The Decoherence Engine: Reframing Biological Complexity as Quantum Information P

DandelionPheasant

The predominant view in quantum biology sees decoherence as a destructive obstacle that life must overcome. This essay challenges this paradigm. I propose that biological systems are "Decoherence Engines", which have evolved to actively use and structure environmental noise to perform computation. Decoherence is feature - a selection process that collapses vast spaces of quantum possibilities into functional and classical results with unmatched efficiency. I present a new metric, Bio-Quantum Algorithmic Complexity (BQAC), to quantify this process and proposes a new experimental methodology using nitrogen vacancy (NV) central probes to "hear" the real-time computational rhythm decoherence. This structure reformulates the "warm,wet and noisy" cellular environment from a quantum computing obstacle in its essential operating system.

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EmeraldBeetle

DandelionPheasant

The author's initial claim that “This essay postulates a radical inversion of this vision” with respect to de-emphasizing the problem of biological systems maintaining coherence and instead focusing on decoherence effects doesn't appear to me to be 'radical'? It's a position widely covered in the 'Environment-assisted quantum transport' (ENAQT) literature, which the essay doesn't really engage with (although related work is referenced).

The central concept of the “Decoherence Engine” also appears to me to conflate decoherence with ‘collapse’:

"The Decoherence Engine model proposes that it’s a collapse and not a search."

The model for this ‘collapse’ – i.e., actualization of a single outcome from a decohered superposition (the measurement problem) – remains largely unspecified. Selection here is said to depend on a “dynamic field,” i.e., the decohering cellular environment:

The unfolded protein does not “search” for its final state; It’s in a quantum superposition of many possible conformations. Surrounding water molecules, ions and phonons - the “noise” - aren’t random. They form a highly structured dynamic field.

This coherent superposition of protein states is sustained in a 'highly structured' cellular environment which then:

interacts with the superposition, rapidly decohering pathways that lead to non-functional and unstable states, while resonantly stabilizing the way towards the native, functional state. The environment acts as a massive parallel quantum Zeno-like selection mechanism.

The decohered (quasi-classical) superposition of protein states remains a decohered mixture until 'collapse' yields a single empirical outcome per the Born rule. The author suggests, however, that rather than a probabilistic outcome, only the most 'functional' state is selected by its biological environment via a 'Zeno-like' process:

Imagine a quantum system, like an exciton in a photosynthetic complex, in a superposition of pathways. Some roads are more “in tune” with the resonant vibrational frequencies of surrounding protein scaffold. Interaction with these evolved phonons can be sustaining coherence along a specific and eﬀicient energy transfer channel, while decohering less optimal pathways. This is not noise cancellation; It is noise sculpting. The environment becomes a filter, a computational guide wire.

This statement of 'decoherent selection' I find rather confusing. In physiological conditions, coherence in molecules typically decays on femto to picosecond timescales. And more to the point, this rapid decoherence does not eliminate "less optimal" pathways but just suppresses interference between components of the superposition. 'Collapse' is a different mechanism, and environmental decoherence is neutral on how the outcome selection occurs – which is the measurement problem (via spontaneous collapse, Everettian, de Broglie–Bohm etc. interpretations). The essay appears to conflate interference suppression (decoherence) with the actualisation of a single outcome. Decoherence isn't collapse!

My question to the author would then be: By what concrete physical mechanism does the cellular environment “select” a single optimal pathway outcome from a rapidly decohered mixture of possible protein states, given that environmental decoherence merely einselects a quasi-classical pointer basis of protein states without invoking a measurement 'collapse'?

Benz

DandelionPheasant The Decoherence Engine (MD) thesis is a critical step forward, and we strongly agree with its core premise: Biological computation is highly efficient collapse guided by structured noise, not a random search.
The DSRR framework shares foundational synergy with the MD model, and I believe DSRR thesis can offer several solutions and refinements for the experimental and theoretical development of the MD framework:
Points of Fundamental Agreement

