Phyllotaxis
the spirals are counted, not admired
Concept

Evidence — where it appears

An observation that would have come out differently if the claim under test were false. Several familiar phyllotaxis observations are not evidence in this sense, because every account on offer predicts them equally.

Named by 32 essays across 5 fields — each of them below, with the objects they name alongside it.

Which patterns grow on a ring of circumference 0.80. Modes 2 to 8 have positive growth rates and mode 4 is fastest. Integrating the full equations from a disordered start gives 4 peaks.

What a mechanism would have to show

Every model of phyllotaxis comes with the caveat that reproducing a pattern is not explaining it. That is easy to repeat and hard to make precise. Here it is made precise — a list of what an account of phyllotaxis would have to establish, with each item marked according to whether the models drawn in these essays establish it.

mechanism · Mechanism claims A tree built at an exponent of 3, measured band by band. Six bands of daughter ratio, 300 junctions in each, all from trees built at an exponent of exactly 3 with the same 2% measurement error. The median implied exponent falls from 3.00 at an even fork to 1.58 at a twig, and the share of junctions that have any exponent at all falls from 100% to 53% over the same range. The rule across the top is a single fit over 200 junctions spanning the whole range: 2.85. A mixed sample is safe because least squares already weights by leverage — 42% of it sits in the most symmetric band and 0.06% in the twigs. The sample that is not safe is the one a person can reach.

The band decides the answer

A fit over a whole tree's junctions returns the exponent the tree was built at, even though most of its junctions are from bands that on their own return 1.6. Least squares is already weighting by leverage. The dangerous sample is not the mixed one — it is the one a person can reach.

branching · Exponent The same lattice with no rule in it. A cylindrical lattice at a divergence of 137.826° and a rise of 0.005, built by placing node i at exactly i times the divergence and then displacing each azimuth independently by 0.5°. Its photograph is the photograph of the stem in the figure beside it and its parastichy pair is the same pair. The largest comb mean in it is 0.03 against a sampling band of 0.07, and the readout refuses.

A comb is evidence of a rule

Build the same lattice kinematically — every node at an exact multiple of the divergence, an independent error on each azimuth, no feedback anywhere — and the spectrum is empty. The photograph is identical and the parastichy pair is identical. The comb is not a property of the arrangement.

mechanism · Mechanism claims A lattice with independent errors. The autocorrelation of 759 divergence angles from a kinematic lattice at a divergence of 137.8261° and a rise of 0.005, with 0.5° of scatter on each azimuth. There is no placement rule anywhere in it: node i is put at exactly i times the divergence and then displaced. The only thing that differs between this figure and the control is the structure of the displacement — here, independent errors — that earlier work's control at 0.5° of independent scatter. The largest comb mean is 0.029 against a sampling band of 0.073, and the readout refuses.

A disturbance with a memory

That earlier work's control assumed that a plant's errors are independent from organ to organ, and nobody had tested it. Give the errors a memory — each one a fraction of the last, up to a coefficient of 0.97 — and the comb does not appear. The obvious threat to the result turns out to be empty, and the algebra says why before the measurement does.

mechanism · Noise colour A lattice with an error inherited from the two contact neighbours. The autocorrelation of 759 divergence angles from a kinematic lattice at a divergence of 137.8261° and a rise of 0.005, with 0.5° of scatter on each azimuth. There is no placement rule anywhere in it: node i is put at exactly i times the divergence and then displaced. The only thing that differs between this figure and the control is the structure of the displacement — here, an error inherited from the two contact neighbours at coupling 0.7. The largest comb mean is 0.514 against a sampling band of 0.073, and the readout returns 8/13.

