Science Funders From 11 European Nations Adopt Radical Open Access Plan

11 European science funding agencies, from as many nations, which collectively contribute nearly $9bn U.S. worth of research grants annually, have joined together on an ambitious Open Access Plan: 'Plan S'.

Plan S calls for immediate, free-to-read access to research published under grant funding from any of the organizations involved, along with liberal (typically free-of-cost) licenses to download, reuse, and translate research findings. Most radically, it bans researchers from publication in about 85% of major research journals, which typically lock this research up behind paywalls.

It is no exaggeration to say that this plan spells doom for the major Subscription Journal Publishers as we know them, and they're not happy. The decision is facing push back, of course, but the journals are rather powerless against the people who actually write the cheques. Much of this research is at least partly publicly funded, anyways, which makes the presence of paywalls all the more galling.

I, for one, say good riddance to Science paywalls! May they die swiftly and ingloriously! Science depends on the free and open exchange, review, and reuse of findings, as well as anything relevant to the findings, such as the procedures used to obtain them, the personnel and organizations involved, etc...

Research behind paywalls is research that cannot benefit the collective whole of humanity's great Enlightenment Project known as Scientific Inquiry.

#BlindMeWithScience #PlanS #OpenAccess

Old Age Is No Modern Invention

You may have heard a variation on the following claim: Ancient people lived hard and died young. They were often 'old' by the standards of their day and age, where we would still be young or in our middle ages. They left behind a lot of beautiful corpses, and few with gray hairs on their heads, or at least with few gray hairs earned by the passing of years. Thanks to modern technology, though, we now live to ripe old ages our ancestors could scarcely imagine, apart from a very small, fortunate minority.

It sounds so plausible and convincing, that there is only one small problem: it's not true. Not really. What is true, is that average lifespans tended to be shorter, but their numbers were dragged down in this regard by high early mortality rates, i.e. miscarriages, stillbirths, and childhood mortality. There are substantial lifespan differences in the world today, which are also heavily determined by early mortality, moreso than the longevity of those who survive childhood. The difference between modern and ancient, as it turns out, is not so different from the difference between Third World and First World is today.

In fact, and depending a lot on the particular peoples we are referring to, it was not at all uncommon for many people, if they reached adulthood at all, to live to ripe old ages even by our modern Western standards. Despite all the threats of disease, malnutrition, and injury, and other risks to survival, people still managed it, and not rarely either. Old people were not some quasi mythical sort of creature in antiquity, but were common enough that the form and symptoms of senescence were as well known then as they are today. Even "dying of old age", as we call it, was not an uncommon event.

So by all means, celebrate the many things modern society has achieved to preserve, prolong, and enhance life! But make no mistake: surviving childhood is most of the battle in the war for a long life, and always has been.

#BlindMeWithScience #Archaeology #History

Twitter Bots and Russian 'Trolls' Spreading FUD About Vaccines

A new study published in the American Journal of Public Health compared Twitter Bot accounts, Russian 'Troll' accounts, 'Content Polluters' (spammers, malware dissemenators, etc...) and average Twitter user accounts on vaccine-related content.  Their findings reveal that whereas Bots and Content Polluters tended to spread antivaxxer messages, Russian Troll accounts, as the term 'Troll' classically implies, were more interested in sewing divisiveness by posting highly polarized and politicized anti- and pro-vaxxer messages.  And each group posted far more vaccine-related content than average user accounts, perhaps unsurprisingly.

The researchers concluded that these accounts, posing as real users, can create uncertainty, false equivalence, and otherwise contaminate the public discourse, leading to an excess of skepticism in what is, undeniably, a technology which has saved more lives than nearly any other modern medical technologies, even wiping out diseases our species once frequently suffered.  This helps fuel the rise of the antivaxxer movement, which is almost single-handedly bringing back measles and other readily preventable diseases.

While there are other ways in which Twitter, and social media in general, can help connect and strengthen the resolve to antivaxxers, there can be little doubt that the proliferation of accounts which are either not really operated by humans, or are operated by humans deliberately spreading misinformation and sewing socio-political division, are playing a substantial role in this.  Given that more than a few of these accounts are unofficially-officially backed by a major government, whose operatives cannot be said to have the best interests of their international target audiences at heart, this should be especially concerning, i.e. that a foreign nation may, for their own (likely nefarious) purposes, be undermining public health issues and putting large chunks of the global population at risk of preventable health crises.