Collapse as Computation: We agree that the speed and selectivity of the decoherence process itself is the computational mechanism (e.g., protein folding). This rejects the traditional view of decoherence as mere information loss.
The Structured Medium: We concur that the environment (phonons, structured water) acts as an active, structured filter—the computational hardware—that makes controlled collapse possible.
Economic Principle: Both models operate on an economic principle: MD uses entropy to buy functional certainty. DSRR applies this same principle to perception, asserting that reality is rendered with an economy (the Lost Frames, IF) to conserve informational resources.
DSRR Solutions for the MD Framework
Since DSRR views consciousness as the Meta-Engine managing this local system, we offer the following suggestions based on the νz parameter, which may strengthen the MD's QBP (Quantum Biological Probe) methodology:
Optimization of the QBP Trigger (Faster Collapse)
The MD's QBP test focuses on measuring changes during substrate binding. If νz (Conscious Sampling Frequency) dictates render speed, then modulating the subject's νz during the experiment could optimize the collapse rate:
• Proposal: Introduce a simultaneous high-cognitive load task (measured via MEG/EEG) to the observing scientist or the system interacting with the enzyme.
• Hypothesis: An externally induced high νz state will increase the urgency for functional certainty in the local informational field, leading to a faster, more definitive decoherence in the QBP/NV center measurement than can be explained by the substrate binding kinetics alone. This essentially uses consciousness to 'turbocharge' the MD.
Refinement of the BQAC Metric
The Bio-Quantum Algorithmic Complexity (BQAC) metric is excellent, but DSRR suggests incorporating a term for the Subjective Cost of Focus:
• Proposal: Add a νz factor to the BQAC equation. BQAC = f(…νz …). This term would reflect the informational energy required from the conscious observer to sustain the functional collapse.
• Implication: A system might have high functional complexity, but if the local consciousness can achieve that functional collapse with a low, relaxed νz, the BQAC suggests a highly evolved and efficient coupling between the consciousness and the biological decoherence engine.
DSRR views the MD as the physical implementation layer for the conscious rendering process. Exploring this causal link through controlled modulation of νz offers a direct path to empirically validating the hierarchical relationship between organism-level consciousness and cellular-level computation.

https://doi.org/10.5281/zenodo.17533873

Riddler

Due to errors in the site while submission the references and a typo could not be updated.

Its not Decoration it's Decoherence.

References:-
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Collini, E., Wong, C., Wilk, K. et al. Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature. Nature 463, 644–647 (2010). https://doi.org/10.1038/nature08811

G. Panitchayangkoon, D. Hayes, K.A. Fransted, J.R. Caram, E. Harel, J. Wen, R.E. Blankenship, & G.S. Engel, Long-lived quantum coherence in photosynthetic complexes at physiological temperature, Proc. Natl. Acad. Sci. U.S.A. 107 (29) 12766-12770, https://doi.org/10.1073/pnas.1005484107 (2010).

Rebentrost, Patrick, et al. “Environment-Assisted Quantum Transport.” New Journal of Physics, vol. 11, no. 3, Mar. 2009, p. 033003. Crossref, https://doi.org/10.1088/1367-2630/11/3/033003.

Huelga, S. F., and M. B. Plenio. “Vibrations, Quanta and Biology.” Contemporary Physics, vol. 54, no. 4, July 2013, pp. 181–207. Crossref, https://doi.org/10.1080/00405000.2013.829687.

Jianshu Cao et al. ,Quantum biology revisited.Sci. Adv.6,eaaz4888(2020).DOI:10.1126/sciadv.aaz4888

A Model for Photoreceptor-Based Magnetoreception in Birds
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TY - JOUR
PB - American Physical Society
ID - 10.1103/PhysRevLett.106.040503
DO - 10.1103/PhysRevLett.106.040503
TI - Sustained Quantum Coherence and Entanglement in the Avian Compass
PY - 2011/01/25/
UR - https://link.aps.org/doi/10.1103/PhysRevLett.106.040503
JF - Physical Review Letters
JA - Phys. Rev. Lett.
J1 - PRL
VL - 106
IS - 4
SP - 040503
EP -
A1 - Gauger, Erik M.
AU - Rieper, Elisabeth
AU - Morton, John J. L.
AU - Benjamin, Simon C.
AU - Vedral, Vlatko

TY - JOUR
PB - American Physical Society
ID - 10.1103/RevModPhys.89.035002
DO - 10.1103/RevModPhys.89.035002
TI - Quantum sensing
PY - 2017/07/25/
UR - https://link.aps.org/doi/10.1103/RevModPhys.89.035002
JF - Reviews of Modern Physics
JA - Rev. Mod. Phys.
J1 - RMP
VL - 89
IS - 3
SP - 035002
EP -
A1 - Degen, C. L.
AU - Reinhard, F.
AU - Cappellaro, P.

