BioLogic

Louis H. Kaufman, UIC kauffman@uic.edu www.math.uic.edu/~kauffman

What is the relationship between logic and biology?

Classical Aspects: Self-Reference, Recursion, Imaginary Values. Symbols and reproducibility of symbols. Separation of object and reference.

The Non-Locality of Impossibility

will converge to one of the roots when the roots are real, b convergence when the roots are imaginary. Nevertheless, this K 34,1/2 eigenform are very closely related to the complex solutions, an a conceptual center for the investigation of these relationship 136 We end this section with one more example. This is th fractal (Kauffman, 1987). In this case, one can symbolica equation
Figure 3. Geometric conguration of the re-entry

The Framing of to indicate that the Koch Fractal re-enters its own indicationa ding m Imaginary Space. nite
Figure 4. Recursion corresponding to the Koch eigenform which leads to the innite self-reecting eigenform (Koch snowake fractal)

K K{K K}K

orm tal)

made up of four copies of itself, each one-third the size of brackets in the center of this equation refer to the fact that the the fractal are shown. To the eye, the last stage vividly illustrates to the another and with inclined with respect how one Five stages of recursion are ideal fractal form contains copies. Figurefour copies of itself, each one-third the size of the whole.conguration of the re 3 shows the geometric The abstract schema K recursion, each line segment at a given In the geometric K{K K}K for segments of one-third its length, arranged according to linethis fractal itself can be iterated to produce a skeleton of the geometric recursion:
Five stages of recursion are shown. To the eye, the last stage vividly illustrates how the ideal fractal form contains four copies of itself, each one-third the size of the whole. The abstract schema

Fixed Point and Self-Replication

about the With the

A = AA this interpretation we would With this interpreta =

Hence form. manner, we may solve the equation for J crossed form. of boxe by an infinite nest =
crossed

reentering

reentering mark. But we about the reentering

mark, taken allmark the reentering by

= =

...

...

his form of the solution, layered like an onion, the = entire infinite form = (all by itself) (all ational space. It is indeed a solution to the equation

Church-Curry Fixed Point Theorem gx = F(xx)

gg = F(gg)

Building Machine B,x B,x X,x

(x is the blueprint for X) Let b be the blueprint for B. Then B,b builds itself. B,b B,b B,b

Indicative Shift A Then #A BA

After

"HVF"

A refers to B.
"#HVF"

Before
HVF

Suppose that M #. Then #M #M. self-reference And if g then #g F#, F#g. Godelian self-reference

M #M

# #M

Self Reference occurs at the Shift of the Name M of the Meta-Naming Operator #. I am the Observed link Between myself And Observing myself. (Heinz von Foerster)

In a Nutshell: Rx ---------> xx then RR---------->RR

So far, this is the story of the classical logic of self-replication and self-reference. We know that DNA engages in self-replication. How does the DNA self-rep compare with our familiar self-replication at the level of logic and recursion?

abstract form of DNA replication.

DNA consists in two strands of base-pairs wound helically ar backbone. It is is a Self-Replicating Form of these Wa DNA customary to call one separated in vivo, strands thebeing new duplex DNAs. Each strand, nds its complement the other the Crick built naturally are AT (Adenine and Thymine)the well-known topological C The strand. inAbstractly we can write (Guanine and base pairs the environment. This picture ignores and GC
4

the other the occurs locally and Crick strand. Abstractly we can write propagates. Local sectors of separation can amalgamate larger pieces of separation as well. DN A =< W |C > Once the strands are separated, the environ to can provide each the two strands into the single DNA duplex. the base of the cellsymbolize the binding of with complementary bases to formReplication pa occurs via the separation of the two strands via polymerase enzyme. This separation new duplex DNAs.and propagates. Local sectors ofin vivo, nds amalgamate into Each strand, separated separation can its complement occurs locally built naturally in the environment. Once the strandsignores the well-known topolo larger pieces of separation as well. This picture are separated, the environment of present to the each with complementary bases to form strands. dicultiesthe cell can provideactual separation of the daughter the base pairs of diculties sine). Thus if present to the actual separation of the daughter strands.

