I’m starting with a bit on “metascience” this afternoon, because in a sense it’s what we’re doing. By being here, by spotlighting some articles over others, by reading these articles, I, you … we are affecting the reach and impact of the research contained in these articles.
Right here, right now, I’m acting as a filter, as an amplifier and as an interpreter. That means an article about the expression of adenosine receptors isn’t here because I found it both challenging to read and difficult to express in relatable terms, even though that article is directly connected to basic research on breast cancer. It means that an article on an ancient group of creatures known as the Ediacaran and a biochemical analysis of one of their fossils is here, because I’ve long had an interest in the area and find the latest news exciting.
While I’m trying to select a broad range of articles each week, I invariably grab those related to issues that I think will have broad interest, or generate the most excitement. In doing so, I’m mimicking the process that turns “journal science” into “popular science.” That adenosine receptors article? It’s also not in the New York Times this week. Or Discover Magazine. That puzzling ancient fossil, esoteric as it may seem, can be found across a broad spectrum of media.
And of course I’m not just bringing forward articles, I’m putting my own — often clumsy — spin on them. Even when not intentionally bringing forward something that supports a position I already hold, I’m interpreting these articles through the lens of my own bias and (very) limited knowledge. That’s a very big deal. The consequences of selecting the wrong article to support and giving it the wrong spin can result in wholesale changes in people’s diets that are counter to good health. It can result in thousands of kids dying because their parents became convinced that vaccines can’t be trusted.
So I’m trying to be careful, to be catholic in my selections, and to be more careful in my interpretations. I encourage you to do the same. Go back to the original sources. Bring in articles that I missed. Lend your own expertise to the conversation.
And most of all, call me out when you think I’m wrong, dead wrong, or simply bullshitting. Because, seriously, I appreciate it.
Science: The growing number of researchers researching research
Given the billions of dollars the world invests in science each year, it's surprising how few researchers study science itself. But their number is growing rapidly, driven in part by the realization that science isn't always the rigorous, objective search for knowledge it is supposed to be. Editors of medical journals, embarrassed by the quality of the papers they were publishing, began to turn the lens of science on their own profession decades ago, creating a new field now called “journalology.” More recently, psychologists have taken the lead, plagued by existential doubts after many results proved irreproducible. Other fields are following suit, and metaresearch, or research on research, is now blossoming as a scientific field of its own.
Climate Change
Science: Deadly storms break records, damage research facilities
Weather and marine scientists were awestruck last week as they watched two deadly, record-breaking storms evolve on opposite sides of the globe: Hurricane Florence in North America, and Typhoon Mangkhut in Asia. Now, they are scrambling to analyze a torrent of information on the origins and impacts of the storms, collected by satellites, gauges, robotic submarines and other instruments. They are also assessing damage to research infrastructure. Roofs were peeled off laboratory buildings and dormitories at Duke University in Durham, North Carolina, and the University of North Carolina in Wilmington. Weather buoys and storm gages from U.S. government research institutions were dragged by high-speed winds and overtopped with floodwaters. Institutions in China, Taiwan, and the Philippines were similarly battered by typhoon-strength winds and waves.
There are going to be cases for both Florence and Mangkhut, just as with Maria last year, where the “record” isn’t really the record at all. It’s the point where the measuring device failed.
Science: Amazon flooding reaches new levels
The Amazon basin is the largest watershed on Earth. Although the variability of the Amazon hydrological cycle has been increasing since the late 1990s, its underlying causes have remained elusive. We use water levels in the Amazon River to quantify changes in extreme events and then analyze their cause. Despite continuing research emphasis on droughts, the largest change over recent decades is a marked increase in very severe floods. Increased flooding is linked to a strengthening of the Walker circulation, resulting from strong tropical Atlantic warming and tropical Pacific cooling.
A warmer Atlantic, from human-driven climate change, is driving a drought-flood cycle in the Amazon Basin that’s growing worse over time. That’s a threat to both communities in the region and to a critical ecosystem.
Metascience
Science: Progress through death.
Don’t let the “metascience” tag scare you off. You’re going to like this macabre little number.
Max Planck wrote that “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die.” Despite all of their contributions to science, might “superstar” scientists also use their central position to stymie the arrival of new ideas? To shed empirical light on this issue, we turned to a ghoulish natural experiment, assessing impacts of the premature deaths of 452 eminent life scientists (median age at death = 61 years). We implemented a procedure (drawing on automated analysis of keywords in publications) to delineate the boundaries of the intellectual neighborhoods in which eminent scientists worked and conceptualized the premature deaths as shocks to the structure of these neighborhoods. We found that after the deaths, the stars' expansive rosters of collaborators tend to drastically reduce their scientific output, whereas noncollaborators increase their output in the deceased stars' field.
