an autodidact meets a dilettante…

‘Rise above yourself and grasp the world’ Archimedes – attribution

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some stuff about dinosaurs and their relationship to birds

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Archaeopteryx lithographica with its long bony tail – I took this pic myself at London’s Natural History Museum

Jacinta: Let’s talk about dinosaurs. Are they a thing?

Canto: Of course they are, what are you talking about?

Jacinta: Well I read recently in a New Scientist article that for quite some time in the recent past dinosaur experts didn’t really think ‘dinosaur’ existed as a scientific classification. A new way of classifying was needed because some dinosaurs were bird-hipped and some were lizard-hipped, though they were neither birds nor lizards. So, new names were required.

Canto: Right, so some had hips like lizards, but were clearly not lizards because they had anatomical features that set them apart, and the same went for those that had hips like birds?

Jacinta: Yes I think that’s right. Let’s talk as we learn. Bird-hipped dinos are ornithischians – think ornithology – and the lizardy ones are called saurischians. It was Harry Seeley who shook up the dinosaur-loving world back in 1887 when he argued, before the Royal Society, that what they’d thought were dinosaurs (a term coined by Richard Owen) were really two separate groups, based on those hip bones. Seeley was right about the two groups, but the term ‘dinosaur’, which of course has never disappeared in popular writing, has been rescued over time for science by agreement on other features which bespeak ‘dinosaur’. This has much to do with cladistics, which we may or may not discuss later.

Canto: So the first dinos appeared some 235 mya in the late triassic period, but interestingly they flourished between two major extinction events, the Triassic-Jurassic extinction event about 201 mya, a very sudden event that allowed dinosaurs to fill vacated ecological niches on land, and the Cretaceous-Paleogene (or Cretaceous-Teriary, or K-T) extinction event of 66 mya, which wiped out all the non-avian dinos.

Jacinta: And it should be mentioned that birds are now considered feathered avian dinosaurs, descended from earlier therapods, which strangely are saurischians (lizard-hipped), though a very recent and still controversial paper has reclassified them as ornithischians. I should also mention that dinosaur researchers are a notoriously feisty and bickering tribe, from what I’ve heard.

Canto: I’ve started ploughing through a course on dinosaurs via youtube – The Natural History of Dinosaurs – and I’ve already learned some words, just as background: lithify, diagenesis and coprolite. I’ll let you know if anything exciting crops up, but tell me more about birds being the only remaining dinosaurs and how we know that.

Jacinta: Well, it’s been known since at least the discovery of Archaeopteryx, the type specimen of which was found just two years after Darwin published The Origin of Species, that there are clear anatomical similarities between birds and non-avian dinosaurs. Feathers and hollow bones, for example. There’s also evidence that they share nesting and brooding behaviour. There are also relations with non-avian dinosaurs, some species of which also had feathers, and these discoveries are raising fascinating questions about the origin of flight in these creatures. Of course it’s all very controversial and some researchers are still holding out on the dinosaur-bird link, suggesting other archosaurs were the ancestors.

Canto: What’s an archosaur?

Jacinta: It means ‘ruling reptile’ and these are creatures which first emerged some 300 mya, and they’re the ancestors of living reptiles today. They’re also the ancestors of birds, and dinosaurs. So they’re a larger and older group. Presumably the hold-outs have reason to think birds emerged out of some reptilian line that was distinct from theropod dinosaurs. But that’s nothing to the arguments about the evolutionary steps that led from maniraptoran theropods (perhaps) to modern birds, or the arguments about the origin of flight. Now let me point out that theropods are a suborder of dinosaurs with hollow bones and three-toed limbs, which have long been classed as saurischians until this very recent paper discussed in the New Scientist article, which reclassifies them as ornithiscians. And this seems to be another step – if it holds – towards our understanding of the relationship between birds and their ancestral dinosaurs. An earlier but still pretty recent step were the discoveries, particularly out of China, of a number of fossilised dinosaurs with evidence of feathers, or proto-feathers, and all this, together with advances in analysing and categorising existing specimens using cladistics described in Wikipedia as ‘a method of arranging species based strictly on their evolutionary relationships, using a statistical analysis of their anatomical characteristics’.

Canto: I get very confused about all this. Weren’t there flying dinosaurs – we used to call them pterodactyls – and did they have feathers, or were their means of flight completely different? I seem to remember them depicted like gliders – I mean of the animal kind, with great flaps of skin to catch the wind… Of course that was long before any talk of feathered dinos.

Jacinta: Well hopefully I’ll get to that. Let me talk first about Archaeopteryx, which they reckon dates back to about 150 million years ago. It was probably about the size of a magpie, though there may have been different species of different size (only 11 fossil specimens have been discovered so far). They had feathers, but it’s not known whether they flew like modern birds (flapping flight) or merely glided. A recent study (which I’ve not read) has argued that their flight capabilities were quite limited. They had long, bony tails, which I’m assuming would’ve hampered long-term flight. Interestingly, complex and, for me, impossible-to-verify coloration analyses have presented evidence that the feathers of these critters were a matte black, at least predominantly. Of course it’s hard to prove all this conclusively with 150 million-year-old animals, but speculation and analyses continue, for example on the brain-case of one Archaeopteryx specimen, to determine whether it had a brain for flight (e.g. adequate eyesight, hearing and muscle manipulation). Most of this converges on a limited flight ability, but just how limited will be endlessly argued. And concerning the evolution of birds and flight, there’s a ‘trees-down’ theory (think of sugar gliders etc) and a ‘ground up’ theory. Where does Archaeopteryx fit with those alternatives? That’s still up for grabs.

Canto: Okay, so what about pterodactyls, are they still a thing? Dactyl means digit or finger, doesn’t it?

Jacinta: Winged finger. Yes, they’re a species of pterosaur, with thirty known specimens. They presumably achieved fame among the children of the world as the first-known flying dinosaurs – but they’re not dinosaurs. It’s confusing because ‘saur’ means ‘lizard’, and ‘dinosaur’ means ‘terrible lizard’ and ‘pterosaur’ means ‘winged  lizard’ and they all seem to be connected…

Canto: So what about their relation to birds? Any sign of feathers?