DNA replication loops

then < W strands into the single DNA du to symbolize the binding of the two| =< ...T T AGAAT AGGT ACGCG...| |C >= |...AAT CT T AT CCAT GCGC... > . then occurs via the separation of theoversimplify the whole process as > . |C >= |...AAT CT T AT CCAT polymerase enzym Symbolically we can two strands via GCGC... Symbolically we can occurs locally and propagates. oversimplify the whole processof separation can Local sectors as < W W++ E <W |C|C >= DN A < | | E < W >= DN A larger pieces of separation as well. Once the strands are separated E |C >< W >= DN A E complementary A of the cell can provide each with + + |C><W |C|C >= DNbases to form < W |C >< W | + E + |C >=< W |C >< W new duplex DNAs. Each<strand, separated environment, |C > nds its c in |C >< a > W |C >< W | the help of >=< Wvivo, W |C full DNA. Either half of the DNA can, with + E + |Cthe become We can the DNA can, W | be a symbol for the process by which thebecome a full D let E |C >< with the help of the environment, environment built naturally in Either environment. This picture ignoresCrick strands. the half of the complementary base pairs AG, T C to the Watson and the wellsupplies We can let E |C >< W | be a symbol for the process by which the environ Self Replication Schematic diculties present to the complementary base pairs AG,ofCthe daughterCrick str supplies the actual separation T to the Watson and stran
topo I topo II DNA topo II DNA
Figure 1 - DNA Replication In logic there is a level beyond the simple copying of symbols that contains a non-trivial description of self-replication. The (von Neumann) schema is as follows: There is a universal building machine B that can accept a text or description x (the program) and build what the text describes. We let lowercase x denote the description and uppercase X denote that which is described. Thus B with x will build X. The building machine also produces an extra copy of the text x. This is appended to the production X as X, x. Thus B, when supplied with a description x, produces that which x describes, with a copy of its description attached. Schematically we have the process shown below.

The base pairs are AT (Adenine and Thymine) and GC (Guanine and Cytosine). Thus if < W | =< ...T T AGAAT AGGT ACGCG...|

DN A =< W |C >

DNA = <Watson|Crick> The base pairs are AT (Adenine and Thymine) and GC (G E = Environment sine). Thus if
< W | =< ...T T AGAAT AGGT ACGCG...| |C >= |...AAT CT T AT CCAT GCGC... > .

then

Either half of the DNA can, with the help of the envir full DNA. We can let E |C >< W | be a symbol which the environment supplies the complementary base p 7 Watson and Crick strands. In this oversimplication we environment as though it contained an already-waiting st The base pairs are AT (Adenine and Thymine) and GC (Guanine and with < W Cytosine). Thus if | and an already-waiting strand < W | to pair wi In fact it is the opened strands themselves that command the < W | =< ...T T AGAAT AGGT ACGCG...| mates. They conjure up their mates from the chemical soup Then |C >= |...AAT E is CCAT GCGC... > . The environment CT T ATan identity element in this algebra Symbolically we can oversimplify the whole process as background and can be tion. That is, E is always in the spontaneously |in E < W |Cbetween Watson and Crick: the cleft >= DN A <W + < W |C >< E + |C >< W |C >= DN A

W ||C >< W |E|C >

Either half of the DNA can, with the help of the environment, become a full DNA. We can let E |C >< W | be a symbol for the process by This is the formalism of DNA replication. which the environment supplies the complementary base pairs AG, T C to the Watson and Crick strands. In this oversimplication we have cartooned the Compare contained an already-waiting strand |C > the environment as though itthis method of replication with to pairmovemen with <building already-waiting strand < W | to pair with |C > . W | and an machine supplied with its own blueprint. Here In fact it is the opened strands themselves that command the appearance of their