I’m from a generation of geologists who were still grumbling about “that damn German weatherman” — even though the plate tectonics theories put forward by German meteorologist Alfred Wegener in 1912 had long been supported by literal mountains of proof. And they were a long way from ready to buy into the proposals of “that f#$*ing physicist” even though from the beginning it was clear Luis Walter Alvarez was onto the truth about the dinosaur-killing asteroid. People can be hard-pressed to let go of ideas in science, and nowhere more than a science where people get used to talking about processes that take tens of millions of years.
But, as this research shows, attaching yourself to a “star” scientist can be a issue that lingers even after that star dies. It’s interesting stuff, and surely applicable outside of science.
Nature: Galileo put a spin on his research to hide ideas from the Inquisition
See, this metascience stuff is both older and more interesting than you thought it would be.
It had been hiding in plain sight. The original letter — long thought lost — in which Galileo Galilei first set down his arguments against the church’s doctrine that the Sun orbits the Earth has been discovered in a misdated library catalogue in London. Its unearthing and analysis expose critical new details about the saga that led to the astronomer’s condemnation for heresy in 1633.
The seven-page letter, written to a friend on 21 December 1613 and signed “G.G.”, provides the strongest evidence yet that, at the start of his battle with the religious authorities, Galileo actively engaged in damage control and tried to spread a toned-down version of his claims.
In this letter, Galileo argues that “references in the Bible to astronomical events should not be taken literally” because both the people who recorded them, and the audience for their writing, didn’t understand the nature of the Solar System. And he argues that the sun-centered system proposed by Nicolaus Copernicus isn’t incompatible with those Biblical references. The letter was definitely edited to “soften” the language.
Nanotechnology
The Proceedings of the National Academy of Sciences has a special report this week on “molecular machines” — where engineering touches on chemistry and biology. Because they were nice enough to have these articles outside the firewall, I’ve grouped several of them here.
PNAS: What’s the best way to build a molecular machine?
The idea of using molecules to build minuscule machines that perform useful tasks dates back at least to a lecture given in 1959 by physicist Richard Feynman titled “There’s Plenty of Room at the Bottom.” More recently, demonstrations of artificial molecular machines offer good reasons to think that such devices are feasible. Researchers have forged motors, shuttles, elevators, walkers, and pumps out of molecules, and powered them with electrical energy, chemical reactions, or light. Tiny motor by tiny motor, these demonstrations are inching toward future applications that could range from molecular electronics to artificial muscles.
We have big expectations for the possibilities of molecular machines. Fleets of micro-robots could prowl our blood streams for bacteria or enter our cells to mend DNA. They might also turn the entire world into grey goo (or, as Culture fans might prefer, a hegemonizing swarm). But at the moment, we remain not too far past the tech level of the Mayans who built wheeled toys, but never quite put those rolly things to work. We’re not sure of the materials or the methodology that provides the best approach. Which is why there are so many teams taking so many different tacks. It’s a very, very small wild west down there. And some researchers are insisting that it stay wild.
Building machines that operate at the molecular scale brings a raft of different problems and opportunities that will take decades to explore. “The biggest challenge for molecular machines is to avoid the trap of delivering something useful, now,” says chemist Wesley Browne at the University of Groningen in The Netherlands. “It has to stay fundamental.”
Come on in, we’ll look at some of the approaches being taken … and don’t worry, there’s “big” science, too.
PNAS: Looking to biology for nanotech ideas.
There are two, fundamentally different, philosophies for designing molecular machinery. One is to scale down classical mechanical elements from the macroscopic world, an approach advocated in many of the Drexlerian designs for nanomachines and also the inspiration behind “nanocars”, “molecular pistons”, “molecular elevators”, “molecular wheelbarrows”, and other technomimetic molecules designed to imitate macroscopic objects at the molecular level. An advantage of this approach is that the engineering concepts behind such machines and mechanisms are well understood in terms of their macroscopic counterparts; a drawback is that many of the mechanical principles upon which complex macroscopic machines are based are inappropriate for the molecular world.
The effect of things like surface tension, friction and gravity can be so different at a small scale that techniques that work for “everyday” items simply won’t function down in the microscopic world.
An alternative philosophy is to try to unravel the workings of an already established nanotechnology, biology, and apply those concepts to the design of synthetic molecular machines. A potential upside of this, biomimetic, approach is that such designs are clearly well-suited to functional machines that operate at the nanoscale, even when limited, as nature is, to the use of only 20 different building blocks (amino acids), ambient temperatures and pressures, and water as the operating medium. However, a major issue in pursuing this second strategy is that the only “textbook” we have to follow is unclear: Biological machines are so complex that it is often difficult to deconvolute the reasons behind the dynamics of individual machine parts.