Jacinta: They may have had downy feathers here and there, but not for flight. Their wings were more like those of bats, and they were originally classified as an archaic type of bat. In fact, in the early days of taxonomy, many fossils that had vague similarities to the first pterodactyl fossils discovered in the late 18th century were wrongly designated as pterodactyls, which probably explains their general popularity. It has taken years and many improvements in analysis and dating to sort out the mess, and apparently it still hasn’t been sorted. Anyway, they’re not seen as ancestral to birds. But I may be wrong.

Canto: Wow. Disappointing.

Jacinta: So getting back to the origin of birds, the question of clavicles (collar bones) is important. Birds have wishbones (furculae), which are fused clavicles. The question of bird ancestry has hung on these clavicle bones to a large degree. They’re delicate bones, not easily preserved, and it was long thought that they didn’t exist in dinosaurs. This view has been completely overturned, and in fact most of our understanding about the relationship between birds and earlier dinosaurs come from skeletal studies, or re-examinations, as well as studies of musculature and internal organs, though of course it’s feathers that capture the public’s imagination. But of course there’s a lot of controversy about the how and when of bird evolution, and the evolution of flight, which you’d expect from such scant solid evidence together with intense scientific and public interest.

Canto: Well, I’ve learned something more than the little I knew before about dinosaurs. And their hips. I’ll watch the rest of The Natural History of Dinosaurs’, and we’ll speculate some more in a later post.

Written by stewart henderson

September 4, 2018 at 1:03 pm

Always chemical: how to reflect upon naturopathic remedies

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most efficacious in every case

So here’s an interesting story. When I was laid up with a bronchial virus (RSV) a few weeks ago, coughing my lungs up and having difficulty breathing, with a distinct, audible wheeze, I was offered advice, as you do, by a very well-meaning person about a really effective treatment – oregano oil. This person explained that, on two occasions, he’d come down with a bad cough and oregano oil had done the trick perfectly where nothing else worked.

I didn’t try the oregano oil. I followed my doctor’s recommendation and used the symptom-relieving medications described in a previous post, and I’m much better now. What I did do was look up what the science-based medicine site had to say about the treatment (I’d never heard of oregano oil, though I’ve had many other plant-based cures suggested to me, such as echinacea, marshmallow root and slippery elm – well ok I lied, I found the last two on a herbal medicine website).

I highly recommend the science-based medicine website, which has been run by the impressively-credentialed Drs David Gorski and Steve Novella and their collaborators for years now, and which thusly has a vast database of debunked or questionable treatments to explore. It’s the best port of call when you’re offered anecdotal advice about any treatment whatsoever by well-wishers. Not that they’re the only people performing this service to the public. Quackwatch, SkepDoc, and Neurologica are just some of the websites doing great work, but they’re outnumbered vastly by sites spreading misinformation and bogus cures, unfortunately. It’s almost a catch-22 of the internet that you have to be informed enough to use it to get the best information out of it.

As to oregano oil specifically, Scott Gavura at science-based medicine proves a detailed account. I will summarise here, while also providing my own take. Firstly people need to know that when a substance, any substance –  a herb or a plant, an oil extracted therefrom, or a tablet, capsule or mixture,something injectable or applied to the skin, whatever – is suggested as a treatment for a condition, they should consider this simple mantra – always chemical. That’s to say, a treatment will only work because it has the right chemistry to act against the treated condition. In other words you need to know something (or rather a lot) about the chemistry of the treating substance and the chemistry of the condition being treated. It’s no good saying ‘x is great for getting rid of coughs – it got rid of mine,’ because your cough may not have the same chemical cause as mine, and your cough in February 2007 may not have the same chemical cause as your cough in August 2017. My recent cough was caused by a virus (and perhaps I should change the mantra – always biochemical – but still it’s the chemistry of the bug that’s causing the problem), but no questions were asked about the cause before the advice was given. And you’ll notice when you look at naturopathic websites that chemistry is very rarely mentioned. And I’m not talking about toxins.

Gavura gives this five-point test for an effective treatment:

When we contemplate administering a chemical to deliver a medicinal effect, we need to ask the following:

  1. Is it absorbed into the body at all?
  2. Does enough reach the right part of the body to have an effect?
  3. Does it actually work for the condition?
  4. Does it have any hazardous, unwanted effects?
  5. Can it be safely eliminated from the body?

The answer to Q1 is that oregano oil contains a wide variety of chemical compounds, particularly phenolic compounds (71%). It’s these phenolic compounds that are touted as having the principal beneficial effects. However, though we know that there’s some absorption, we don’t have a chemical breakdown. We just don’t know which phenolic compounds are being absorbed or how much.

Q2 – No research on this, or on absorption generally. Topical effects (ie effects on the skin) are more likely to be beneficial than ingested effects, as the oil can maintain high concentration. This would have no effect on a cough.

Q3 – According to one manufacturer the oil has ‘scientifically proven results against almost every virus, bacteria, parasite, and fungi…’ (etc, etc, but shouldn’t that be bacterium and fungus?). In fact, no serious scientific research has ever been conducted on oregano oil and its effectiveness for any condition whatsoever. So the answer to this question is  – no evidence, beyond anecdote.

Q4 – There have been reports of allergic reactions and gastro-intestinal upsets, but the naturopathy industry is more or less completely unregulated so you can never be sure what you’re getting with any bottle of pills or ‘essential oils’. As Gavura points out, the lack of research on possible adverse effects, for this and other ‘natural’ treatments, is of concern for vulnerable consumers, such as pregnant women, young or unborn children, and those with pre-existing conditions.

Q5 – At low doses, there’s surely no concern, but nobody has done any research about dosing up on carvacrol, the most prominent component of oregano oil, which gives the plant its characteristic odour. Other organic components are thymol and cymene.

 

So there’s no solid evidence about oregano oil, or about the mechanism for its supposed efficacy. But what if my well-wisher was correct, and something in the oregano oil cleared up his cough – twice? And did so really really well? Better than several other treatments he tried?

Well, then we might be onto something. Surely a potential billion-dollar gold-mine, considering how debilitating your common-or-garden cough can be. And how, if not cleared up, it can leading to something way more serious.

So how would a person who is sure that oregano oil has fantastic curative properties (because it sure worked for him) go about capitalising on this potential gold-mine? Well, first he would need evidence. His own circle of friends would not be enough – perhaps he could harness social media to see if there were sufficient people willing to testify to oregano oil curing their cough, where other treatments failed. Then , if he had sufficient numbers, he might try to find out the causes of these coughs. Bacterial, viral, something else, cause unknown? It’s likely he wouldn’t make much headway there (most people with common-or-garden coughs don’t go to the doctor or submit to biochemical testing, they just try to ride it out), but no matter, that might just be evidence that the manufacturer was right – it’s effective against a multitude of conditions. And yet, it seems that oregano oil is a well-kept secret, only known to naturopathic companies and health food store owners. Doctors don’t seem to be prescribing it. Why not?