marcovici alexandru

Riddler
take out - cosmology speculation
Levinthal’s paradox might have something to do with how large numbers are being estimated , in spite of regularity this makes room for rare events to happen suddenly - to apparently be fine tuned in an other essay there was a mention about cyclical universe , a closed rotating universe with starting - annihilating rules that can return to an initial state, might place those historical events in some symmetry group

take for example climate change why it does seems to be counter balanced with the rapid expansive technological evolution

at the structured noise chapter is there is there a way to look for other times beyond/ sideways to thermodynamic
lets call this situation - living time crystals organism

Riddler

marcovici alexandru

Your points on Levinthal’s paradox, cyclical universes, and “living time crystals” converge on a key insight: complexity can generate sudden order within apparent randomness. Levinthal reminds us that vast search spaces do not preclude fast convergence when hidden constraints exist. Similarly, climate and technology may act as coupled variables in a larger symmetry, balancing unpredictably yet systematically. The notion of “living time crystals” is compelling—a biological analogue of non-equilibrium phases that sustain structure while resisting entropy. Exploring such analogies could sharpen our understanding of undecidability in both physics and life.

Anonymous

@EmeraldBettle You’re absolutely right that decoherence is not collapse. My proposal is not a new collapse mechanism, but a biological biasing process. In cells, the environment is not a random thermal bath—it is highly structured and evolved. Hydration shells, ionic gradients, scaffold vibrations, and chaperone proteins couple non trivially to the protein’s conformational space. These couplings do not treat all conformations equally: unstable folds dissipate rapidly, while near-native states resonate with environmental modes that stabilize them. In this sense, the environment shapes the pointer basis and skews the distribution, creating a strongly biased quasi-classical mixture where the native fold dominates. The final “choice” is still probabilistic, but overwhelmingly weighted toward functional states. Collapse remains a foundational question, yet biology leverages structured decoherence as a sieve—sculpting noise into a directional filter that makes functionality the path of least resistance.

EmeraldBeetle

Anonymous Thank you for the clarification wrt 'decoherence vs collapse' – as a nonspecialist I can only work from basic concepts towards your intended 'biological biasing process'. So in terms of the highly structured non‑equilibrium bath that is the cellular environment driving environment-induced selection of relatively stable pointer states, I can understand this intuitively in terms of quantum Darwinism where information about the most stable pointer states is redundantly recorded in the local environment.

As for the 'highly structured' nature of that environment, are you drawing an analogy to qubit 'reservoir or dissipative state engineering' where the idea is that engineered (or here, evolved) environments guide a system towards specific steady or metastable quantum states? The cellular environment (hydration shells, ionic gradients, scaffold vibrations, and chaperone proteins) has evolved to bias quantum dynamics that generally provide an evolutionary advantage in some sense (a selection preference vs less advantageous outcomes). I'm just trying to build a 'picture' of your model from a general informed reader's perspective (i.e., mine!) so please correct me if I'm wandering off in the wrong direction.

The difficulty I have with this picture is the same for many of the quantum coherence proposals submitted so far, and that is that quantum coherence in biomolecules in cell environments apparently decays on femtosecond–picosecond scale (outside of microtubules?), whereas doesn't protein folding occur on a microsecond–millisecond scale? How do you bridge roughly 6–12 orders of magnitude between coherence decay and folding? And given this mismatch, isn't the "quasi-classical mixture where the native fold dominates" more effectively modelled in classical stochastic terms?

DandelionPheasant

@EmeraldBeetle You’re spot on about the coherence–folding timescale gap; no one expects millisecond-scale quantum coherence in warm, wet cells. The idea isn’t a “quantum marathon” but a relay: femto–picosecond coherence windows recur at key junctures (hydration shell fluctuations, scaffold vibrations, chaperone cycles), nudging the conformational landscape before classical stochastic dynamics take over. In that sense, the environment is more like an evolved reservoir-engineered bath—structured noise that recurrently biases folding pathways rather than sustaining coherence throughout. So yes, classical stochastic models remain powerful, but the “pointer basis” they explore may already have been sculpted by these fast, structured quantum–environment interactions.