< W |C >< W | + E + |C >=< W |C >< W |C >

< W ||C >< W ||C >< W |C >< W |

( < W | and |C > ) are each both the machine and th

There is not space here to go into all these relationships, but the Russell paradox will give a hint of the structure. Let ab be interpreted as b is a member of a. Then RX = (XX) can be taken as the denition of a set R such that X is a member of R exactly when it is not the case that X is a member of X. Note the repetition of X in the denition RX = (XX). Substituting R for X we obtain RR = (RR), which says that R is a member of R exactly when it is not the case that R is a member of R. This is the Russell paradox. From the point of view of the lambda calculus, we have found a xed point for negation. Where is the repetition in the DNA self-replication? The repetition and the replication are no longer separated. The repetition occurs not syntactically, but directly at the point of replication. Note the device of pairing or mirror imaging. A calls up the appearance of T and G calls up the appearance of C. < W | calls up the appearance of |C > and |C > calls up the appearance of < W |. Each object O calls up the appearance of its dual or paired object O . O calls up O and O calls up O. The object that replicates is implicitly a repetition in the form of a pairing of object and dual object. OO replicates via O OO O OO whence OO O O OO OO .

paradox. From the point of view of the lambda calculus, we have found a xed point for negation. Where is the repetition in the DNA self-replication? The repetition and the replication are no longer separated. The repetition occurs not syntactically, but directly at the point of replication. Note the device of pairing or mirror imaging. A calls up the appearance of T and G calls up the appearance of C. < W | calls up the appearance of |C > and |C > calls up the appearance of < W |. Each object O calls up the appearance of its dual or paired object O . O calls up O and O calls up O. The object that replicates is implicitly a repetition in the form of a pairing of object and dual object. OO replicates via O OO O OO whence OO O O OO OO .

The repetition is inherent in the replicand in the sense that the dual of a form is inherent in the form.

ntainertwo brackets of the container as representatives for the regard the DNA =<> .

ched DNA strands. We let the extainer E =>< represent the cel ronment with its supply of available base pairs (here symbolized by vidual left and right brackets). Then when the DNA strands separate, ounter the matching bases from the environment and become two DN

brackets= <> < E container DNA DNA. DNA of the > <><> = as represen itself is We let the search and learn nds. about systems thatenvironment. andE =>< rep E is the extainer become. Perhaps a bol like E =>< with is replaced bythat EE =><>< produces conta E the property ><.base pairs (here ts retains its own integrity in conjunction with the autonomy of <> and supply of available If <> is a container, A) could be a step toward bringing formalism to life. ight brackets).><Then when the DNA str then is an extainer. These concepts of concatenation of extainers and containers lead, in Sec hing approach tofrom=theofenvironment and b bases the structure and generalizations of the Temp <><> < >< > o a new
>< >< = ><><

algebra. In this Section we discuss how projectors in the Temperley bra can be regarded as topological/algebraic models of self-replica we take this point of view to characterize multiplicative elements P o

= <> < E > <><> = DNA D

problem. with H. There is e projective space associated The classical world is known through our biology. a In this sense product of complex is the foundationB only one superposition of H. biology vectors A, for physics. He also separated the parts gle state |v > with itself.

the bracket into the bra < A | and the ket |B > . Thus

of

Dirac [5] introduced the bra -(c)-ket If a quantum system>= twoB for the superposition the ket |B > is identied with distinct states |v > and while of states. notation < A |B has A the vector B H, In this interpretation, A, ner product of complex>, then it has B H. many also separated the > +b|wof where a and |w vectors innitely He states of the form a|v parts > < numbers taken Thus the bra < Ab < complex the as the > up to common multiple. States are space in is regarded ket |B element dual e bracket into the bra|are A | and A |B >=<. A | a|B > to A in the dual really H . The