Clearly it’s because Big Pharma doesn’t support the stuff. Doctors are in cahoots with Big Pharma to sell attractive pills with long pharmacological names and precise dosages and complex directions for use. Together they like to own the narrative, and a multi-billion dollar industry is unlikely to be had from an oil you can extract from a backyard plant.

Unless

Our hero’s investment of time and energy has convinced him there’s heaps of money to be made from oregano oil’s miraculous properties, but that same investment has also convinced him that it’s the chemical properties that are key, and that if the correct chemical formula can be isolated, refined and commercialised, not only will he be able to spend the rest of his life in luxury hotels around the globe, but he will have actually saved lives and contributed handsomely to the betterment of society. So he will join Big Pharma rather than trying to beat it. Yes, there would have to be a massive upfront outlay to perform tests, presumably on rats or mice at first, to find out which chemical components or combinations thereof do the best job of curing the animals, who would have to be artificially infected with various bugs affecting the respiratory system, or any other bodily system, since there are claims that the oil, like Lily the Pink’s Medicinal Compound™, is ‘most efficacious in every case’.

But of course it would be difficult for any average bloke like our hero to scratch up the funds to build or hire labs testing and purifying a cure-all chemical extract of oregano oil. Crowdsourcing maybe, considering all the testimonials? Or just find an ambitious and forward-thinking wealthy entrepreneur?

Is that the only problem with the lack of acceptance, by the medical community, of all the much-touted naturopathic cures out there? Lack of funds to go through the painstaking process of getting a purefied product to pass through a system which ends with double-blind, randomised, placebo-controlled human studies with large sample sizes?

Permit me to be sceptical. It’s not as if the chemical components of most herbal remedies are unknown. It’s highly unlikely that pharmacologists, who are in the business of examining the chemistry of substances and their effects for good or ill on the human body, haven’t considered the claimed cornucopia of naturopathic treatments and the possibility of bringing them into the mainstream of science-based medicine to the benefit of all. Yes, it’s possible that they’ve missed something, but it’s also possible, indeed more likely, that people underestimate the capacity of our fabulous immune system, the product of millions of years of evolution, to bring us back to health when we’re struck down by the odd harmful bug. When we’re struck down like this, we either recover or we die, and if we don’t die, we tend to attribute our recovery to any treatment applied. Sometimes we might be right, but it pays to be skeptical and to do research into a treatment, and into what ails us, before making such attributions. And to do so with the help of a good science-based medical practitioner. And remember again that motto: always chemical. 

 

Written by stewart henderson

August 24, 2018 at 10:18 am

is there life on Mars? – encore

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Don’t worry Davey, we’ll find out

The recent announcement about a large lake of water beneath the ice near the south pole of Mars has naturally engendered great excitement among those desperate to find life ‘elsewhere’, and with good reason. Mars, our closest planet, has long been a haven of hope for this sort of thing, but it has also engendered the ‘too good to be true’ response. It’s almost been seen as a lazy conjecture, as if we should expect to work really hard, and over unimaginably long distances, to find this precious and surely extremely rare stuff called life. But in recent decades we’ve managed to discover life surviving and even thriving under the most extreme circumstances in odd nooks and crannies of our own planet, which has widened our view of life’s diversity and tenacity. And the fact that we’ve been discovering new life on our own planet, is a testament to our developing skills and technology in the search for life – because, of course, the life we’re discovering isn’t new at all, what’s new is our technology and our deeper awareness of life’s range and possibilities.

And what we know about life on Earth is all about water. We’re full of the stuff, as are the plants and animals around us, and we now know that our ancestors emerged from the stuff, and we’ve never stopped being dependent on it. So it’s not surprising that the question about life on Mars is also all about water.

In previous centuries it was much speculated that water lay on the surface of Mars, in what appeared to be canals or waterways of some kind. Nowadays what we’ve learned about the atmosphere at Mars’ surface – low temperature and pressure – has rendered the possibility of liquid water increasingly unlikely. However, water below the surface is another matter. Lake Vostok, four kilometres below the surface in Eastern Antarctica, is just the largest of a number of subsurface lakes – at least 400 found under that continent – and they support thousands of living species.

So for some time there’s been a search for subsurface water on Mars. A radar instrument called MARSIS, orbiting the planet on the European Space Agency’s Mars Express, and purpose-built to search for underground water, has been sending out radio waves which are reflective to liquid water but not to ice or rock. A particularly reflective patch near the south pole appears to reveal a layer of water about 1.5 kilometres below the surface. However, MARSIS is limited in the data it can provide. The depth of the water, and what other material is mixed in with it, are not known – though we know that it’s about 20 kilometres across, and the the Italian research team that has published the findings estimates the water to be at least a metre deep, indicating a genuine lake rather than meltwater. It’s expected that the water will contain salts, which lower the freezing point of water, as would pressure from the material above the lake.

There are still many unknowns here, but the various Mars rovers and orbiters are building evidence, for example that Mars was once warmer and wetter, and that even now liquid water can still be found at periods on the surface. What we haven’t found so far is evidence of life. So how can we get this evidence? First, we need to look for life ‘as we know it’, carbon-based life, because that’s very likely the kind of life we’ll find on our nearest neighbour, and because we have no way of knowing how to look for completely alien life.

Mars’ Curiosity rover has already found organic molecules, specifically methane, which may or may not be produced by biological activity beneath the surface. The rover has been sampling the atmosphere and has found methane at varying levels as the seasons have changed. However, it’s generally believed that the thin atmosphere at Mars’ surface would be insufficient to deflect life-harming radiation. The discovery of a specific and more or less substantial body of water below the surface, perhaps sufficiently protected from radiation, provides a target for future researchers to aim at.

The next step would be to obtain samples from the lake, which is easier said than done. It would require some sort of robotic drill to be sent out there and operated remotely, a task beyond current capabilities. Meanwhile, a Chinese probe is set to be flown to Mars in 2020. It will have radar instrumentation similar to MARSIS, but operating at a slightly different frequency. It may confirm the MARSIS findings or discover other underground bodies of water, further piquing our interest in the very real possibility of life on the red planet.