Anyone who ever had to diagram the Kreb’s Cycle will understand the bone-crushing complexity that can be involved in what appears to be a very simple task down in the world of the itty-bitty. But the good thing about starting with the biologic approach is that human researchers can draw both from the clever solutions evolution produced over billions of years of working these things out, and a much broader set of materials than can be generated from proteins and amino acids.
PNAS: Pumps, motors, and a biological–mechanical hybrid.
Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment—walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents.
If all that sounds like damn-the-biology, full speed ahead with micro-gears and tiny steam locomotives! It’s not. Because the approach to pumps and motors in this piece is drawn from on of biology’s great complex structures — the cell membrane.
The molecular machines necessary for life must carry out their function in the fluctuating environment of a biological cell. Nowhere is the dynamic aspect of biology at the molecular level more evident than in the bilayer membrane surrounding most cells and organelles.
That membrane exists in broad terms as three separate systems that allow for the movement of ions, transport some large molecules (but only some) across the boundary, and use energy from ATP to keep the system in balance. Embedded in these systems are individual mechanisms that can be hijacked and mimicked to build components of simple, or complex, mechanical systems. Systems that could be powered by the same energy sources that power our cells, leaving open the possibility that these machines could operate inside the body and need no additional power source. But behind these apparently simple systems are some pretty big “gee, and how does that work?” questions.
PNAS: And have some motors to go with those pumps.
Rotary molecular motors hold great promise for achieving dynamic control of molecular functions as well as for powering nanoscale devices. However, for these motors to reach their full potential, many challenges still need to be addressed. In this paper we focus on the design principles of rotary motors featuring a double-bond axle and discuss the major challenges that are ahead of us. Although great progress has been made, further design improvements, for example in terms of efficiency, energy input, and environmental adaptability, will be crucial to fully exploit the opportunities that these rotary motors offer.
Rotary motion is one of those things that’s pretty darn rare in biology, but common in the larger world where electric motors rule. Duplicating them at nanoscale is definitely a mechanical not biological solution, but it also opens up a lot of systems that biology simply doesn’t have.
PNAS: Adding some controls to micro-machines.
If you’re going to build a machine that’s incredibly small, it’s nice to have some controls on the system. Controls that turn it on. Or off. Maybe especially off (after all, another name for an aggressive hegemonizing swarm is cancer). So how about some switches for all those pumps and wheels and motors.
Progress in chemically and photoinduced switches and motors is summarized and contextualized such that the reader may gain an appreciation for the novel tools that have come about in the past decade. Many of these systems offer distinct advantages over commonly employed switches, including improved fidelity, addressability, and robustness. Thus, this paper serves as a jumping-off point for researchers seeking new switching motifs for specific applications, or ones that address the limitations of presently available systems.
This isn’t so much new research as a catalog of all the mechanisms that have been employed to date in making nano-scale switches. There’s a considerable set of different technologies employed here, some of which are obviously more suitable for inside-the-body systems vs. go-grow-me-a-computer dreams. And the authors admit that this is just a small subset of what’s becoming a very full toolbox. We may not yet be building complex nanomachines, but we’re certainly assembling a big collection of potential parts.
And now I’m going to move on, though there are still a stack of actual fresh research articles in this section with titles like “Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem” (consider translating just the title your assignment for the afternoon).
Paleontology
Nature: More Denisovan bones found
A tiny bone fragment recovered from Denisova Cave in Siberia caused a big stir last month, after scientists showed that it belonged to an ancient-human hybrid they named Denny, who had a Neanderthal mother and Denisovan father.
Now, the researchers who uncovered Denny’s remains have discovered four more hominin bones from the same cave.
These discoveries are part of an effort to identify early hominins by combing through thousands of unidentified pieces of animal bone, many of which have been left to gather dust in warehouses belonging to museums and research institutes.
We’re getting past the point where you can store everything we know of Denisovans in a shoe box. Now it’s going to take two.
Nature: Precambrian fossil turns out to be early animal
Researchers first discovered the pancake-shaped creatures — a group known as Dickinsonia — in the late 1940s. The species were among the most common residents of the world’s oceans 558 million years ago, during the Ediacaran period. Whereas most living things during that time ranged in size from microscopic to a few millimetres long, some Dickinsonia grew up to 1.4 metres in length.