Errors that pass between organs

An organ's neighbours are the ones eight and thirteen places back — that is what a parastichy pair is. So a disturbance transmitted by contact is correlated at exactly the two lags the readout examines, and it does not have to be told them. Driven into a lattice with no rule in it, it returns the counted pair on eight stems out of eight.

mechanism · Noise transport The two combs, in the proportions the rule gives them. The ratio of the second comb to the main one, for a kinematic lattice whose errors are inherited from its two contact neighbours, against how unevenly that inheritance is split. The horizontal line is where the placement rule's own stems sit, at 0.65. Weighted by distance — the coupling a d⁻³ interaction would give, which at this rise favours the 13-neighbour by 1.26 to one because the 13-hop is the shorter — the forgery sits at 1.46, well above the rule. It reaches the rule's value only at about 3 to one the other way, which is a factor of 4 against what distance supplies and in the opposite direction.

What a forgery has to know

A lattice with transported errors reproduces the comb and the pair, so one quantity is left: the two combs' relative strength. Weighted by distance the forgery puts more in the second comb than the first; the rule does the opposite. It matches only if the coupling is turned three to one towards the further neighbour, which no falloff supplies.

mechanism · Noise transport Murray's law and Da Vinci's become one measurement at 12% of radius error on the informative band. Two trees measured the same way: 50 junctions of daughter ratio 0.6–1, 300 replicate samples at each of 15 error levels, one tree built at exactly 3 and one at exactly 2. Each shaded band is the central 90% of the recovered exponents. Both run downward, but the tree at 3 runs down faster — -113σ² against -29σ² — so the two close on each other. At 11% they are still apart; at 12% the bands overlap and one study's answer could have come from either tree; at 20.5% the means cross, and above it a tree built at 3 measures lower than a tree built at 2.

Where three and two become one

Two trees, one built to obey Murray's law and one to obey Da Vinci's, are measured through the same fifty junctions with the same instrument. At twelve per cent of error on each radius the two answers overlap, and above twenty and a half the tree built at three measures lower than the tree built at two.

branching · Exponent error A lattice with an error that repeats every 8 organs. The autocorrelation of 759 divergence angles from a kinematic lattice at a divergence of 137.8261° and a rise of 0.005, with 0.5° of scatter on each azimuth. There is no placement rule anywhere in it: node i is put at exactly i times the divergence and then displaced. The only thing that differs between this figure and the control is the structure of the displacement — here, an error that repeats every 8 organs at period 8, weight 0.7. The largest comb mean is 0.592 against a sampling band of 0.073, and the readout returns 8/10.

A periodicity is not a lattice

Give a lattice's errors a period of eight and a comb appears at spacing eight, on an arrangement with no rule in it. But the partner it names is 10, then 12, then 11, then nothing — an accident of the disturbance rather than a measurement of the pattern. The forgery is caught by reading a second stem, and by nothing else.

lattices · Noise colour Take away the organ eight places back, and the next one goes into the hole. The last 34 organs of a stem at a rise of 0.005, unrolled. The open circle is the organ removed — eight places before the tip. The ring at the top is where the rule puts the next organ with every organ present; the filled mark beside it is where the rule puts it with that one missing. The two are 16.4° apart, against a local spacing of 25°, and the vacancy itself is 22.7° from the undisturbed answer. Nothing else differs between the two runs: same rise, same history, same rule.

The organ that was taken away

Every observable this site has is read off an arrangement that was finished before the reading began, and earlier work here showed what that costs. So remove one primordium from a settled stem and place the next one against what is left. The rule has to answer. The rival account cannot, because in it no organ's position was ever computed from its neighbours.

mechanism · Ablation What the experiment costs, in internodes. The combined sampling band of two autocorrelations falls as one over the root of the sequence length. The difference to be resolved is 0.76 — between noise that arrives before the primordium is placed and noise that arrives after — so the count needed is 56 internodes on a single stem. Every other open question in this collection is priced in tens of specimens.

