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reading matters 12: food mysteries

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New Scientist 3292 July 25 2020

Jacinta: So this cover story reminds me of something I read or heard a few years back  – that if you were to list the chemical ingredients of a hen’s egg, you’d never come to the end, or something like that. 

Canto: Well you’re on the right track, the cover story is titled ‘the dark matter in your diet’, but instead of a hen’s egg it starts with garlic. Both of these commonly consumed edibles, like just about everything else we eat, contain ‘nutritional dark matter’ that scientists have only recently started to focus on, surprisingly considering that we are, to a fair degree, what we eat. 

Jacinta: Yes, so we all know that food components or nutrients are usually divided into fats, carbohydrates and proteins, though these three can be subdivided to a near-infinite degree, but there are also vitamins, minerals and other biochemical elements in various quantities, and with variously vital effects. Currently the US Dept of Agriculture (USDA) has a database of 188 nutritional components of food, under which some info is provided on many thousands of chemical elements. 

Canto: So garlic, the USDA reckons, is found in 58,055 foodstuffs, including, uhh, garlic. Raw garlic itself is described as containing 67 nutrients, both macro and micro, some of which can only be found in very minute quantities. And yet many components, such as allin, which helps to give garlic its particular odour and flavour, aren’t listed on the database. 

Jacinta: Allin is converted into allicin, through the enzyme allinase, when you crush or chop garlic. That’s when that lovely/notorious stink hits you. 

Canto: Right, and this is apparently a major problem across the whole database. They added a few dozen flavonoids – plant compounds that can lower the prevalence of cardiovascular disease – in 2003, but recent researchers have been frustrated by the many gaps, and are building their own more comprehensive database, based on their own chemical analyses. It’s called FooDB, which now lists almost 400 times the number of nutritional compounds as the USDA database. 2306 for garlic, for example, compared to the USDA’s 67. But there’s a lot of work still to be done, even on garlic. Only a tiny fraction of those compounds have been quantified – we don’t know the exact concentrations. And this is a problem for the whole of FooDB, with about 85% of compounds unquantified.

Jacinta: Sounds like we need an equivalent of the old human genome project – but for every single edible product? Nice, a few hundred lifetimes’ work, if you can get the funding. 

Canto: Well, it suggests that we’ve massively overlooked the complexity of our food – and not only the foods themselves, but their interaction with the microbes and enzymes in our body. But here’s the thing – brace yourself – some nutritionists disagree!

Jacinta: OMG! Scientists are disagreeing?

Canto: The counter-argument is that ‘dark matter’ in nutritional terms is a beat-up. That, though much research is still needed in nutritional epidemiology, in relation to particular conditions and so forth, we know what the essential nutrients are, so the ‘dark matter’, which tends to exist in ultra-minute quantities, would make little difference. But the researcher who coined the term ‘nutritional dark matter’, Albert-Laszlo Barabasi, begs to differ – of course. He points out, for example, that vitamin E, or its absence, can have adverse effects at minuscule quantities, and it may be that all the flip-flopping advice we’re given about nutrition may have much to do with the gaps in our knowledge. Taking garlic again, it was found that of the 67 compounds listed for it on the USDA database, 37 had health effects one way or another, but of the 2306 on FooDB, some 574 had what they called ‘potential’ health effects. In any case, it seems to me that a more complete knowledge of what’s in our food can’t be a bad thing, and will very likely be of benefit in the long run. 

Jacinta: That makes sense, but isn’t everything even more complicated, when you think of how all these nutrients interact with our individual microbiota, and the enzymes that break down our food more or less efficiently, depending on how numerous and healthy they are, which no doubt varies between individuals? 

Canto: Yes, Barabasi and others working on all this ‘dark matter’ are well aware of these complex interactions, but they reckon that doesn’t detract from the need to know much more about this particular component of the food-nutrient-digestion-health cycle. And Barabasi does in fact compare the current state of knowledge with the days before the human genome project, when much DNA was considered ‘junk’. It’s just not a good idea to assume that such a large proportion of nutrients are barely worth knowing about. Let’s return to garlic again. It features quite a lot in the Mediterranean diet, which seems protective against cardiovascular disease. Steak, on the other hand, can be problematic. Our gut bacteria breaks down red meat, in the process producing a compound, trimethylamine, which our liver converts into trimethylamine-N-oxide (TMAO). High levels of TMAO in the bloodstream are linked to heart and vascular problems. But allicin, from garlic, which we’ve mentioned before, and which wasn’t on the USDA database, is known to inhibit the production of trimethylamine, so a diet containing red meat – not too much mind you – can be rendered a wee bit safer, and tastier, with a nice garlic dressing. 

