-themed social website SAGANet.org, and is a member of the Board of Directors of Blue Marble Space. She is active in public engagement in science, with recent appearances on “Through the Wormhole” and NPR’s Science Friday.

Admittedly, she only had a few short minutes, but it would have been nice if she’d started out with a precise definition of information. I suspect the majority of her audience didn’t know the definition with which she’s working and it would have helped focus the talk.

Her description of Speigelman’s Monster was relatively interesting and not very often seen in much of the literature that covers these areas.

I wouldn’t rate this very highly as a TED Talk as it wasn’t as condensed and simplistic as most, nor was it as hyper-focused, but then again condensing this area into 11 minutes is far from simple task. I do love that she’s excited enough about the topic that she almost sounds a little out of breath towards the end.

There’s an excellent Eddington quote I’ve mentioned before that would have been apropos to have opened up her presentation that might have brought things into higher relief given her talk title:

Suppose that we were asked to arrange the following in two categories–

distance, mass, electric force, entropy, beauty, melody.

I think there are the strongest grounds for placing entropy alongside beauty and melody and not with the first three.

Sir Arthur Stanley Eddington, OM, FRS (1882-1944), a British astronomer, physicist, and mathematician
in The Nature of the Physical World, 1927


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🔖 Origins of Life: A Problem for Physics

Bookmarked Origins of Life: A Problem for Physics by Sara I. Walker (arXiv)
The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the origin of life for those new to the origin of life field, with a forward look towards considering what it might take for a physical theory that universally explains the phenomenon of life to arise from the seemingly disconnected array of ideas proposed thus far. The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.
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👓 Can Darwinian Evolution Explain Lamarckism? | Quanta Magazine

Read Can Darwinian Evolution Explain Lamarckism? by Pradeep Mutalik (Quanta Magazine)
Answering three questions can help reveal how the “inheritance of acquired characteristic” fits into modern evolutionary theory.
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