Is this paper on quantum propeties of the brain bad science or not?
May 31, 2024 8:30 PM   Subscribe

I have seen a lot of people interested in the idea of quantum consciousness making a big deal of this paper: Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures. And I am not sure if it is good science or says anything especially novel.

I have seen a lot of reactions to it, ranging from Stuart Hameroff saying it is powerful support for his and Penroses's theories about consciousness to people saying the experiment was badly carried out and the results are likely meaningless noise. And I would really like to know where on this spectrum it actually lay. Unfortunately I don't have any background in spectroscopy or quantum physics and so I can't tell who is right. I'd appreciate it if someone with more expertise could let me know what they think.
posted by The Manwich Horror to Science & Nature (11 answers total) 1 user marked this as a favorite
 
Journal is credible. I know a lot about the physics of fluorescence, and am an "expert" on transmembrane proteins and the role that tryptophan plays in their physical chemistry. I'll be reading this in a bit and will chime in again soon.
posted by mr_roboto at 9:16 PM on May 31 [1 favorite]


Best answer: It's not a good paper. Poorly written, and the "connect-the-dots" shit going on in the plots is big-time amateur hour. Some of the text reads a little cargo-culty: they're using very, very, very basic tools and defining them like they should be new to us. There is unnecessary mathematical notation ('∈') that reads like someone has just learned this mathematical notation and is very excited to use it. But this could be a pedagogical choice or writing by an excited new scientist that the PI chose to let shine through. Figure 5 is a fucking trainwreck. Label your panels, dood. Astounding that this was published in this journal.

I don't think the modeling is credible. As I understand it, they're trying to model the collective excitation of the system as coupled dipoles. This is fine, but it's not "quantum". If you wanted to understand the quantum mechanical properties of the system, you'd probably need to use a density functional theory approach, which would likely be computationally intractable for a system of this size. So the modeling is right, but it's probably not relevant to phenomena like superradiance, and would not be expected to capture any relevant effects.

I don't have a deep understanding of superradiance, but I think you need to characterize it with time-domain spectroscopic techniques. They do not do this here. They acknowledge this deficiency (I think it's a critical deficiency?) in the second-to-last sentence of the conclusions section.

Again, I must reiterate how poorly written this paper is. It is very difficult to read. But it seems like the main result is focused around this parameter they call "superradiance linewidth". This is not a standard term and it is not defined in the text of the paper: it appears only on axis labels on the plots. It's very difficult to understand the connection between data and interpretation.

If they were trying to test a hypothesis here, there would be some kind of statistical argument or error analysis. There is none. That makes this work automatically dismissible in my mind, but I'm trying to keep an open heart.

The experiments themselves are trivial. They just bought some commercially available proteins and put them in a couple of standard instruments. There are 10,000 labs in the US that could do this tomorrow. So if the data are *really* important, reproducibility can happen.

Finally, a couple of comments for the implications of this work on quantum consciousness:

This result depends on the interaction of biological matter with light, and the skull is famously opaque.

I used to follow the Penrose stuff and was pretty excited about QM as an explanation of consciousness. If this is the kind of work they're reaching at though. This is pretty sad. It's not even anything. Sometimes you need to go with your gut, and my gut is telling me that if this is all the QM people have, consciousness is probably best explained by complexity.
posted by mr_roboto at 10:41 PM on May 31 [31 favorites]


I have seen a lot of people interested in the idea of quantum consciousness making a big deal of this paper:

That on its own is enough for me to view it with deep suspicion.

Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures

Title has an ultra, a super, and a mega! SCIENCE!
posted by flabdablet at 11:26 PM on May 31 [6 favorites]


Response by poster: Wow, thanks mr_roboto! That was a really thorough analysis. I really appreciate the time you took to read the paper and reply!
posted by The Manwich Horror at 3:42 AM on June 1


I read Penrose's treatise The Emperor's New Mind over 30 years ago when I was still a physics undergrad and, while I learned a lot about Turing-completeness and the like, it was pretty clear to me even then that his main argument amounted to nothing more than "I don't understand consciousness, and I don't understand quantum mechanics, therefore quantum mechanics must explain consciousness!!1!"
posted by heatherlogan at 6:09 AM on June 1 [2 favorites]


Best answer: A few comments from a more biological perspective:

Consider how much UV light is reaching cells other than the exterior-most cells (skin etc.) Environment matters: things that can happen to a protein in a cuvette don't always happen the same way (or at all) to a cell in a dish, let alone a cell in an organ. And several of their "zomg there is previous work connecting light and microtubules" citations are cells in a dish and bacteria - and nothing in this paper involves anything more than freefloating proteins.

Some of the citations are just... weird. That bacteria citation (21), for example, is ostensibly supporting the idea that the centriole (a microtubule bundle) is "the subject of several studies (18−21) examining the cellular orientations to a light stimulus." The citation does not appear to have anything to do with that: it's about bacteriochlorophyll near-infrared autofluorescence in photosynthetic bacteria. Entirely different compound, entirely different biological process, no microtubule connection, and no brain connection for that matter. The cytoskeleton is mentioned briefly, but solely to say "some people worry that using GFP to view things in cells could be a problem, because the wavelength used for exciting it is too close to wavelengths that lots of cellular material (DNA, proteins) absorb energy from; what if we used bacteriochlorophyll as a near-IR fluorescence marker instead?" (Note: this didn't take off as a useful approach.) But I get concerned when I see citations that don't seem to be related to or to support the concepts they're being attached to - even if it's just the result of them sloppily mis-citing something or not really understanding the bio side of things, that's not great.

Almost nothing is experimental: basically, they have some very basic fluorescence data for tryptophan (and some other amino acids), tubulin dimers, and tubulin microtubules. They state "it was not possible for us to prepare solutions with exact concentrations", to which I would unsympathetically suggest that they talk to biologists or chemists (and possibly work with a different vendor), because when you have a single set of experimental data, it's probably important that that data be reliable. And while they're at it, they should get someone to loan them a real quartz cuvette, seriously, and a stopped-flow device or a collaborator with a fancier ultrafast spectroscopy rig to get that time-domain data. As mr_roboto says, that seems like a critical deficiency.

Everything that follows based on a single crystal structure determined ages ago by another group. I do want to highlight that the crystal structure is from bovine tubulin heterodimers (cows) but all their experiments use tubulin from pigs - are they actually interchangeable? Who knows (the authors certainly don't address it) but when you're assuming there are specific numbers of a specific amino acid present and that there are specific distances between tryptophans, it matters. They also computationally build the microtubule from that single heterodimer structure. Why not use actual microtubule structures (porcine ones, even, at various sizes and lattice assembly states?) Unclear, they just cite another paper that did the same, also with little explanation - but to evaluate the biological relevance of their work, you'd want to know whether the simulated microtubule actually is a solid match for the actual structure of the protein they used (from the same species!).

After this, it's all simulations. As mr_roboto points out, there are some real limitations to the kind of techniques they use. Some of their descriptors are not great - they misleadingly describe "Simulations of MT Bundles in Neuronal Axons". No actual neurons are involved. At best, this could be described as "simulations of microtubule bundles at lengths relevant to axons" - though based on Figure 6 that seems a little misleading still since the simulated microtubule lengths seem to be <5>
On the balance: I do want to be clear that I am personally not super qualified to say anything about superradiance or about their computational approaches for anything beyond protein structure. I'm just a protein biochemist, so I could certainly be missing something, particularly on the physical chemistry side. However, the kinds of simulations I run into in my bit of the biochem world (e.g. DFT in an enzyme active site) require high quality data going in and careful design and evaluation - garbage in, garbage out - and some of the weird details in this paper have me worried about the quality of everything pre-simulation. The clear over-hyping also makes me concerned: it's a long way from "we measured some quantum yields and ran some simulations" to claims that superradiance in tryptophan networks "may serve a photoprotective role in pathological conditions such as Alzheimer’s disease and related dementias." And it's a long way from "we ran one set of fluorescence measurements with one protein and ran some sims" to "numerous possibilities for superradiance- and subradiance-enabled metabolic regulation, communication, and control in and between cells." (Some of the stuff in puff pieces you can dig up in the Altmetrics looks even worse, oof.) Hopefully other groups will be able to follow up with some more careful experimental work to explore this and to explore whether this is a phenomenon that can be experimentally observed in actual biological systems. This paper alone, though, seems more like hypothesis generation than "powerful support" for anything.
posted by ASF Tod und Schwerkraft at 12:24 PM on June 1 [5 favorites]