Is it an underground lake? We can’t be entirely sure.

References

http://www.abc.net.au/news/science/2018-07-26/vast-liquid-lake-found-under-mars-south-polar-ice-cap/10030264

https://theconversation.com/discovered-a-huge-liquid-water-lake-beneath-the-southern-pole-of-mars-100523

http://www.abc.net.au/news/science/2018-07-26/mars-life-evidence-organic-carbon-methane-liquid-water/10038324

https://www.bbc.com/news/science-environment-44952710

 

Written by stewart henderson

August 11, 2018 at 10:38 pm

Useful stuff on extremophiles and their tricks

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A tardigrade or water bear, emblematic creature for extremophile-philes everywhere. Look em up, cause they’re not mentioned in this article

I’ll try to wean myself from the largely thankless task of writing about politics by picking a topic, almost at random, though one that I know will keep me engaged once I get started.

I was reading an article on the geology of the Earth’s crust and upper mantle (aka lithosphere) the other day, which mentioned the possibility of life in the mantle. Little is known for sure about the mantle’s composition and activity, because until recently drilling down to that level has been just a pipe dream, so to speak. The mantle’s distance from the earth’s surface varies considerably from region to region, but the average depth of the crust at its thinnest, ie under the ocean, is about 6 kilometres. In 2011, microscopic nematodes, or roundworms, were found some 4 kilometres below the surface in a gold mine in South Africa. Other single-celled micro-organisms were found in the region, at depths of 5 kms. Since we’ve rarely plumbed such depths, it’s not unreasonable to suppose that life down that far may be commonplace. We already know that life exists under the sea floor, at immense pressures. At the bottom of the Mariana Trench in the western Pacific, bacteria thrive 11 kilometres below sea level, and some bacteria have been tested in the lab as tolerating 1000 atmospheres of pressure.

Of course, the term extremophile, applied to such life forms, is typically anthropocentric, as they would presumably shuffle off their mortal coils tout de suite when subjected to our torturous environment. Then again…

Extremophiles are of course termed as such when found in conditions that are far from what we would term normal. Such conditions include extremely hot or cold environments, highly acidic or alkaline environments, anaerobic environments, and extreme pressure. They include archaea, the earliest living organisms we know of, some of which have been found to be halophilic (thriving in high salt conditions) or hyperthermophilic (lovers of temps around 80°C).

So how far down can these organisms go? What do they live on? What do they look like and how do they relate to other organisms on the bush of life?

This article from National Geographic online suggests the possibility of an ecosystem existing some eight or nine kilometres below the Mariana Trench. The trench is a subduction zone, a region known to provide pro-life environments of sorts. Analysing such regions requires geological as well as microbiological expertise. A geological process known as serpentinisation provides an ecosystem for methane-consuming microbes. Serpentine is a mineral formed deep in the lithosphere ‘when olivine in the upper mantle reacts with water pushed up from within the subduction zone’, according to the article. Hydrogen and methane are by-products of this reaction, and this serpentinisation process is already known to create microbial habitats at oceanic hydrothermal vents. Furthermore, in recent years, serpentinisation has been found ‘everywhere’, at subduction zones and within mountain ranges, suggesting that methane-supported life may be commonplace, and may even exist elsewhere in the solar system where there is tectonic activity, and an abundance of olivine.

Organisms living at great depths, under great pressure, are called piezophiles. So what is it that permits these bacteria, archaea and other unicellular organisms to thrive – or perhaps only just survive – in such conditions? There’s no one-size-fits-all answer, as some, such as xenophyophores, which are found at depth throughout the world’s oceans, are relatively complex creatures that appear to have adapted over time to increased pressure in order to benefit from benthic provender, while others like Halomonas salaria, a proteobacterium, are obligate piezophiles, unable to survive in under 1000 atmospheres. Unsurprisingly the outer membranes of these organisms are necessarily different in structure and composition from your common or garden microbes, but also unsurprisingly, it has proved difficult to analyse the structural features of piezophiles under lab conditions, though it’s clear that regulation of membrane phospholipids is key to maintaining a stable internal environment, which can not only withstand pressure, but also extremes of heat or cold or acidity. Proteins are also modified to maintain function. Although little is yet known about these organisms, the variety of their environments suggest a variety of adaptations independently arrived at. Most are autotrophs, or self-feeders, able to build organic compounds such as proteins through chemosynthesis in the absence of light. Many of them appear able to slow their metabolism and their reproduction rate by many factors.

Researchers are becoming increasingly interested in extremophiles in general, as they’ve widened the possibilities of life in environments hitherto dismissed as unviable – in boiling water or under mountains of ice for example – just as we’ve begun to discover or further explore other planets (and moons) within and beyond our solar system. The field of microbiology has also made great strides in recent decades. Don Cowan, a senior researcher at the University of Pretoria, describes the microbiological ‘revolution’ of the eighties:

In less than a decade, a combination of conceptual, scientific and technical developments all came together. These included the ability to purify total environmental DNA, the development of special marker sequences that can identify different microbial species, and the advent of very fast, very cheap DNA sequencing techniques.

Collectively known as metagenomics, these developments hugely stimulated the field of microbiology. They have done so across diverse areas of science, from biological methods for cleaning up environmental pollution and contamination, to human disease.

Researchers are applying these techniques to the examination and possible exploitation of extremophiles, for example to improve drought or temperature tolerance in plant species, for various pharmaceutical applications and possibly for the development of biofuels, as heat-tolerant enzymes enable plant tissues to be broken down more readily. The range of products and processes that can be improved by tapping into the enzyme production of various types of extremophiles is potentially vast, according to James Coker, a researcher at the University of Maryland’s Department of Biotechnology. In a 2016 paper, Coker admits that research in this field is new, but real progress has already been made:

Four success stories are the thermostable DNA polymerases used in the polymerase chain reaction (PCR) 17, various enzymes used in the process of making biofuels 18, organisms used in the mining process 19, and carotenoids used in the food and cosmetic industries 20. Other potential applications include making lactose-free milk 1; the production of antibiotics, anticancer, and antifungal drugs 6; and the production of electricity or, more accurately, the leaching of electrons to generate current that can be used or stored 21

That last-mentioned application is of particular interest (as are all the others), as clean electricity production and storage is a high priority issue for some. Extremophile microbial catalysts can be used to drive microbial electrochemical systems (MES), a new TLA which may or may not catch on. Related TLAs include the MFC (microbial fuel cell) and the MEC (microbial electrolysis cell). Without losing myself in too much detail here, the exploitation of these microbes to help drive reactions at the electrodes has a number of useful applications, such as the remediation of waste-water, desalination, biosensing and ‘generating electrical energy from marine sediment microbial fuel cells at low temperatures’ (Dopson et al, 2016). None of this is, as yet, set to revolutionise the clean energy industry, but these are just some of the largely unsung incremental developments that are, in fact, moving us towards more clever and efficient use of previously untapped renewable resources. I was about to use the metaphor ‘at the coalface’ – which would’ve been appropriately inappropriate.