The test a plant could settle

Every other open question in this collection is priced in tens of specimens, and one of them in a hundred and sixty. This one is priced in internodes on a single stem, and the number is fifty-six — because it is a statistic of one sequence rather than a share of a population.

wrong · Sequence The ratio follows the disturbance, not the rule. The ratio of the second comb to the main comb on stems grown by the placement rule and jostled by seven different disturbances, all at 0.25° of displacement per organ and all on the same rule. Independent errors and errors with a memory return 0.76–0.81, which is the value this site measured for the rule. A periodicity at the smaller parastichy number takes it down to 0.45; errors inherited from the contact neighbours take it up to 1.09, most of the way to the 1.24 a transported disturbance gives with no rule in it at all. So the quantity separates arrangements by how their errors are related, not by whether anything computed the positions.

The ratio was never about the rule

The comb has already been retracted here as evidence that a plant computes its pattern, and one quantity was exempted from the retraction: the ratio of the two combs, which a placement rule and a transported disturbance divide differently. Drive seven disturbances through the same rule and the ratio spans 0.45 to 1.09. The exemption does not hold, and the angle sequence has nothing left.

mechanism · Noise transport What the sequence sees that the scatter cannot. Each point is an ensemble at one amplitude, placed at the scatter it produces. A stem at three quarters of a degree of scatter has a lag-one correlation near zero if its noise arrived after the primordium was placed, and near 0.7 if it arrived before — and no measurement of the scatter can tell those apart. The separation closes above about a degree, because what the other two kinds preserve is the correlation of a lattice.

What a quiet plant is worth

Almost every measurement gets easier as the effect gets larger. This one gets harder — a stem's divergence sequence stops carrying information about its noise at precisely the scatter where the noise becomes obvious. The specimens worth measuring are the ones that look least interesting.

wrong · Survey spec Two combs, at a rise of 0.005. The autocorrelation of 760 divergence angles from one stem held at a rise of 0.005. The filled teeth are the lags at multiples of 8; the open teeth are the second comb, at the same spacing offset by 5. Reading the spacing off the first and the offset off the second gives the pair 8 and 13, which is what the position counter reports for the same stem — from angles alone, with no coordinate anywhere in the calculation.

A disturbance that is not passed on

The disturbance that forges every observable measured here does two things at once — it correlates an organ's error with its contact neighbours', and it hands that error on to be handed on again. Every result about it has been unable to say which half did the work. This is the control that takes the second half away and keeps the first.

mechanism · Noise colour The damage is the sharing; the forgery is the history. Three disturbances of the same size, measured four ways. The two left columns are stems grown by the placement rule and jostled at 0.25° per organ: a disturbance shared between the contact neighbours scatters the lattice by 0.71° against white noise's 0.57°, and one inherited from them — the same sharing, passed on again at every organ — by 0.97°. The two right columns are kinematic lattices with no rule in them at all, where the whole question is what a disturbance can manufacture. The inherited one returns the pair on 8 seeds of 8 with a main comb of 0.205 against a band of 0.073; the shared one, at the same coupling and the same scatter, returns it on 1 and makes a comb of 0.099, which is the band. So sharing an error with the organs you touch does the damage, and only passing it on and on forges the evidence.

The forgery needs a history

A disturbance passed between touching organs manufactures the comb, the second comb and the parastichy pair on an arrangement with no rule in it — which is why the comb stopped being evidence. Give the organs the same correlation with no accumulation in it and the forgery collapses: one seed in eight returns a pair, and the comb is the noise floor.

mechanism · Noise transport What a swelling does to the exponent read from the informative band, by where the swelling is. 50 junctions of daughter ratio 0.6–1, built at exactly 3 and read with no random error, but with one or more radii measured fat. A parent read fat lowers the reading: 1% gives 2.864, 3% gives 2.631, 10% gives 2.075, and at 11.3% the tree reads Da Vinci's 2. Daughters read fat raise it: 1% gives 3.150, 3% gives 3.499; from 8% some junctions have a daughter measured wider than their parent, which no exponent balances, and the line stops. All three radii read fat by one factor return 3.000 at every swelling — the unswollen reading exactly.