(Mostly) separate from the actual paper:

I want to emphasize that many biological chemicals have a range of chemical features. However, their use in a given biological system may not actually rely on every single one of those features.

Tryptophans do have a bunch of interesting roles in biology. Some of them are completely unrelated to fluorescence: you see a lot of them in transmembrane proteins because they are hydrophobic, and can happily co-exist with the hydrophobic bits of the phospholipid bilayer. They're thus often conserved and conserved in larger numbers in those environments. A second distinctive tryptophan characteristic involves the energetics of "pi stacking", a kind of interaction between certain kinds of chemical rings - like the ones in tryptophan - that can help stabilize interactions within and among biological macromolecules. Again, because of how this works, you can often see "networks" of conserved tryptophan or tyrosine sidechains for this. In some circumstances, tryptophans are useful because they're just really big compared to other amino acids, and that bulk can help position things within a biological macromolecule. They're also involved in electron transfer (more on that in a sec), with chains of tryptophans and tyrosines helping this to happen over longer distances.

In any of those contexts, tryptophan UV absorption and fluorescence is still present and is something we'll be able to observe and manipulate and even co-opt, but it may or may not be relevant to what the tryptophan is actually doing in a natural biological system. So "tryptophan networks are conserved in lots of biological systems" and "tryptophan networks can exhibit weird photochemistry" can both be true, but does not mean that a given tryptophan network in a biological system is going to be engaged in weird photochemistry. Even if we can artificially induce weird photochemistry in that system, it doesn't mean it's what's actually going on in the relevant biological system.

One additional note on tryptophan involvement in redox chemistry: Tryptophans and tyrosine chains are often involved in mediating electron transfer in enzymes - you can get ~direct electron tunneling over distances under 15 Å, but beyond that, you need chemical intermediaries that can stabilize various radical states, and tryptophans and tyrosines can do this well in a protein environment. In enzymes where long-distance electron transfer is needed, you'll see tryptophan/tyrosine networks conserved to mediate this (potentially aided by various non-protein chemicals). Niftily, there's an associated suggestion that many redox enzymes also have additional chains of these residues acting as an escape hatch, a shunt for channeling out reactive species to the surface of the protein when something goes wrong in the active site.

I bring this up partly because it's cool to dorks like me, and partly because the superradiance paper actually has another dubious citation connected to this - they mention "the Trp network as a photoreduction mediator in cryptochrome" as an example of "extended protein scaffolds that harness the symmetries of hierarchical Trp networks to promote biological function." The paper's description of these Trp networks as "hierarchical" is sorta weird and non-standard but seems to be associated with the lattice-based supramolecular assembly of microtubules & their function at various scales (based on Fig. 1 etc.) That's... not at all what's going on with cryptochromes, though. They're a great example of electron/electron hole hopping, happening within a small-ish single-enzyme context and not reliant on any supramolecular symmetry. It's also not really relevant to tryptophan superradiance as far as I can tell: photoactivation is happening at a different chemical group (a flavin cofactor) and plain ol' electrons are getting transferred from a plain ol' biochemical reductant through the tryptophans to reduce the flavin. In this context, it sorta feels like the citation is implicitly misusing a not-quite-related paper & phenomenon to say "see?!?!?!? here's a biological system involving light and tryptophans, so our conclusions must be legit!"
posted by ASF Tod und Schwerkraft at 12:52 PM on June 1 [8 favorites]