There’s an entire set of Ediacaran fauna, known initially from a site in Australia where some of the first fossils were found in numbers. The best way to describe all of them is that they look like what you might get if your beach float fossilized. The look for all the world as if they were composed of little individual, soft chambers that might have been inflated in life. There were quite a variety — a world full of blow-up animals. Some of them, but not many, survived the beginning of the Cambrian around 500 MYA and the onslaught of scaly, hard-shelled things with claws.
A team led by Jochen Brocks, a palaeobiogeochemist at the Australian National University in Canberra, examined ring-like fat molecules called sterols that infiltrate the membrane surrounding a cell to keep it flexible and fluid. Plants, animals, fungi and bacteria all contain sterols, but the type of sterol that predominates in each group differs. Animals mainly make cholesterol, and the fungi that form colourful, crusty lichens found on boulders have only ergosterol. Under the right conditions, these chemicals can persist for millions of years, and so help to determine a fossilized organism’s evolutionary relationships.
Call me one of those old stuck-in-the-mud scientists, but I like it when the latest research confirms the theory I’ve been putting forward for decades.
PNAS: Evolution of animal body plans
The animal kingdom exhibits a great diversity of organismal form (i.e., disparity). Whether the extremes of disparity were achieved early in animal evolutionary history or clades continually explore the limits of possible morphospace is subject to continuing debate. Here we show, through analysis of the disparity of the animal kingdom, that, even though many clades exhibit maximal initial disparity, arthropods, chordates, annelids, echinoderms, and mollusks have continued to explore and expand the limits of morphospace throughout the Phanerozoic, expanding dramatically the envelope of disparity occupied in the Cambrian.
Decades ago, Stephen Jay Gould celebrated the whacky diversity of Cambrian organisms in several of his essays and books. Though Gould (along with most others) got his interpretations of some organisms wrong, the basic theme still holds — right from the beginning, animals pressed out into some extreme and radical body designs as evolution tested the limits of what would work. This new research shows that life has continued to push the boundaries, though never at the breakneck pace of that first bloom.
Archeology
PNAS: Monumental architecture may have started in Kenya
Archaeologists have long sought monumental architecture’s origins among societies that were becoming populous, sedentary, and territorial. In sub-Saharan Africa, however, dispersed pastoralists pioneered monumental construction. Eastern Africa’s earliest monumental site was built by the region’s first herders ∼5,000–4,300 y ago as the African Humid Period ended and Lake Turkana’s shoreline receded. Lothagam North Pillar Site was a massive communal cemetery with megalithic pillars, stone circles, cairns, and a mounded platform accommodating an estimated several hundred burials. Its mortuary cavity held individuals of mixed ages/sexes, with diverse adornments. Burial placement and ornamentation do not suggest social hierarchy. Amidst profound landscape changes and the socioeconomic uncertainties of a moving pastoral frontier, monumentality was an important unifying force for eastern Africa’s first herders.
As famous archeologist Indiana Jones once said “They’ve been looking in the wrong place.” Rather than starting with Middle Eastern cultures that were piling up those pyramids and ziggurats, it looks like massive architecture may have started, problematically enough, with people who were not settled in cities and tows. But then, Gobekli Tepe — 11,000 years old up in Turkey — shows that people who are not fixed in a location can be involved in some pretty spectacular constructions. And heck, Çatal Höyük shows you can also have cities without agriculture. Actual archeology always seems to destroy our neat assumptions.
Astronomy
PNAS: Direct evidence of water ice on the moon
We found direct and definitive evidence for surface-exposed water ice in the lunar polar regions. The abundance and distribution of ice on the Moon are distinct from those on other airless bodies in the inner solar system such as Mercury and Ceres, which may be associated with the unique formation and evolution process of our Moon. These ice deposits might be utilized as an in situ resource in future exploration of the Moon.
I know. It seems like this one gets announced about twice a year. But consider this a really, really, yes, absolutely following years of “it looks like” research.
Environment
PNAS: Air pollution makes you stupid
This paper examines the effect of both cumulative and transitory exposures to air pollution for the same individuals over time on cognitive performance by matching a nationally representative longitudinal survey and air quality data in China according to the exact time and geographic locations of the cognitive tests. We find that long-term exposure to air pollution impedes cognitive performance in verbal and math tests. We provide evidence that the effect of air pollution on verbal tests becomes more pronounced as people age, especially for men and the less educated. The damage on the aging brain by air pollution likely imposes substantial health and economic costs, considering that cognitive functioning is critical for the elderly for both running daily errands and making high-stake decisions.
And the older you are, the worse it hits you.
Image
Today’s image comes from Mike brunning at Compound Interest. Visit his site for a larger, easier to read version.