A swelling at the fork

A branch thickens where it forks, so a parent measured just below a junction and daughters measured just above it carry three different amounts of the same swelling. A swelling that fattens all three alike moves a fitted exponent by exactly nothing. A parent read one per cent fat moves it by as much as 3.6 per cent of random error on every radius, in a sign known in advance, and a tenth of a radius turns a tree built at Murray's three into one that reads Da Vinci's two with no noise at all. Added to the noise, it does not bring the two rules together any sooner: the two errors do not add.

branching · Exponent error The wander is in the disturbance and not in what a plant lets you measure. Each disturbance measured twice, in the same statistic. On the left, the variance of the block means of the disturbance's own deviates, over blocks of 100, as a multiple of what independent draws would give; on the right, the same quantity for the divergence sequence those deviates produce, over blocks of 128. The left column is what this site measured when it proposed a slow wander as a second observable. The right column is what a botanist would have: a divergence is the difference of two organs' errors, and differencing is exactly the operation that removes power at low frequencies. The disturbance inherited between touching organs goes from ×49.1 — the largest here — to 0.83, which is what independent errors give. The one with a memory in time keeps most of its own.

A difference forgets a drift

This collection proposed a second observable and priced it as free: if a plant's errors are inherited between touching organs, the divergence sequence should carry a slow wander as well as a comb. The disturbance with the largest wander of any built here leaves none at all in the sequence, because a divergence is a difference and differencing is what removes a drift.

mechanism · Noise transport Adding error to carry a fitted exponent back to none, at 12%. At 12% of error on every radius each replicate is refitted with more error added at four levels, and the dots are the means over 300 replicates, the tree at 3 above and the tree at 2 below. Uncorrected they read 2.035 and 1.676. Carried back to no error through the mean points, the tree at 3 reads 2.695 by a quadratic curve, 2.380 by a linear curve, 2.914 by a rational curve; the tree at 2 reads 1.961 by a quadratic one, 1.877 by a linear one, 1.982 by a rational one. The curve carried back is a choice the method does not make.

A correction that keeps the overlap

The duel between a tree built at Murray's exponent and one built at Da Vinci's ended by saying the displacement is the geometry, and that no better estimator removes it. Correcting every replicate by simulation-extrapolation removes 92 per cent of the tree at three's displacement at five per cent of error and 68 per cent at twelve, and the error at which the two means cross leaves the measured range altogether. It pays in spread — the corrected readings are twice as wide at twelve per cent — so the error at which the two trees' intervals overlap does not move. Of the duel's two numbers, the inversion was the estimator's and the overlap is the question's.

branching · Exponent error Both statistics, on the same stems, at a rise of 0.005. Five seeded stems at each disturbance, held at a fixed rise. Bars are how many returned the pair the position counter finds; open portions are refusals. The pair comes out from 0.1 to 0.25, and across that whole range the lag-one correlation of the same sequences is -0.33, -0.58, -0.59 — decisive, negative and flat. There is no trade between the two: one stem supplies both. Below the window the sequence has locked onto the sampling grid and is a cycle rather than a sample; above it there is no lattice left, at 117° of scatter.

What a refusal does not say

The readout can decline for four different reasons — too quiet, too disturbed, too fast, or a window in the wrong place — and a stem that returns nothing does not say which. That is the third time this thread has failed to close the mixture problem, and the first time the failure has a shape.

wrong · Survey spec Through the rule, the drift survives and the inheritance still does not. How much of a divergence sequence's variance survives being averaged over blocks, on stems the rule grew. The vertical quantity is B² times the variance of the block means divided by the variance of the sequence, which is one at every block size for independent errors — the arithmetic is normalised for a differenced stream, since a divergence is the difference of two organs' errors. A line that climbs is a sequence with power at frequencies below one per block. The disturbances that remember the last error climb to 46 at a block of 64. The ones inherited between touching organs do not climb at all — 1.51 and 1.90 at the same block — although their own deviates carry ×— and ×— an independent stream's variance in exactly this statistic. What they do instead is dig a hole: at block sizes of 8 and 13, which are the offsets they couple at, the statistic falls to 0.06 and 0.12.