EmeraldBeetle

DandelionPheasant Ok cool, that 'quantum relay' picture sounds a lot more plausible than some of the other essay narratives submitted so far!

So for your Decoherence Engine model, a protein fold isn't a simple 'one and done' process (which makes sense) but a cascading series of decohering interactions each shaping the next quasi-classical step ... a sort of decoherent ratchet?

Folding is thus mostly classical but punctuated by very short femto–picosecond coherence bursts that quickly decohere in the cellular bath, with each burst slightly reshaping which local conformations are favoured (the 'pointer' states) and then classical dynamics carries the system forward until the next burst.

But this 'decoherent ratcheting cascade engine' isn't actually spelled out in the essay is it? You argue for “collapse not search” and a Zeno-like environment-shaped selection process, which I guess could be framed as a ratchet-like cascade. And the section on the Quantum Biological Probe (QBP) might be a good place to add specific, testable predictions?

If only you had another month to submit an extra 15,000 characters for a new submission! 🙂

DandelionPheasant

Ha! Yes — “decoherent ratcheting cascade engine” actually captures the essence aptly. The Decoherence Engine isn’t meant as a single event but as a temporally distributed process: coherence bursts acting like quantum nudges at critical inflection points, each re-biasing the conformational search space before decohering into the next quasi-classical plateau. Over time, this cascade yields what appears as a smooth, directed classical fold, but beneath it lies a structured sequence of quantum–environment negotiations.

You’re also right — that mechanism wasn’t explicitly formalized in the essay, though the Zeno-like framing hints at it. I like your idea of embedding this in the Quantum Biological Probe section — as testable predictions about transient coherence bursts shaping folding pathways. Will do a follow up essay later.

Ulla Mattfolk

I like this thought of a decoherence engine. it sounds almost like it uses the quantum as an energy source and 'decompose' it? That is something new.

I have also thought of using entropy as such sourcee, so life would be expert on making quantum output coherent? But How?

Congrats to a good essay.
Ulla.

DandelionPheasant

Thank you, Ulla — that’s a perceptive question. The Decoherence Engine doesn’t “decompose” the quantum as an energy source, but rather treats decoherence as a structured information-to-function conversion process. Quantum superpositions contain vast configurational possibilities, but the cell cannot “use” them directly; instead, the environment (the thermal, chemical, and electromagnetic bath) continually measures the system, collapsing local degrees of freedom into classically actionable configurations.

In this sense, decoherence becomes a directional entropy exchange — not energy extraction from the quantum, but energy through it. The cellular milieu shapes the flow of entropy such that random decoherence events bias toward conformations with lower functional uncertainty. This is similar to principles explored in quantum thermodynamics and reservoir engineering, where noise can be harnessed to drive systems toward ordered steady states.

So yes — life may indeed “make quantum output coherent,” not by resisting entropy, but by choreographing it into productive, self-stabilizing cascades.

Ulla Mattfolk

DandelionPheasant say, we have a system containing very efficient enzymes (proteins) as a ringformation (torus) and they are in that bath. the efficiency they show is exactly the flow from quantum to classicality?
In biology we also have many cascades or 'orchestrating' scenarios.

This is similar to principles explored in quantum thermodynamics and reservoir engineering, where noise can be harnessed to drive systems toward ordered steady states. -can you give some exx.?
Ulla.

DandelionPheasant

@Ulla Mattfolk, yes, a toroidal enzyme ring immersed in a fluctuating bath could indeed act as a quantum-to-classical transducer, where catalytic efficiency reflects how well the system channels environmental noise into functionally coherent states.
In quantum thermodynamics, this is analogous to dissipative structure formation — systems like photosynthetic reaction centers (e.g., the Fenna-Matthews-Olson complex, Engel et al., Nature, 2007) maintain quantum coherence long enough to enhance exciton transfer before decoherence stabilizes the reaction path.
Another case is reservoir engineering in superconducting qubits or trapped ions (e.g., Poyatos, Cirac & Zoller, Phys. Rev. Lett., 1996), where controlled noise or coupling to a tailored environment drives the system into non-trivial steady states — even pure entangled ones.
By analogy, enzyme cascades and allosteric networks may operate as biochemical reservoirs that sculpt decoherence — the “bath” is not a destroyer but a sculptor. Evolution may have optimized these feedback loops so that decoherence pathways themselves become the computation.
In short: life’s efficiency might not be despite decoherence, but because of how it exploits it.