ranging from Stuart Hameroff saying it is powerful support for his and Penroses's theories about consciousness
"The project was supported by The Guy Foundation Family Trust." is how the Acknowledgements section begins. this is from one of the Guy Foundation pages:
"It has been said that the brain is not simply a computer system, and as the Nobel prize winning scientist, Roger Penrose has proposed somewhat controversially, it may utilise quantum principles to enable it to process information and generate awareness (Hameroff and Penrose 2014)."
posted by HearHere at 1:56 PM on June 1 [2 favorites]


Response by poster: ASF Tod und Schwerkraft, thank you. I really appreciate that perspective. That is really fascinating stuff about the variety of roles Tryptophan can play in biology. Thanks for taking the time to explain it.
posted by The Manwich Horror at 2:44 PM on June 1


Whoops crappy HTML mangling on one sentence there. Sorry! One of those statements above should have been:
[B]ased on Figure 6 that seems a little misleading still since the simulated microtubule lengths seem to be smaller than 500 nm, i.e. small enough to be in ~every eukaryotic cell, making it unclear why this is being described as specifically axon-related. (The clarity of some of their figures and captions leaves something to be desired.) In any case, simulating microtubule bundles of various lengths and densities is still very different from simulating how things would work for microtubules in actual axons (and if DFT is a problem at the full-macromolecule scale, let me tell you simulating cells is another level of difficulty entirely.)
posted by ASF Tod und Schwerkraft at 4:27 PM on June 1 [1 favorite]


it was pretty clear to me even then that his main argument amounted to nothing more than "I don't understand consciousness, and I don't understand quantum mechanics, therefore quantum mechanics must explain consciousness!!1!"

Crystal clear. And I've yet to see any Quantum Consciousness booster since then offer anything more convincing.

All attempts to explain consciousness via assorted forms of reductionist inquiry involve examining stuff that goes on in the brain at smaller and smaller scales. The trouble with that approach is that pretty much everything that goes on in the brain at cellular scale also goes on in a lot of other structures, and by the time we start to consider molecular scale and smaller, goes on pretty much everywhere.

The other thing that makes this approach essentially pointless is that it will never satisfy those who insist that consciousness is inherently non-physical: any attempt to explain subjective experience by measuring its externally measurable correlates runs into the brick wall of "yes, you've reliably identified some stuff that goes on while conscious experience is also going on, maybe even only while conscious experience is going on, but that doesn't amount to an explanation of conscious experience itself".

This insistence that subjective experience is The Hard Problem and therefore requires a wholly different kind of understanding and/or explanation from any other kind of natural phenomenon is the real problem, and it's one I've personally solved to my own complete satisfaction simply by deciding not to insist on that.

To my way of thinking there is nothing the slightest bit unsound about the idea that "physical correlates of consciousness" are subjective experience as described from outside the particular system having that experience. I don't think there's anything more mysterious or unexpected going on there than the kind of point-of-view shift that accounts for my own inability to see my own face or lick my own elbow.

The way I think of consciousness is as a process characterized by the ongoing synthesis of a world-model from sensory information, that world-model then being used to explore both factual and counterfactual scenarios in order to make, among other things, survival-enhancing predictions about the behaviour of the world. If I have consciousness, as it appears that I do, then I am inevitably going to turn up as a feature of my own world-model. And if I choose not to make a distinction between my self-in-the-world and my self-in-the-model, the nature of my self is inevitably going to collapse into an infinite regress and seem infinitely deep. I think that's all there is to subjectivity, and I don't think that's particularly mysterious.

From that perspective, all the quantum-consciousness microtubule stuff is meaningless noise because all of it addresses a wholly confected problem. To me, it's the same kind of think as astrology or homeopathy. I'm happy that it's fun for those people, but it's not something my own world-model has me expecting to need to take seriously.
posted by flabdablet at 7:58 PM on June 1 [4 favorites]


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