What the rule does to a drift

A placement rule was supposed to leave no slow wander in a divergence sequence, because its errors are corrections rather than inheritances. Driven by a disturbance that drifts, it leaves a larger one than a lattice with no rule in it at all — while cutting the per-organ scatter by more than half. The rule removes what is relative between neighbours, and a drift is not.

mechanism · Noise colour Measured radii against the tips each branch carries, at 12% of error on every radius. One replicate of a 50-junction tree, 101 segments, every radius measured with 12% of relative error and drawn against the number of tips that segment carries. The count has no error in it, so the slope is not displaced: the tree built at 3 gives a slope of 0.3404, an exponent of 2.937, and the tree built at 2 a slope of 0.5071, an exponent of 1.972. On the same measured radii the junction-by-junction fit reads 2.218 and 1.736.

A count carries no error

Fitting r₀ᵏ = Σrᵢᵏ junction by junction puts a measured radius on both sides of every equation, and at twelve per cent of error a tree built at Murray's three and one built at Da Vinci's two stop being told apart, however the fit is corrected. Fit the same measured radii against the number of tips each branch carries instead — a count, which nobody measures with error — and the two trees read 2.996 and 1.997 at twelve per cent and 3.015 and 2.001 at thirty, never overlapping. The twelve per cent belonged to the junction fit, not to the tree. The count fails in its own way, and the way is stated.

branching · Exponent error A periodicity reports a different partner every time. eight kinematic lattices, differing only in the seed of their disturbance, each read by the same instrument. The disturbance repeats every 8 organs at a weight of 0.9: it puts a strong comb at spacing 8 — 0.75 against a band of 0.07 — and the partner it names is 8/10, 8/12, 8/11 across the 8 stems and never 8/13, which is what the position counter finds in every one of them. There is no placement rule in any of these arrangements.

The control a survey would need

A comb no longer shows that a plant computes its pattern, so the survey this site has been specifying for a long time has to change. What it loses is its headline; what it gains is a measurement a botanist can actually make — six requirements, four of them already in the specification, and a quantity nobody has ever reported.

wrong · Control spec The next organ moves for the last 13, and for no others. One row per organ removed, counted back from the tip of a stem at a rise of 0.005 whose counted pair is 8 and 13. Removing any of the last 13 moves the next organ by 2.6° to 167.6°; removing an older one moves it by at most 0.47°, which is under the azimuth grid. The boundary is at 13, and 13 is the larger parastichy number — so the experiment counts the spirals without measuring an angle.

An experiment a needle could run

For eight instalments the outstanding item has been a survey — photographs, a protractor, hundreds of specimens — and it has not been done. The intervention is a different kind of ask, and a cheaper one: a needle, one apex, and a yes-or-no per ablation. Here is what it would cost, what it would settle, and the four ways it could come out.

wrong · Ablation The exponent read from a tree that has lost tips, tips lost one at a time. The 50-junction tree built at 3 and at 2, 12% of error on every radius, 300 replicates of loss and measurement at each level. Shaded: the central 90% of the exponent read against the tips still there. Dotted: the mean read against every tip ever grown. Solid: the junction fit's mean over the junctions that survive. The count's two intervals are still apart with 70% of the tips gone, reading 2.366 and 1.576, and overlap by 80%. The junction fit's intervals overlap by 20%. At the heaviest loss drawn, 90%, the scars still read 2.998 and 1.997.