< A |B >=< A.| Thus acket into the braA< A | and thequantum information viewpoint is the notion of the ket |B > |B > key concept in the

dual element to A corresponds to the Formalism one superposition the vector transpose the projective space associated with conjugate only of a Quantum H. There is the vectorAB of H, while s interpretation, thestate|B|Bwith expressed in conventional language by the matrix is identied with single product > itself. A, and the inner< ket > is A | |B > A |v >=< a < A | is regarded as[5]is a elementbra B isto column vector). Having H . The A in the dual space the product A theDirac|Bthe identied dual introduced since -(c)-ket notation < A while this interpretation, B (which > is scalarthe with theavector B H, |B >= A B for separated ket inner ket, of complex conjugate element | to regardedtheproduct Dirac dual vectorsin thedual He alsoH . The the |parts AB . In the is Aand as the element the to A A,the ket-bra separated B theofvector bra corresponds to can write B H.transpose >< of = |A A e bra < A space the bracket into the bra < A | and the ket |B > . Thus al element to A corresponds expressed in istranspose Anot the vector by we matrix d the conventional notation, the conjugateconventional language and thehave the inner product is to the ket-bra a matrix, of a scalar, and the inner product a scalar since B < P column vector). Having separated ct A following formula for the square of Aa = languageB | :the matrix B (which is is expressed in conventional |A >< > is |B >=< A | |B by

oduct A B (which is In this interpretation, the ket |B > is identied with separatedB H, while a scalar since B is a column vector). Having the vector ra and the ket, Dirac write the ket-bra |A >< B | = AB . B = AB >< e bra and the ket, Dirac can can write the ket-braA |Athe dualIn | H . The . In the bra < A | is regarded as the element dual to in space 2 ntional notation, dual ket-bra to><matrix,matrix, not (Btranspose A=< B vectorP. nventionalnotation, >< B ||Ais A corresponds toathe conjugate scalar, theof the|Ahave the the element a is = not scalar, and A)AB P = |A the ket-bra B | a A(B A)B = a we have and we > owing formula for A, square inner = |A >< B | :>< conventional language by the matrix ing formula for the andsquare product =expressed inB | : the the of P of P is |A
Having separated the bra and the ket, Dirac can write the ket-bra |A >< B | = AB . In P 2 = |A >< B ||Aconventional A(B A)B = (B A)AB =< B |A > P. and we have the >< B | = notation, the ket-bra is a matrix, not a scalar, P 2 = |A >< the square B = |A>< 2 following formula forB ||A ><ofP |= |A >< B | :B |A >< B | P 2notation|A >< |A| = A(B A)B = B |A > P. B |A > P. = |A ><B ||A > have =< B we B >< B| =< (B A)AB =< Dirac product A B (which is a scalar since B is Written entirely in Dirac notation we have a column vector).

itten entirely in Dirac notation we have

= |A >< B ||A >< B | = A(B A)B = (B A)AB =< B |A > P.

Written entirely a ket-bra P we have The standard example isin Dirac notation= |A >< A| where < A |A >= 1 so that P 2 = P.==< BP is B projection matrix, B>< B |Ato theB| | 2 >< B |A |A ||A= B| =< ||A |AP. = |A >< >< subspace of H that P 2 Then ><> a|A P>< |A >< B|B=>< projectingB |A >< B |A > | is spanned by the vector |A >. In fact, for any vector |B > we have

en entirely 2in |A >< B ||A >< B | = |A >< B |A >< B | P =

e standard example is a ket-bra P = |A >< A| where < A |A >= 1 so that = P. Then P is a projection matrix, =< B |A > |A >< B| =< B |A > P. that projecting to the subspace of H

P=< standard> |A| |Ba>= |AP><B >< A| whereA |B > |A > that |B >= |A >< A >< B| =< |A |A >=< < A |A >= 1 so . The B |A example is ket-bra = A |B > P.

P 2 = |A >< B ||A >< B | = |A >< B |A >< B | =< B |A > |A >< B| =< B |A > P.