You can also read the study itself here:
https://ajph.aphapublications.org/doi/10.2105/AJPH.2018.304567

#BlindMeWithScience #Vaccination #SocialMedia

How A Software Bug Fueled a 7-Year Scientific Debate About Water

In 2011, a team of researchers at Berkeley, led by the renowned chemist David Chandler, announced the results of model simulations their team had performed on supercooled pristine water: at every temperature measured, they claimed, the liquid water remained fairly homogeneous in structure. In short, their models suggested that, if kept pure of dust and other contaminants, liquid water remained the same until reaching a rapid freezing point.

Given his widespread acclaim, Chandler's teams findings were widely accepted, much to the chagrin of a team of researchers at Princeton, led by Pablo Debenedetti. The Princeton Team, seemingly using the exact same modeling, had come to a quite different conclusion: at supercool temperatures, before freezing into ice crystals (which, in pristine water, do not form until temperatures are extremely supercool due to a lack of impurities for ice crystals to form on, but form quickly when they finally do form), the water appeared to take on two different liquid states, high-density and low-density. As this resembled the transitional stage at higher temperatures where liquid water and water vapor become indistinguishable, they took this to indicate a low temperature critical period between solid and liquid water.

Seeing the issue of getting different results from apparently the same data and modeling, the two teams began to collaborate, trying to find the source of the disagreement. This fell apart, though, when the Princeton team continued to publish results, before a consensus on the source of the disagreement could be reached. The relationship between the two then turned contentious, and at times openly hostile, with each side accusing the other of an error, but neither side agreeing on what that error might be.

Eventually, Debenedetti had an insight: although the two teams had used the same mathematical models to simulate supercooled water behaviors, Chandler's team had used an algorithm to speed up their processing, allowing them to run simulations over longer periods. While Chandler believed this gave their results an edge, subsequent speed up efforts by Debenedetti had matched them for duration, but not matched their results. It had, thus, occurred to Debenedetti that there may be a bug in the Berkeley code.

Had Chandler and his team quickly turned over their code for inspection, the matter could have been resolved quickly, but instead it would be another couple of years before they published it. When they did, Debenedetti and his team were vindicated: the Berkeley algorithm used an unconventional and, as it turned out, improper technique to initialize their molecular dynamics simulations, which among other things inflated the simulated temperatures by tens of degrees.

As a result, Chandler's team had failed to see the transitional state of high- and low-density liquids, as one would fail to see water turn to ice at the freezing temperature if your thermometer was in fact wrong and the real temperature was above that. In failing to publish their code right away, Chandler's team had, in fact, violated the scientific principles of transparency and reproducibility, since no one could truly have replicated their findings. In the process, they had wasted a lot of time and energy, for themselves and other researchers.

While opinion has now shifted in favor of Debenedetti's simulations, it is worth noting that despite 7-years of debate over this, neither side in the end has yet proven anything. Their simulations were just that, simulations, using models of liquid molecular dynamics known to be imperfect (as all such models are). Only real tests, on real pristine water, at the right temperatures will resolve this.

While there can be no doubt that algorithms will play an increasingly invaluable role in scientific research, they are no less in need of transparency than any other material or method used in conducting research. One cannot argue effectively against results from a Black Box (i.e. a mechanism whose inner means of operation are opaque), after all.

#BlindMeWithScience #Chemistry #Algorithms

Offspring Inherit More Than Genes From Sperm

It was long believed, in the reproductive sciences, that the contribution of sperm to fertility, reproduction, and the future health of the child was limited to direct genetic contribution. Whereas the mother, bearing the child in the womb, could also contribute environmental influences on development. Thus, the male's role apart from genetic health (over which he has little, if any, control, or even knowledge barring modern genetic tests) could be over in a matter of moments, and it then became the responsibility of the mother to ensure healthy development prior to birth.

In recent years, this paradigm has shattered, as evidence has accumulated suggesting that males, too, pass down environmental influences to offspring, in the form of Epigenetics: changes to the output of genes, in response to environmental input. Yet, despite this, countless offspring are produced each year through in vitro fertilization, involving extraction of sperm prior to ejaculation and in some cases prior to maturity, which begs the question as to whether these procedures may influence Epigenetic contributions from fathers.

Now, Researchers can finally offer insight into how these Epigenetic influences are passed down, and their role in not only the Epigenetics of the offspring, but in fertility itself.  The key may lie in what are known as small RNA's, which can conceal information from our genetic machinery, even 'ghosting' the outputs of certain genes entirely.  After entering the early part of a 6-meter long part of the male reproductive tract called the epididymis, sperm discard many of their small RNA's, then apparently reacquire these later in the process from the epididymis cells themselves, thereby inheriting Epigenetic influences from the father.