It’s impossible for we dilettantes to keep up with all these discoveries and developments in a detailed way, but we can at least feel the excitement of work being done and advances being collaboratively made, as well as sensing the many obstacles and unforeseen complexities involved in transforming the viability of these amazing life-forms and their products into something viable and possibly life-transforming for the humans who have discovered them and unlocked their secrets. When politics and our inhumanity to others (human and non-human) lets us down, we can still marvel at our relentless drive and ingenuity.

 

Written by stewart henderson

July 14, 2018 at 8:50 am

Is free will a thing? Apparently not.

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Science appears to be cutting the gordian knot of philosophical isms

Canto: The subject of free will often comes up, and I’ve recently read Sam Harris’ booklet on it, so I want to state right now my view that if we do have free will, it’s a far more circumscribed thing than many prefer to believe, and I’m open to the view that it doesn’t exist at all.

Jacinta: Yes I’ve read a fair bit on the subject over the years, including Dennett’s Elbow Room in the eighties, and a collection of essays edited by Bernard Berofsky, dating back to the sixties, but like everyone I’ve forgotten almost all of any book I’ve read within weeks of having read it, so it’ll be good to get back to the subject enfin. 

Canto: But have you been exercised by the actual subject, intellectually speaking?

Jacinta: Very much so. Let’s return to our old friend the Dunedin longitudinal study, which indicates that the various personality types – roughly characterised as well-adjusted, confident, reserved, under-controlled and inhibited – are established very early on and rarely change outside of neurological damage. These constrain free will, as does your broad environment, for example whether you’re a scion of the British aristocracy or the offspring of Mongolian goat-herders. You’re not free to choose these things or your genetic inheritance or, presumably, your neuronal wiring, at least not as a youngster.

Canto: I think the free will people would concede all that, but their best argument would be that in spite of all the determining factors that make you who you are, your moment-to-moment decisions – whether to get out of bed or sleep in for a while, whether to break your diet or stick to it, whether to watch a TV program or go to the pub, whether to study physics or psychology at uni (assuming you’re qualified to do either), and so on – these decisions are made of your own volition, so you are responsible for them and nobody else. If there’s no free will, there’s no responsibility, therefore nothing or nobody to praise or blame. And then where would we be with our ethics?

Jacinta: That’s interesting because we often get confused about that, or some people do. I would say most people believe we have free will, so we’re happy to punish people for criminal acts. They chose to commit them after all. But take those serial paedophiles that the tabloid press like to call ‘monsters’. They describe them as incorrigible – that’s to say, uncorrectable. So they should never be released again into the public, once they’ve been proven to commit some heinous paedophile act. What’s being claimed here is that the paedophile can’t help but commit these acts again and again – he has no choice, and presumably had no choice to begin with. But prison is a terrible punishment for someone who has no choice but to be what he is. They’re denying that he has free will, but punishing him for acts that should only be punished if they’re undertaken freely. You can’t have it both ways.

Canto: Well put, and my own tendency towards what used to be called hard determinism comes from reading the writings of ‘compatibilists’ or ‘reconciliationists’ who wanted, I thought, to give themselves as much credit for their success as they possibly could, seeing that they were successful academic philosophers earning, I assumed, the kind of salaries I could only dream of. On the other hand, as a hard determinist, I naturally wanted to blame everyone else, my parents, my working class environment, my lack of wealthy and educated connections, for my abject failures in life.

Jacinta: You jest a little, but I know you’re being essentially serious, in that the Gina Rineharts of the world, inheritors of millions, are the biggest spruikers of the notion that everyone is free to be as rich as everyone else but most people are just too slack, or, for reasons unfathomable to her, aren’t sufficiently interested in material self-enrichment, so they get precisely what they deserve.

Canto: Or what they’re destined to get. Just reading through some of that old philosophical material though, I find myself reliving my impatience with the academicism of philosophy. For example, the endless analysis of ‘able to’, as in ‘she’s able to play the piano’ but she can’t because she hasn’t got one right now. So she has the skill but not, right now, the equipment. Perhaps because she’s fallen on hard times and has had to sell it. Which leads to having ‘potential ability’. She might have been one of the world’s greatest soccer players, having the requisite skill, speed, drive, etc, but she was never introduced to the game or was discouraged from playing it.

Jacinta: She was told to study piano instead. Or more importantly, potential scientific geniuses who just didn’t get the opportunity due to a host of external circumstances, to attain that potential. They say geniuses are made not born, but they require external material to make themselves into geniuses, if that’s what they do. The point is that you can get caught up with words like ‘able to’ or ‘could have done otherwise’, which you can then interpret in varieties of ways, and it becomes almost a philosophy of language thing. But the main point is that although it seems obvious that you can choose between having a piece of cake before bedtime or not, these aren’t the most important choices..

Canto: And maybe even these choices aren’t as freely made as we might think, according to research Sam Harris cites in his essay. It seems science is catching up with what I knew all along. Not only do we have no control whatever over our genetic inheritance, but the way those genes are expressed, based largely on environmental factors, which lead to our brains being wired up in particular ways to release particular levels of hormones and neurotransmitters in patterned ways, leading to those character types identified in the Dunedin study, all of this is way beyond our conscious control. In fact it’s fair to say that the gradual retreat of the notion of free will is largely the result of the assault on the primacy of consciousness. Far more of what we do is less conscious than we think.

Jacinta: Yes the neurophysiological research around everyday ‘decisions’ is compelling, and disturbing to many. It suggests that our feeling of having freely decided on something is a delusion, though perhaps an evolutionarily useful one. Believing in free will usually entails belief in personal moral responsibility, and thus supports punishment for damaging acts and reward for heroic or beneficial ones. And  some research has actually shown that people primed to disbelieve in free will are more prepared to cheat and pilfer than those who aren’t.