The standard example is a ket-bra P = |A >< A| where < A |A >= 1 so that P 2 = P. Then P is a projection matrix, projecting to the subspace of H that is spanned by the vector |A >. In fact, for any vector |B > we have

Sum over Paths (Possibilities)

If {|C1 >, |C2 >, |Cn >} is an orthonormal basis for H, and Pi = |Ci >< 12 Ci |, then for any vector |A > we have
|A >=< C1 |A > |C1 > + + < Cn |A > |Cn > . Hence < B |A >=< C1 |A >< B |C1 > + + < Cn |A >< B |Cn > =< B |C1 >< C1 |A > + + < B |Cn >< Cn |A > =< B | [|C1 >< C1 | + + |Cn >< Cn |] |A > =< B | 1 |A > . We have written this sequence of equalities from < B |A > to < B |1 |A > to emphasize the role of the identity n Pk = n |Ck >< Ck | = 1 k=1 k=1 so that one can write

P |B >= |A >< A | |B >= |A >< A |B >=< A |B > |A > .

=< B | [|C1 >< C1 | + + |Cn >< Cn |] |A > =< B 1 |A =< B || 1 |A > .> .

We have written this sequence of equalities from < B |A > to < B |1 |A > t mphasize the role of the identity = n |Ck >< Ck | = 1 n Pk k=1 k=1
so that one can write

We have written this sequence of equalities from < B |A > to < B |1 |A > to emphasize the role of the identity

that one can write

< B |A >=< B | 1 |A >=< B |n |Ck >< Ck ||A >= n < B |Ck >< Ck |A > . k=1 k=1

n Pk = n |Ck >< Ck | = 1 k=1 k=1

B |A >=< B | 1 |A >=< B |

In the quantum context one may wish to consider the probability of startin state |A > and ending in state |B > . The square of the probability fo If there are intermediate states between the intermediate states this formuis event is equalcan be|continued |A > |2summing over all possiblerened if we have mor < B until one is . This can be paths from A lation to nowledge. If to B. This becomes the pathone can go from amplitudeCiB|A >= 1, , n) an it is known that integral expression for the A to < (i . om Ci to B and that the intermediate states |Ci > are a complete set o thonormal alternatives then we can assume that < Ci |Ci >= 1 for each

In the quantum context one may wish to consider the probability of starting in state |A > and ending in state |B > . The square of the probability for this event is equal to | < B |A > |2 . This can be rened if we have more knowledge. If it is known that one can go from A to Ci (i = 1, , n) and n from Ci to B and that the n intermediate states |Ci > are a complete set of k k k=1 orthonormal alternatives then we can assume that < Ci |Ci >= 1k=1each i for and that i |Ci >< Ci | = 1. This identity now corresponds to the fact that 1 is the sum of the probabilities of an arbitrary state being projected into one of these intermediate states.

|C >< C ||A >=

< B |Ck >< Ck |

 < W | |C >< W | |C > < W |C >< W |C > Here is the form of intermediate state expansion. < B |A > < B | |A > < B | 1 |A > < B | k |Ck >< Ck | |A > k < B |Ck >< Ck |A > . We compare E = |C >< W | and 1 = k |Ck >< Ck |. That the unit 1 can be written as a sum over the intermediate states is an expression of how the environment (in the sense of the space of possibilities) impinges on the quantum amplitude, just as the expression of the environment as a soup of bases ready to be paired (a classical space of possibilities) serves as a description of the biological environment. The symbol E = |C >< W | indicated the availability of the bases from the environment to form the complementary pairs. The projection operators |Ci >< Ci | are the possibilities for interlock of initial and nal state through an intermediate possibility. In the quantum mechanics the special pairing is not of bases but of a state and a possible intermediate from a basis of states. It is through this common theme of pairing that the conceptual notation of the bras and kets lets us see a correspondence between such separate domains.

Quantum Formalism and DNA Replication

5.2

Quantum Copies are not Possible

Finally, we note that in quantum mechanics it is not possible to copy a quantum state! This is called the no-cloning theorem of elementary quantum mechanics

theme of pairing that the conceptual notation of the bras and kets lets us see a correspondence between such separate domains.