Apart from affecting the subsequent development of the offspring, the Researchers found that these small RNA's play a critical role in implantation, and by extension fertility itself, such that mouse embryos from early and mature sperm implanted successfully in a surrogate, whereas those from the middle stage did not.

It is still somewhat unclear what this may mean for in vitro offspring using techniques that extract immature sperm prior to the shedding of small RNA's. Despite thousands of babies being conceived this way, the offspring are at most 3-4 decades old by now, and not all such techniques utilize immature sperm.  Consequently, this may be very meaningful in considering the use of such technologies, or meaningless, or it may vary by the particular technique employed in any given conception.

It is as yet unclear why the sperm go through this shedding and reacquiring process, but a likely answer is that the reacquired small RNA's encode relevant instructions preparing the offspring for post-natal life. If, for example, dad's diet was bereft of some vital nutrients, this may signal the offspring's body to reduce or suspend processes depending on these nutrients, such that babies influenced by this process survive better than those born with a 'clean slate'.  Epigenetics, then, would function like the kind of Cheat Sheet to prepare the child for the external world they'll likely encounter.

This finding should also have profound ramifications for how society understands the roles of each parent in producing offspring. Whereas women have traditionally shouldered the responsibility for environmental influences on developing offspring prior to their birth (if not afterwards, as well), and have shouldered the blame for anything but genetic contributions by the father (if even), these findings suggest that the lifestyle choices of fathers play a substantial, if somewhat less decisive, role as well, which cannot be overlooked.

#BlindMeWithScience #Genetics #Biology

Researchers Find Way To Turn Type-A Blood Into Type-O Blood

Type O- Blood is the so-called Universal Donor blood type, because it can be given in emergency transfusion situations to people of any blood type, without rejection. Consequently, medical demand for this blood type outstrips its proportion in the general populace.

So, any way to increase this supply can only be a good thing, saving potentially countless lives. It is fortunate, then, that Researchers from the University of British Columbia may have found a way to convert at least one other blood type into the Universal Donor type.

Specifically, the researchers identified a type of gut microbe (i.e. which naturally lives in the human gut) which secretes an enzyme that, when introduced to Type-A blood samples, strips away the specific Type-A markers, leaving behind a substance seemingly indistinguishable to the body from Type O-. This process is also remarkably efficient, because it works on whole blood, rather than requiring any sophisticated chemical processing techniques.

Of course, there will need to be proper human clinical testing before this can become an approved solution, but the Researchers seem fairly confident that human bodies will accept this 'artificial' O- Blood just as it would any conventional sample of Universal Donor blood. If their confidence proves justified, it may well solve in a single stroke the issue of Universal Donor blood shortages in modern medicine. It also suggests that future techniques may well be developed for converting other blood types, as well.

#BlindMeWithScience #MedicalScience #Biology

The Importance of Energy Efficiency for Natural Selection

It has been said that, in nature, "the race is to the quick and the dead", i.e. those who don't work hard for their survival, don't survive.

Many Evolutionary Theorists have long challenged whether this bit of colloquial wisdom applies to Adaptation by Natural Selection (Evolution). Instead, it has been argued, that in the race to survival a tortoise may well beat a hare, by conserving energy more efficiently. (As in the original story, wherein the hare gets out to a big lead, only to nap it away.)

New research published in Proceedings of the Royal Society B looked at nearly 300 species of mollusc, some of which are extinct, and some of which are not, and compared their Basal Metabolic Rates. In general, they found that molluscs with low BMR's were less likely to go extinct.

To be sure, the correlations with BMR may reflect other underlying differences which may more directly explain the findings, and it is not assumed that all species will show this to the same degree.

In general, however, it is to be expected that, holding all else equal, a species with a lower BMR, due to its lower needs for resources such as food, air, sunlight, etc... will be more resistant to pressures to its survival than one with a higher BMR in most circumstances. This is akin to running a bunch of cars against each other in a race that ends only when their engines stop running, and finding out that the most fuel efficient ones lasted longest. Not surprising.

This is also the basis of the Adaptive Inactivity Theory of Sleep: that sleep is not a compensation for effort and energy expended when awake, though it doubles as this, but is primarily a means by which Natural Selection favored creatures that expended less energy at times when threats (including the basic 'threat' of wasting energy unproductively) are high relative to resources, as in the case of the Hairy Brown Bat, which sleeps 20-hours each day and awakens only during a 4-hour period when its food supply (mosquitoes) are awake and active. In short, we sleep not because we must, but because any creature that didn't sleep when the costs of remaining awake were higher than the benefits, tended to die.