Canto: So if this continues, this spread of disbelief or skepticism about free will, it may lead to a spike in criminal activity, large and small?

Jacinta: Well I don’t know if there’s been a rise in crime, but there has certainly been a rise in ‘my brain made me do it’ defenses. The effect of all this might be a ‘go with the flow’ attitude to pursue self-interest because your brain’s wiring supposedly impels you to.

Canto: So, that’s interesting, maybe a solution to this is more knowledge. The understanding that we’re the most social mammals on the planet, and that what we do, such as cheating and pilfering, adversely affects others, which will ultimately rebound on us. Even our brain’s own wiring has been caused by environmental factors, primary among those being human factors. So emphasising that our ‘self’ is more of a social self than our privileged access might lead us to believe will encourage us to consider what we owe to the wider society that helped shape us.

Jacinta: Yes, that’s a good point. And I think, as Harris and others point out, jettisoning the free will notion should help us reduce our tendency to blame and hate. I struggle myself with this – I ‘hate’ Trump, but I quickly realise he’s always been like this, and I can’t even blame his parents, who are what they are, etc. So I turn, as I think I should, to a US political system that enables such a person to reach the position he’s reached. In focusing on this system I can heap blame upon blame to my heart’s content, which I always love to do, without getting personal, which may have rebounding consequences for me. It’s a great solution.

Canto: Anyway, I think we’ve just scratched the surface with this one. Don’t we sometimes appear to agonise over decisions? People make lists of pros and cons about whether to spend x money or whether to travel to y, or whether or not to break up with z. How does this sort with a lack of free will? There must be a lot more to say.

Jacinta: It’s determined by our brain’s wiring that we agonise over some of our decisions and not over others. And how often do we make those lists you speak of, often prompted by others, and then just go with our original intuition?

Canto: Hmmm, I still think this is all worth further consideration…

Jacinta: I don’t think there’s any way you can seriously argue for free will. The argument is essentially about the consequences.

References

https://www.theatlantic.com/magazine/archive/2016/06/theres-no-such-thing-as-free-will/480750/

Sam Harris, Free will

https://theforeveryears.wordpress.com/2016/06/30/dunedin-study-findings-the-importance-of-identifying-personality-types-at-a-young-age-by-kirsteen-mclay-knopp/

Bernard Berofsky, ed, Free will and determinism

 

Written by stewart henderson

May 15, 2018 at 10:16 am

Archimedes, the Mathematikos and the birth of science

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Rise above yourself and grasp the world.

Archimedes (attributed: inscribed on the Fields Medal)

One of Archimedes’ most spectacular inventions, the gravity-defying spiral-in-a-cylinder, or screw – still effective

Canto: So we spent some time at the Waikato museum in Hamilton, braving the school holiday crowd to view an exhibition celebrating the work of Archimedes (c 287-212 BCE) and his fellow mathematikos, and noting how it inspired the likes of Leonardo some 1800 years later. So let’s talk about their breakthroughs and about why there was such a gap between their clever contrivances and the maths on which they were based, and the scientific revolutionaries of the sixteenth and seventeenth centuries.

Jacinta: These are intriguing and vital questions. Many modern scientists have been dismissive of the science of the ancient Greeks because they think of Aristotle as representative. I think it was Lawrence Krauss I heard complaining of Aristotle’s belief that women had less teeth than men – apparently he never thought to count them! But the fact is that, though Aristotle is sometimes known as the father of empiricism, he probably doesn’t deserve that title except in respect of ethics, and politics, which he based on what actually works for societies and city-states, which is why he collected and analysed their constitutions. The mathematikos, on the other hand, eschewed ethical issues in favour of mathematics – geometry in particular (think Euclid). And, especially in the work of Archimedes, they enjoyed phenomenal success in many practical areas.

Canto: Especially warfare apparently. It seems Archimedes in particular was called on more than once to defend his city, Syracuse, with war machines. In the blurb to the exhibition, they mention ‘torsion ballistae’. Can you please explain?

Jacinta: Well, I’ll tell you about the torsion siege engine. It replaced the earlier tension siege engine, possibly invented in Syracuse in the time of Dionysius the Elder (c 432-367 BCE) – so the engineering of weapons of war was already a big thing at the time. It was basically a massive catapult. The first torsion device of this kind is generally dated to the time of Philip II of Macedon, Alexander’s dad, circa 340 BCE. The first extant evidence of its use comes from a list of items in the arsenal of the Acropolis in Athens dating to 338-326 BCE. So what is torsion? It’s the energy created by winding something up, like a spring. In earlier times, human hair, horsehair and animal sinews were used for this purpose.

Canto: So plats give you energy?

Jacinta: Torsion basically means twisting. The Greeks apparently used specially cured sinew combined with human or animal hair to create a ‘torsion bundle’ – we don’t know what the exact recipe was – which was fixed to a wooden frame and could be twisted and released regularly via levers without breaking. But the key development was the mathematics of these devices. This military website describes:

The critical dimension was the diameter of the sinew “spring” or torsion bundle. For a bolt shooter, the ideal diameter was one-ninth the length of the bolt. For a rock thrower the ratio was more complex; the diameter (d) of the bundle in dactyls (about 3/4 inch) should equal 1.1 times the cube root of 100 times the mass of the ball (m) in minas (about a pound). Saddled with a numerical notation system even more awkward than Roman numerals, the Greeks developed sophisticated geometric methods to compute cube roots.

Canto: So how were these maths – these geometric methods – derived. Euclid was the great geometer of the time, wasn’t he?

Jacinta: Actually, though the exact time-frame of Euclid’s life isn’t known, his Elements came out after this invention, but before the work of Archimedes. Clearly it must’ve been drawn from earlier mathematikos, such as Eudoxus, who worked out, via an early version of integral calculus, that areas of circles relate to squares of their radii, and volumes of spheres relate to the cubes of their radii, and various other relations between volumes and dimensions of pyramids, cylinders, cones etc, which obviously had practical applications as described above.

Canto: Okay, so tell us about Archimedes’ particular contributions, and about why the great work of the mathematikos was apparently discontinued after Archimedes. Considering that the Roman Empire didn’t become christianised until some 500 years after Archimedes’ death, we can’t really blame the Christians – can we?