5.2

14

Quantum Copies are not Possible

Finally, we note that in quantum mechanics it is not possible to copy a quantum Theorem. state!Proofa of is called thestate we needIn unitary mappingquantum process quantum mechanics This the No Cloning no-cloningorder to have aofUelementary theorem make copy of a quantum a : H H [13]. H H where H proof: vector space such that there is a xed state Here is the is a complex
|X > H with the property that U (|X > |A >) = |A > |A > for any state |A > H. (|A > |B > denotes the tensor product |A > |B > .) Let T (|A >) = U (|X > |A >) = |A > |A > . Note that T is a linear function of |A > . Thus we have T |0 >= |0 > |0 >= |00 >, T |1 >= |1 > |1 >= |11 >, T (|0 > +|1 >) = (|0 > +|1 >)(|0 > +|1 >). But T (|0 > +|1 >) = |00 > +|11 > . Hence |00 > +|11 >= (|0 > +|1 >)(|0 > +|1 >) = 2 |00 > + 2 |11 > +|01 > +|10 >

From this it follows that = 0. Since and are arbitrary complex numbers, this is a contradiction. 2 The proof of the no-cloning theorem depends crucially on the linear superposition of quantum states and the linearity of quantum process. By the time we reach the molecular level and attain the possibility of copying DNA

Hence |00 > +|11 >= (|0 > +|1 >)(|0 > +|1 >) = 2 |00 > + 2 |11 > +|01 > +|10 >

From this it follows that = 0. Since and are arbitrary complex numbers, this is a contradiction. 2 The proof of the no-cloning theorem depends crucially on the linear superposition of quantum states and the linearity of quantum process. By the time we reach the molecular level and attain the possibility of copying DNA molecules we are copying in a quite dierent sense than the ideal quantum copy that does not exist. The DNA and its copy are each quantum states, but they are dierent quantum states! That we see the two DNA molecules as identical is a function of how we lter our observations of complex and entangled quantum states. Nevertheless, the identity of two DNA copies is certainly at a deeper level than the identity of the two letters i in the word identity. The latter is conventional and symbolic. The former is a matter of physics and biochemistry.

17 the Dirac notation of bras and kets where Dirac takes an inner product written in the form < B|A > and breaks it up into < B | and |A > and then makes projection operators by recombining in the opposite order as |A >< B |. See the earlier discussion of quantum mechanics in this paper. Each left or right bracket in itself makes a distinction. The two brackets are distinct from one another by mirror imaging, which we take to be a notational reection of a fundamental process (of distinction) whereby two forms are identical (indistinguishable) except by comparison in the space of an observer. The observer is the distinction between the mirror images. Mirrored pairs of individual brackets interact to form either a container C = {} or an extainer E =}{. These new forms combine to make: CC = {}{} = {E} EE =}{}{=}C{. Two containers interact to form an extainer within container brackets. Two extainers interact to form a container between extainer brackets. The pattern

On the Mathematical Side { }

and

wo containers interact to form an extainer within container brackets. Two C = {} xtainers interact to form a container between extainer brackets. The pattern f extainer interactionsextainer regarded as a formal generalization of the bra or an can be nd ket patterns of the Dirac notation that we have used in this paper both E =}{. or DNA replication and forforms combine of make: These new a discussion to quantum mechanics. In the quanum mechanics application {} corresponds to the inner product < A |B >, a CC = B |, a matrix that does not ommuting scalar, while }{ corresponds to |A ><{}{} = {E} ecessarily commute with vectors or other matrices. With this application in and mind, it is natural to decide to make the container an analog of a scalar quanEE =}{}{=}C{. ty and let it commute with individual brackets. We then have the equation