A count that has lost tips

Radii read against the tips each branch carries keep Murray's three apart from Da Vinci's two where junction fits cannot, because a count has no measurement error in it. A count of the tips a tree has is not a count of the tips it grew. Losing them lowers both trees' readings by one factor that belongs to the losses and not to the rule, so the count stops being right long before it stops telling the trees apart: on fifty junctions at twelve per cent of error, to seventy per cent of the tips lost one at a time, and only to about a quarter lost in whole limbs. Counting scars repairs single losses exactly. Nothing countable repairs a shed limb.

branching · Exponent error Which arrangements carry a comb, and what each one reports. The largest comb mean in five arrangements at a rise of 0.005, all read by the same instrument at the same length, with the sampling band of 0.073 marked. Only the first is a placement rule; the other four are kinematic lattices with no rule in them, differing from one another only in how their azimuth errors are structured. Independent errors and errors with a memory leave nothing to read. A repeating error puts up a comb and names a partner that is not the lattice's. Errors inherited from the contact neighbours reproduce both the comb and the pair.

The comb was never the rule

A control is only as strong as the alternative it builds, and the earlier work built one that varied the rule while holding the disturbance fixed at independence. Five rounds of the angle-sequence thread, with what each claimed and what still stands — and why the next evidence has to come from an intervention rather than from a longer stem.

cylinder · Noise transport

The survey loses its second outcome

The survey specification written earlier here names three results the survey could return, and the second — a ratio near or above 1.30, read as evidence against the placement rule — is the one that would have been worth publishing. It does not survive the measurements here. The ratio moves with where the plant sits between two transitions, and it moves again with the colour of the plant's own disturbance.

wrong · Survey spec

The order belonged to the method

A residual was left over after the two width laws, and it looked ordered: the most crowded fraction gave the widest dip, in all three families, in the direction a measurement artefact would take. Measured again with an instrument that has no level in it, the order changes with the window, disagrees between families, and in one of them comes out backwards.

wrong · Second statistic

The ablation a plant would survive

The intervention proposed earlier returns a spiral count from a yes-or-no answer, needs no protractor, and was specified at one rise. Measured across the ladder it acquires three conditions a real experiment would have to meet — and one of them is that the plant must not be too coarsely patterned, or nothing will go wrong at all.

wrong · Survey spec

A count set by a delay

An L-system describes a plant and forbids nothing, because none of its parameters is anything a plant has. One branching grammar is the exception: a mature apex makes a new bud every season, and a bud waits d seasons before it branches. Its counts grow at the root of x^(d+1) = x^d + 1, a delay of one season gives Fibonacci's numbers and nothing else does, and the fourth count already separates a one-season wait from every longer one. So a Fibonacci count in a branching plant is a measurement of how long its buds wait. It is also a fragile one: if one bud in ten waits two seasons instead, eleven counts in a row come out Fibonacci's three times in a thousand.

branching · Lsystem

The second statistic was the first

The experiment this collection has been specifying was priced as two readings off one sequence, the second of them free. The two readings turn out to be one function looked at twice, so the specification loses a statistic — and gains a cheaper one, a warning about how observables get priced, and a question it could not previously ask.

wrong · Survey spec

Matching instead of correcting

Two rounds of work failed on one question because every instrument's free parameter was set by the thing under test. The repair was not a better instrument or a model of the bias: it was choosing what to compare so that the confound could not vary. That move is available in four other places here, and three of them have already used it without anybody naming it.

wrong · Instrument ceiling

Six bands, one table

Every rung of this ladder that carries a handover now has a band grown on it and cut at every rise it holds, and four accounts of which bands change their answer are scored on all six at once. The survivor is right on every band that can test it, and the same table read one cell differently kills it.

cylinder · Rung interior

The coarse design scored

Every claim this thread has made about an uncut band rests on a sample of nine rises, and its record was the argument for trusting it. Six whole bands close that record, and two of its six correct verdicts are correct only because there was nothing on those bands to find.

cylinder · Rung interior

Named alongside it

The objects these essays reach for when they reach for this one.

Honest limitsDiscriminationMeasurementNull modelAutocorrelationIdentifiabilityFalsifiabilityMeasurement errorNoiseParastichy pairSample sizeArtefact

All concepts