Jacinta: Well, I mentioned that early version of integral calculus. It was called the method of exhaustion, a kind of geometric calculus which Archimedes took further than anyone before him, both in theoretical terms and via practical applications. Now I’m far from being a mathematician, but I’ve come to appreciate the essentiality of maths in understanding our universe – so much so that I perhaps regret my lack of mathematical expertise more than I regret anything else in my old life. This is by way of saying that I won’t try to explain Archimedes’ maths – but an understanding of maths is essential to understanding the magnitude of his achievement.

Canto: Okay, so what about his inventions?

Jacinta: Well the key is the application of complex and what might have seemed pointlessly abstract maths about the relations of ‘perfect’ shapes such as spheres, cones and cylinders to real world problems and their solutions. The lever is a good example. Archimedes didn’t invent levers but he was clearly fascinated by them. And it shouldn’t take long to realise that they have immense practical applications. Doors are levers, as are nail clippers, nutcrackers and see-saws. Archimedes wrote what we now call a treatise, On the equilibrium of planes, to explain the maths behind them. But the best illustration of Archimedes’ combination of theory and practice is probably what is known as Archimedes’ principle, which essentially launched the field of fluid dynamics, or fluid mechanics:

the upward buoyant force that is exerted on a body immersed in a fluid, whether fully or partially submerged, is equal to the weight of the fluid that the body displaces and acts in the upward direction at the center of mass of the displaced fluid.

It comes from another treatise of his, On floating bodies. Now let me see if I can explain this. Take an object, any object. The downward force exerted on it is its weight. Immerse it in water. It will float or it will sink, and even if it floats it’ll be partially submersed. The principle doesn’t apply to objects that sink, which will have a density of anything over and above a certain level which permits it to float – I think.

Canto: But that principle, though it comes from a treatise about floating bodies, doesn’t distinguish between floating and sinking. It says ‘fully or partially submerged’…

Jacinta: But an object can be fully submerged and still float. To sink means to continue in a downward direction.

Canto: I’ve found that an object that floats – I’m thinking of water as the fluid, and perhaps I shouldn’t – always seems to have a certain proportion above the water level. Think of icebergs, and human bodies. But I think I get it – the force that keeps you up and floating will be equal to the weight of the water your body displaces… So if I was ten kilos heavier, I would still float but the upward force acting on me would be greater, but not by ten kilos, rather by the larger volume of water my larger body displaces measured in kilos, or by some measure of force…

Jacinta: I don’t think that’s wrong, but I’m not sure if it’s right. The problem for me is that the principle as stated doesn’t specify a floating body, only a body immersed – partially or fully in a fluid. Think of a stone dropped in water. It sinks. To the bottom.

Canto: And if the fluid is bottomless will it just keep on sinking? It’s as if there’s no upward force acting on it at all, or very little. I’m imagining a bottomless column of still water here, not an ocean with its currents…

Jacinta: Ha, I was thinking of a bathtub, but with a bottomless well, it will depend on the density of the stone. I think at some point it’ll slow down and be suspended. I’m sure water pressure will play a role, and density – of the water. And density is somehow related to pressure, and I’m getting lost…

Canto: We may need to do a Khan academy course. But getting back to Archimedes and the mathematikos, why was so little of their work built upon, until Galileo and others became inspired so many many centuries later?

Jacinta: That’s possibly too long a story to go into here, not that I’m much equipped to tell it. It no doubt relates to the gradual decline of the increasingly dispersed Greek culture of the Hellenistic and post-Hellenistic era. I wouldn’t want to say Christianity was a major cause but it certainly didn’t help. By the time the Roman Empire became Christianised, the culture that created figures like Archimedes had long passed. Roman culture was a lot more militaristic and less speculative. Blue sky research wasn’t in vogue. Of course, why all this happened I wouldn’t venture to say without many years of research into the cultural changes then occurring. But the slowness of the scientific recovery, that I would attribute to Christianity, and later to the conservative turn in Islam that still prevents original science from being practiced in those countries where it holds sway.

Written by stewart henderson

May 2, 2018 at 9:13 pm

is this the best use of journalism?: attn Katie McBride and Outline magazine

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Rat Park, in colour

Jacinta: Now we’re going to do something slightly unpleasant but wholly necessary: take someone to task, as teachers must occasionally do.

Canto: Yes, it relates to a previous post, a recent one, about Rat Farm and the war on drugs.

Jacinta: In writing that post we happened upon an article entitled  ‘This 38-year-old study is still spreading bad ideas about addiction” – which kind of shocked me with its provocative title. It was written by Katie MacBride and published by Outline, an online magazine. I only skimmed the article at the time, bemused to find the Rat Park experiment still creating such negative vibes after all these years, but some obvious problems in the article stood out, even on the most cursory reading, so I’ve decided to revisit it with a more careful analysis, with Canto’s help.

Canto: Well the first red flag with the article comes with the first words, before even the title. Pop science. In other words, this article, or rather its subject, should be filed in the category of ‘pop science’, as opposed to real science. This is designed to instil prejudice in the reader from the outset, and is clearly a cheap trick.

Jacinta: Yes, and for an immediate antidote to this kind of cheapsterism, I’d advise anyone to read the Wikipedia article on the rat park experiment, which is calmly and reasonably presented, as is usual. And let me here heap praise on Wikipedia for its general reliability, its objectivity and its pro-science approach. It’s one of the greatest gifts the internet has provided to our world, IMHO.

Canto: The next red flag comes with the title – ’38 years old and still spreading bad ideas’…. As if the date of the study is relevant. There are a number of landmark psychology studies even older than Bruce Alexander’s Rat Park, and also ‘flawed’ – of which more later, – which continue to resonate today for obvious reasons…

Jacinta: Yes, for example Stanley Milgram’s electric shock experiments, over fifty years ago now, and the Stanford Prison experiment of 1971. These, and Alexander’s Rat Park experiment, deserve to be regarded as landmark pieces of work because they make you think. And they often overturn previous thinking. They shake our complacency.

Canto: And what about the latter part of the title, that Alexander’s work is still spreading bad ideas?