While this is widely being called 'Survival of the Laziest', to the point that I could not find an article about this which did not include the term 'Lazy', I feel I must correct this: if laziness means not expending energy when to do so would be optimal for survival, then Natural Selection absolutely does not favor the laziest! And, quite frankly, it is not common to use the term Laziness as a synonym for 'Energy Efficient' (except maybe as a joke).

Furthermore, this is being presented as some sort of contrast to 'Survival of the Fittest', but Survival of the Fittest is not an evolutionary principle. That phrase was, in fact, invented by a Social Darwinist named Spencer to justify laissez-faire capitalism. In fact, as anyone who truly understands Evolutionary Theory will rightly tell you, Survival of the Fittest is a Truism, since we can only define a thing as Fit after-the-fact by seeing that it survived. Evolution (or Adaptation) by Natural Selection is the proper Darwinian and Neodarwinian formulation of the principle, and this in no way contradicts Energy Efficiency.

#BlindMeWithScience #Evolution #EvolutionaryBiology

Mysterious Skyglow 'Steve' Not Auroral and is Unknown To Science

Back in 2016, skywatchers in northern Canada beheld a marvelous sight: a thin beam of purple light, slashing hundreds of miles upwards into space. The phenomenon has been noted for decades, though only recently became of interest to the scientific community.

They dubbed the phenomenon 'Steve', and because it coincided with the aurora borealis, it was assumed to be a type of auroral phenomenon. Studies published around that time, including observations by a European Space Agency satellite, seemed to reaffirm this conclusion.

Until now. A new study published in Geophysical Research Letters, involving researchers in Canada and the United States, failed to find any indication of high energy particles raining down on the magnetic field of Earth, i.e. the classical cause of auroral phenomenon.

Consequently, while it is presumed that Steve is a natural phenomenon, it would appear to be an unknown phenomenon, resulting from unknown causes (possibly ionospheric, though this is mere speculation at the moment).

This should further reaffirm that, for all the empirical observations humans have made of the heavens for centuries now, there remains much about our own skies that we still don't understand yet.

#BlindMeWithScience #Meteorology #AuroraBorealis

Researchers In Potential Panic Mode Over 'Bots' on Amazon Turk

In recent years many scientific researchers, especially in the Social Sciences (e.g. Social Psychology, Sociology, etc...), have been turning to online pools of participants as research participants.

While several platforms exist for this purpose, likely the most popular and best known of these is Amazon Mechanical Turk, a crowdsourcing platform geared around small tasks requiring human intelligence, either because only humans can do them, or because only humans are supposed to do them. For Social Scientists, the important part is the latter: access to a pool of human subjects, who are presumed to be human (else their data would be useless).

Since the early days of Mechanical Turk, unfortunately, there have been bots, used to complete tasks and earn money for a human worker with little to no work on their part. Amazon itself tries to prevent this, and good design principles by Amazon Turk's Requesters (i.e. those seeking workers for a job) can prevent most of the latter. Recently, however, some researchers have noted an apparent uptick in nonsense and suspicious data from Turk Workers, some of which may suggest automation by means of bots.

The looming question is: how big a deal is this, and can it be fixed if it is a big deal? Getting some junk data is in itself not a deal killer, as even human participants tested in-person sometimes rush through questionnaires, fail to follow instructions, etc... resulting in junk data. This is especially true for research involving children, or incentivized undergraduates (e.g. those seeking extra credit, especially towards the end of a semester). Nearly every experiment involving humans will deal with some of this, and generally junk data is easy enough to identify and discard, as long as one gets enough good data as well.

But, are researchers getting good data in the first place? If the Bots are getting cleverer at getting around attempts to identify and squash them, and researchers and Amazon itself aren't getting better at identifying them, then it may well become of little to no value to utilize the platform, despite its tremendous convenience (as it is much more difficult to get participants to come into somewhere in person for research, especially if you need particular types of participants in your sample).

As it stands, no conclusions are being drawn in the Social Sciences by means of Turk data alone. It is being used to confirm and supplement in-person research, by-in-large, and thus the answer to this question, while important, will not threaten to overturn any current data. However, as online research may become much more central and important in the future, such issues must needs be resolved now, before anyone mistakenly draws conclusions about human behavior based on automated data sources.

#BlindMeWithScience #SocialPsychology #Crowdsourcing