Jacinta: And allicin appears to be an anti-carcinogen too. And luteolin, another component of garlic not on the standard database, is also reported to protect against cardiovascular disease. We love garlic! But what about processed foods. Surely there are all sorts of ways of processing, that’s to say transforming, foods and their component nutrients that won’t show up on the list of ingredients. And how do we know if those ingredient lists are accurate in the first place?

Canto: Well, baby steps I suppose. Cooking, of course, has vital transformative effects upon many foods. And I recall that when you whisk an egg it becomes ‘denatured’ – how transformative does that sound! The more you think about the interaction of foods, with all their barely recognised components, with transformative processes occurring both outside and within our bodies, the more it makes your head spin, and the more you realise that dietary science has a long long way to go. 

garlic cultivars from the Phillippines

Written by stewart henderson

September 30, 2020 at 7:33 pm

reading matters 10

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New Scientist 3244 August 24 2019

Canto: Being dilettantes and autodidacts, we engage endlessly in educational reading, bootless or otherwise, so I thought we might take the effort to talk/write about, and expand on, what we’re learning from the texts we’ve perused, rather than providing ‘content hints’ as before.

Jacinta: Well of course science mags cover a wide range of topics at very various depths, so we’re going to limit ourselves to the ‘cover story’, if there is one. 

Canto: So today’s topic comes from a New Scientist that’s been hanging around for a while, from a year ago, but since quantum theory is more or less eternally incomprehensible, that shouldn’t matter too much. 

Jacinta: Yes I’ve heard of Lee Smolin, and in fact we can listen to many of his online interviews and lectures via youtube, and he’s described as a ‘realist’ in the field, which doesn’t mean much to me at present, but neither of us know much about quantum mechanics, in spite of having read numerous articles on the topic. 

Canto: You probably have to ‘do the math’, as the Yanks weirdly say.  

Jacinta: Well we won’t be doing much of that. The cover story is titled ‘Beyond weird’, and Smolin’s idea is that we need to move beyond quantum weirdness to something more coherent and unifying. He describes current quantum mechanical theory as comprised of two different laws:

The first… describes quantum objects as wave-like entities embodied in a mathematical construction known as a wave function. These objects evolve smoothly in time, exploring alternative realities in ‘superpositions’ in which they aren’t restricted to being in any one place at any one time. That, to any intuitive understanding of how the world works, is distinctly odd. The second law applies only under special circumstances called measurements, in which a quantum object interacts with a much larger, macroscopic system – you or me observing it, for example. This law says that a single measurement outcome manifests itself. The alternative realities that the wave function says existed up to that point suddenly dissolve.

Canto: So both of these laws – and of course I’m in no position to doubt or to verify their mathematical exactitude or explanatory power – make little sense from a ‘common-sense’ or ‘realist’ perspective, in which objects must always be objects and waves waves, and, if objects, they must be in a particular place at a particular time, regardless of anything observed. So it seems perfectly cromulent to me that Einstein and no doubt many others found something incomplete about quantum theory, in spite, again, of its apparently vast explanatory power. Like it was an intellectual placeholder for something more real or coherent.

Jacinta: Well Smolin seems to be one of those dissatisfied physicists, – he mentions de Broglie and Schrödinger as others – pointing out that the two laws are in apparent contradiction, with the second law unable to be derived from the first. The theory also ‘seems to’ violate the principle of locality, in which forces are dependent on distance. Quantum entanglement does away with that principle. So Smolin sees a way out by trying to incorporate gravity into the quantum world, or at least trying to connect the general theory of relativity and quantum theory into a seamless whole, as their current incompatibility constitutes a major problem. General relativity presents ‘a smooth, malleable space-time’, while quantum theory suggests ‘discrete chunks, or quanta, of space or space-time’.  String theory and loop quantum gravity are some of the attempts to bridge this divide, but these are currently untestable theories. Also, apparently general relativity is compatible with our perception of the flow of time, whereas quantum theory is more problematic, an issue which, I think, Gerard ‘t Hooft attempts to address in his essay ‘Time, the Arrow of Time, and Quantum Mechanics‘ . 