marcovici alexandru

reread more takein-outs

the idea of sudden jump/ collapse (reduction)
is it reflect able in geometry ? take for example drawing a line 📐 out of chaos of the body movements , there goes out something simple and understandable lets say it "discrete"/ sharp ( other example the Heaviside step or the dirac delta)

Bio-Quantum Algorithmic Complexity, and thermodynamic costs:

cell with all its quantumness still takes hours to days to do things
are there thermodynamic branches that spans long time periods and large scale objects or this are called paralel universes superposition inteferences

decoherence or cellular moment by moment welding to environment might accidently get welded to things more remoted or large ? 🐈️

-for algorithmic complexity the idea of the shortest fastest -why not slowest longest or other qualities that might be better suited to characterize changing things

side comment
the emerging of adjectives is a language thing , how humans evolved this particular way of being receptive to what they observe

noise keyword
the noise ain't random, could a cell be cut and "this not random noise" teleportated / to see if this noise maintain the functioning of the remaining part, if it cannot be understood at least to be transported , or rephrased , how do you know the noise is not random

DandelionPheasant

@marcovici alexandru
Well put — yes, geometry can indeed reflect the logic of collapse. The “sudden jump” you mention may be seen as the geometric projection of continuous quantum amplitudes into discrete manifolds of observables — a kind of symmetry-breaking inscription in spacetime. When a hand steadies to draw a line, countless micro-chaotic degrees of freedom are integrated into a single coherent trajectory — much like a decohered pointer state.

In bio-quantum terms, these “jumps” are rarely instantaneous in clock time but occur as entropic convergence events distributed over longer thermodynamic trajectories — a slow collapse, if you will. Large-scale biological processes could thus be viewed as temporal decoherence manifolds, where distant correlations don’t form “parallel universes” per se, but long-range, weakly entangled thermodynamic branches that retain faint phase memory.

And yes — the noise isn’t random. Biological noise is structured, carrying hidden correlations that sustain function. If you could “teleport” that structured noise, you’d likely transfer part of the cell’s informational coherence, not its energy — a quantum biological signature, not a signal.

ShockwaveRider

If the wave-function does not collapse, it means logic and humor must express particle-wave duality in a singularity. Note, dualism is self-contradictory, Relativity is self-contradictory, while quantum mechanics are equally accurate and precise whether you assume they're random or fated. My own work indicates, you must transform your mathematics into words, or you will get nowhere.

DandelionPheasant

Hello @ShockwaveRider,
That’s an intriguing synthesis — and you’re right that the language we use shapes the physics we can describe. If collapse is replaced by continuous entanglement, then our models must carry both logic and paradox — much like humor does. The particle–wave duality becomes not a contradiction but a context switch, a linguistic projection of complementary information channels.

Mathematics gives us precision, but it compresses meaning; words restore dimensionality. In quantum information terms, language adds semantic redundancy — a kind of error-correction that keeps interpretation coherent. So yes, transforming equations into words isn’t anti-scientific; it’s an essential translation layer between quantum formalism and human comprehension — the dialogue where the observer re-enters the equation.

ShockwaveRider

Moderation note: Off-topic political rant removed.

DandelionPheasant

Hello Benz
I find the introduction of νz intriguing as a metaphorical bridge between cognitive dynamics and physical collapse rates. While I remain cautious about positing a direct coupling between neural oscillations and molecular decoherence (given the many orders of magnitude separating their characteristic timescales), your suggestion highlights a deeper question: Can informational load modulate local entropy flows?

This is testable in principle through controlled observer–system interaction experiments — perhaps not as “conscious collapse,” but as informational cross-correlation between human state variables (EEG) and decoherence signatures in QBP probes.

In revising BQAC, I could see νz recast as a measure of systemic informational pressure — quantifying how efficiently a biological or cognitive agent channels uncertainty into function.

The DSRR–MD synergy underscores an exciting frontier: mapping the hierarchical continuity between computation, thermodynamics, and awareness.