Jacinta: It’s interesting that she claims this, considering that the main reason Alexander embarked on this study was to combat bad ideas – particularly the war on drugs itself, and the prevailing view, promoted by the likes of Harry Anslinger and his zero tolerance approach to drugs such as cannabis and cocaine, that use of these drugs led inevitably to a kind of madness that was extremely harmful to self and others. Remember the rat adverts of the time, which showed rats dropping dead after regularly imbibing morphene-laced water, with the message ‘this could happen to you’.

Canto: Yes, and the rats may well have been choosing the drug over plain water because, like many lab rats of the time – hopefully things have changed – the conditions they were kept in made their life something of a living hell. What Alexander’s experiment showed was that, given a far more enriched environment, rats made far less simplistic and self-destroying choices. That’s all. So how could this be a ‘bad idea?’

Jacinta: MacBride doesn’t say. But to be fair, Alexander’s thesis may have been that opiates aren’t addictive at all, which is not what his results showed – they showed that environment matters hugely in respect to the willingness to get hooked on drugs. And that’s a really really important finding, not a ‘bad idea’.

Canto: And we’re still on the title of MacBride’s essay, which is followed by a tiny summary remark, ‘The Rat Park study was flawed and its findings have been oversimplified, but it keeps getting cited.’ Any comments?

Jacinta: Yes – as a regular listener to the podcasts of the Skeptic’s Guide to the Universe (SGU) over the years, as well as a reader of Ben Goldacre and other science-based critics of medical/psychological studies and experiments, I can safely say that every piece of research or experimentation, since the dawn of time, is flawed. Or imperfect. Or limited. Some more than others. of course. So to say the study is flawed is to say nothing at all. Every episode of SGU, and I’ve listened to hundreds, features one piece of published research or other, which Steve Novella picks to pieces to determine whether it’s very or mildly interesting, or a piece of rubbish, but even with the best study, the mantra is generally ‘needs more research’. So a critic needs to show how an experiment is flawed, and how those flaws affect the results. And MacBride’s effort to do this is pretty abysmal.

Canto: Okay, before we examine that effort, I’d like to quote something from early on in MacBride’s article:

The Rat Park study undermined one popular misconception about addiction, that chemistry of drugs is the single most important factor in addiction. But instead of pushing the popular understanding forward, it merely replaced that misconception with a new one: that environment is the most important factor.

What do you make of that? Do you think it a fair description of the study?

Jacinta: It’s an odd description, or mis-description, of the study. The first sentence you quoted isn’t problematic. The study did undermine the idea that it was all about chemistry. Or rather it would have, had anyone paid attention to it. It should have, as MacBride implies, but instead of then regretting that the study didn’t have any impact, she presents it as deserving of oblivion. It doesn’t make much sense.

Canto: The quote claims that it’s a misconception that environment is the most important factor in drug addiction. Do you agree?

Jacinta: I don’t know if it’s the most important factor, but it’s obviously an important factor, and the Rat Park experiment provided strong evidence for this. It seems MacBride is confusing Alexander’s possible claims or commentary on the study with the study itself. The study doesn’t prove that environment is the most important factor, but it certainly makes you think about addiction in a very different way from the horrific but dumb rat ads  that prompted it. It makes you think, as all good studies do, and that’s something MacBride seems extremely reluctant to admit. And I wonder why.

Canto: But MacBride does provide cogent criticisms of the study, doesn’t she?

Jacinta: Well, she quotes one particular critique of the study, by a Dr Sam Snodgrass, who found that the Rat Park environment, in which rats were no longer isolated and therefore mated, as rats are wont to do, would have rendered the findings questionable. According to Snodgrass, “You can’t have one group of subjects mating and with pups and compare it to a group that doesn’t engage in these behaviors and say that the difference between the two groups is caused by environmental differences.” But I beg to differ. An environment in which you’re isolated and unable to have sex is obviously very different from an environment in which you breed as normal – especially for rats. As to the rat pups ruining the experiment, I think if you looked closely at any rat study in which rats get to live together and breed, the actual experiment would be more messy than the published results indicate, but I doubt the problems would be so great as to invalidate those results.

Canto: And what about attempts to replicate the experiment?

Jacinta: Well there seem not to have been enough of them, and that’s not Alexander’s fault. Above all, similar experiments should have been conducted with different drugs and different concentrations etc. And of course rats aren’t humans, and it’s hard to bridge that gap, especially these days, as lab testing of other non-human animals (and rats too) is increasingly frowned upon, for good reason. I note that MacBride briefly mentions that others did replicate Alexander’s results, but she chooses to focus almost wholly on those who found differences. She’s also quite brief in describing the obvious parallel, presented in much greater detail in Johann Hari’s Chasing the scream, of American soldiers taking heavily to heroin in the alienating environment of Vietnam and giving them up on their return to what was for them an obviously more enriched environment. The facts were startling – 20 time the heroin addiction in Vietnam, as MacBride admits – but not much is made of them, as she is more concerned to pour cold water on Rat Park, so to speak.

Canto: Yes it’s strange – MacBride admits that the war on drugs has been an abject failure, but her obsession with criticising Rat Park prevents her from carrying through on that with, for example, the alternatives to this American approach in Europe. She mentions the again startling fact, reported by the Brookings Institute, that the combined hardcore user rate for hard drugs was approximately 4 times higher in the US than in Europe, after decades of the US war on drugs, but fails to note that the Rat Park experiment was one of the main inspirations in implementing more humane and vastly more successful policies, not only in Europe but, more recently, in some US states.

Jacinta: Yes MacBride is clearly concerned to get everyone’s facts straight on the opioid epidemic that’s currently gripping the US, and about which I honestly know little, but I think she has gone overboard in seeking to vilify the Rat Park study, which surely has little to do with that epidemic. The Rat Park experiment hardly promotes drug-taking; what it does strongly suggest, as does Johann Hari’s book, is that environment is one of the most important factors in determining a person’s willingness to escape into drugs. My own personal experience tallies with that, having been brought up in a depressed and disadvantaged region, hard-hit in the seventies by economic recession, and watching the illicit drug trade take off around me, as houses and gardens became more and more derelict.

Canto: Yes, it’s hard to understand why she’s focusing so negatively on Rat Park, when the problem is really one of interpretation, insofar as there is a problem. And I don’t know how it relates negatively to the opioid crisis. Maybe we should find out more about this crisis, and do a follow-up?

Jacinta: Maybe, but it’s so hard trying to fix the world’s problems… but of course that’s what we’re here for…

 

Written by stewart henderson

April 13, 2018 at 11:53 am