Canto: Yes, he feels that time, with its arrow pointing eternally forward, with no need for or possibility of reversibility, must be an essential element of a grand physical theory.

Jacinta: Maybe. He’s saying I think, that any explanation of our world, any theory, is arrow-of-time dependent, as it necessarily involves preceding causes and antecedent consequences. But let’s just stick to Smolin’s article. He argues that both relativity and quantum theory have issues with the conceptualisation of time. And there are problems, such as dark matter and dark energy, which don’t easily fit within the standard model. So he feels we need to go back to first principles, ‘in terms of events and the relationships between them’. So, according to these principles, space is an emergent property of a network of causal relationships through time.

Canto: Well to keep more strictly to Smolin’s description, he has five hypotheses. One – the history of the universe consists of events and relations between them. Two – that time, as a process of present causes and future consequences, is fundamental. Three – that time is irreversible, cause can’t go backwards and ‘happened’ events can’t unhappen. Four – that space emerges from this cause-consequence chain. Five – that energy and momentum are fundamental, and conserved in causal processes. 

Jacinta: Good, and this is an ‘energetic causal set model’ of the universe, as he and others describe it, to which he’s added a sixth hypothesis, derived from ‘t Hooft, which says that ‘when two-dimensional surfaces are defined in the emerging geometry of space-time, their area gives the maximum rate by which information can flow through them’.

Canto: Now that sounds horribly mathematical. I do note that area = space and rate = time, and so this hypothesis somehow marries space-time with information flow?

Jacinta: Yes, it’s all threatening to move beyond our brains’ event horizon here. Smolin says that ‘in this picture’, and I’m not sure if he’s talking about the ‘picture’ derived from the sixth hypothesis or by all six taken together, but ‘in this picture, every event is distinguishable by the information available to it about its causal past’. This he calls the event’s sky, because the sky, or what we see (speaking about horizons) at any one instant, is what he calls ‘a view of its own causal past’. This has to do with the speed of light – we can’t see what we can’t see. And this sixth hypothesis, combined with the first law of thermodynamics, can apparently be used to derive the equations of general relativity, bringing gravity into the picture. 

Canto: I don’t get the laws of thermodynamics.

Jacinta: The first law is about energy used in a closed-system process, which can be transformed in that process but is always conserved. Anyway, we’ll try to quit before we get in too much deeper. We know that there’s a ‘measurement problem’, a problem of causality in quantum mechanics, in which it is said that a measurement, or observation, ‘collapses the wave function’ to define a particle’s specific place at a specific time. This is counter-intuitive, to put it mildly, and highly unsatisfactory to many physicists, because it seems to make a mockery of how we understand causality. It seems to be a long-standing impasse to the unification of the two major theories. So we’ve only described a fraction of what Smolin has to say here, and there’s also the problem of entanglement. In ‘classical physics’ proximity matters in a way that it doesn’t in quantum theory. Smolin describes, or mentions, a lot of work being done on ‘ensembles’ in an attempt to solve this measurement problem.

Canto: I think one of the issues that the ‘realists’ are concerned with, but perhaps deliberately not mentioned in Smolin’s piece, is the many worlds hypothesis, or the multiverse, embraced for example by Max Tegmark in Our mathematical universe. Neil Turok is another skeptic of this apparent solution to the causality impasse. 

Jacinta: Yes, I don’t think Smolin is an embracer of the multiverse, tantalising though it is in a sci-fi sort of way. Of course we don’t have the mathematical wherewithal to give an informed view one way or another, or to know whether mathematical wherewithal is what’s really needed. I’ve heard it said – possibly by Tegmark – that a multiverse fits so neatly with the mathematical equations that we need to accept it against our intuitions, which have been wrong in so much else. I don’t know… we’ll just have to watch with interest this intellectual battleground, and see if anything decisive crops up in what remains of our lifetimes.

Canto: Singular or plural…

Other references

The universe within, by Neil Turok, 2012

Our mathematical universe, by Max Tegmark


Written by stewart henderson

September 12, 2020 at 1:08 pm