Two containers interact to form an extainer within container brack EE =}{}{=}C{= C}{= CE. extainers interact to form a container between extainer brackets. Th of extainer interactions can be regarded as a formal generalization o y denition thereIt is natural to the Dirac notation that we have used in this p will be no corresponding equation for CC. We adopt the and ket patterns of make the container xiom that containers commute withand for elements in of quantum mechanics. In for DNA analog of a scalar quantity replication other a discussion this combinatorial algethe ra. Containers and extainers are distinguished by this to the inner Containers tum mechanics application {} corresponds property. product < ppear as autonomous and make while }{ corresponds to |A Extainersmatrix that entities and commute with commuting scalar, itcan be moved about. >< B |, a are open necessarily individual sensitive or their surroundings. At appl commute with vectors to o interaction from the outside and are brackets. other matrices. With this this mind, it the basis for the to make the container an earlier parts oint, we have described is natural to decide formalism used in the analog of a sca tity and let it commute with individual brackets. We then have the f this paper. EE =}{}{=}C{= C}{= CE.

18 If we interpret E as the environment then the equation }{= E = 1 expresses the availability of complementary forms so that {} {E} {}{} becomes the form of DNA reproduction. We can also regard EE = {}E as symbolic of the emergence of DNA from the chemical substrate. Just as the formalism for reproduction ignores the topology, this formalism for emergence ignores the formation of the DNA backbone along which are strung the complementary base pairs. In the biological domain we are aware of levels of ignored structure. In mathematics it is customary to stop the examination of certain issues in order to create domains with requisite degrees of clarity. We are all aware that the operation of collection is proscribed beyond a certain point. For example, in set theory the Russell class R of all sets that are not members of themselves is not itself a set. It then follows that {R}, the collection whose member is the Russell class, is not a class (since a member of a class is a set). This means that the construct {R} is outside of the discourse of standard set theory. This is the limitation of expression at the high end of the formalism. That the set theory has no language for discussing the structure of its own notation is the limitation of the language at the low end. Mathematical users, in speaking and analyzing the mathematical structure, and as its designers, can speak beyond both the high and low ends. In biology we perceive the pattern of a formal system, a system that is em-

Simplest Replication

cut

Topological Replication

25 innitely many deformations of the identity, each giving rise to a factorization via cutting the deformation in half, and each giving rise to distinct elements P in the multiplicative Temperley Lieb algebra that have the property P P = P.

Why the topological self-rep worked.

A

B P = AB

BA =

B = A

BA = I
Figure 2.3 - P = AB, BA = I.

26

Cut[M] = BA

A P = AB

Figure 2.4 - Constructing a new P with P P = P. It is quite fascinating to note that this solution to the nature of elements P with P P = P depends crucially on a combinatorial and topological view of the algebra. In Figure 2.5 we have illustrated how to take such an element and, by pairing maxima and minima, write it as a product in the standard generators Uk of the Temperley Lieb algebra. Here Uk consists of a paired maximum and minimum with the minimum connecting upper strands k and k + 1 (ordered from left to right), and the maximum connecting lower strands k and k + 1. The remaining strands proceed from top to bottom. While it is easy to obtain sucn a factorization, it is a dicult problem to characterize

The Algebraic Realm

27

P = AB

20
U5 U4 U6

U3 U5 U7 to [15] where this point of view is used to create unitary representations of that U2 U4 U6 U8 algebra for the context of quantum computation. Here we see the elemental U5 U7 nature of this algebra, and how it comes about quite naturally once one adopts U1 U6 a formalism that keeps= track U3 U5 U7 U2 U4 U6 U8 U5 U7of boundaries that underlie the of the structure U1 U6 P U5 U4 U6 mathematics of set theory.- Writing P as a product of standard generators. Figure 2.5
but we should it The Temperley of another paper, a collectionTpoint outislines. isCutting atodeformationthe a commutative ring k Lieb algebra of Lparallelthatan possible generalize of algebra over n element I to I , k to and element P AB with generators {1,Igeneralobtain 2 , to the Un1=}BAandmultiplicative=elements in the U1 ,solution factorization I of nding allan relationsgives the U an ..., problem
k k k

To go to the complete solution from the hints given here will be the subject

Temperley Lieb algebra with P P = P. A modication of this approach yields a characterization of all elements Q with QQ = r Q for some positive integer r. The basic structure behind this classication is the meander, a simple closed 2 curve in the plane that has been bisected by a straight line. Here we have i i illustrated the concept with an open meander consisting in a cutting of a

U = U ,

Ui Ui1 Ui = Ui , Ui Uj = Uj Ui , |i j| > 1,

where is a chosen element of the ring k. These equations give the multiplicative structure of the algebra. The algebra is a free module over the ring k with basis the equivalence classes of these products modulo the given relations. To match this pattern with our combinatorial algebra let n = 2 and let

associated with it, and hence there is an inverse to the mapping P . We dene Q(X) for X a legal parenthesis structure, to be the result of replacing each pair < > in X by < A| |A > where A denotes a specic letter chosen for that pair, with dierent pairs receiving dierent letters. Thus Q(<<>>) =< a| < b||b > |a > . Note that in the case above, we have that Q(P (C)) is isomorphic to C.

Protein Folding

c a

b d

a e

e e

b c c

bd

Figure 3 - Secondary Structure < a| < b| < c||c > |b >< d||d > |a >< e||e > A chain C is said to be a secondary folding structure if P (C) is legal and Q(P (C)) is isomorphic to C. The reader may enjoy the exercise of seeing that secondary foldings (when folded) form tree-like structures without any loops

L =< a| < b||a > |b > . Note that P (L) =<<>> is legal, but that Q(P (L)) = Q(<<>>) =< a| < b||b > |a > is not isomorphic to L. L is sometimes called a pseudo knot in the literature of protein folding. Figure 4 should make clear this nomenclature. The molecule is folded back on itself in a way that looks a bit knotted.

B A A

B B

Figure 4 - A Tertiary Structure - < a| < b||a > |b > With these conventions it is convenient to abbreviate a chain by just giving its letter sequence and removing the (reconstructible) bras and kets. Thus C above may be abbreviated by abccbddaee. One may wonder whether at least theoretically there are foldings that would necessarily be knotted when embedded in three dimensional space. With open ends, this means that the structure folds into a graph such that there is a knotted arc in the graph for some traverse from one end to the other. Such a traverse can go along the chain or skip across the bonds joining the paired sites. The answer to this question is yes, there are folding patterns that can force knottedness. Here is an example of such an intrinsically knotted folding.

32

Cell Self-Assembly Arising From a Substrate of Rules and Interactions

Figure 5 - Proto-Cells of Maturana, Uribe and Varela In the course of time the catalysts (basically separate from one another due to lack of bonding) become surrounded by circular forms of bonded or partially bonded substrate. A distinction (in the eyes of the observer) between inside (near the catalyst) and outside (far from a given catalyst) has spontaneously arisen through the chemical rules. Each catalyst has become surrounded by a proto-cell. No higher organism has formed here, but there is a hint of the possibility of higher levels of organization arising from a simple set of rules of interaction. The system is not programmed to make the proto-cells. They arise spontaneously in the evolution of the structure over time. One might imagine that in this way, organisms could be induced to arise as the evolutionary behavior of formal systems. There are diculties, not the least of which is that there are nearly always structures in such systems whose probability of spontaneous emergence is vanishingly small. A good example is

invented by a group of researchers at MIT in the 1970s (The Gosper Group). It is highly unlikely that a gun would appear spontaneously in the Life board. Of course there is a tiny probability of this, but we would guess that the chances of the appearance of the glider gun by random selection or evolution from a random state is similar to the probability of all the air in the room collecting in one corner. Nervertheless, the gun is a natural design based on forms and patterns that do appear spontaneously on small Life boards. The glider gun emerged through the coupling of the power of human cognition and the automatic behavior of a mechanized formal system. Cognition is in fact an attribute of our biological system at an appropriately high level of organization. But cognition itself looks as improbable as the glider gun! Do patterns as complex as cognition or the glider gun arise spontaneously in an appropriate biological context?

Could the Glider Gun Arise Spontaneously?

Figure 6 - Glider Gun and Gliders

Other Examples

Topological Processes

DNA Recombination

Tangle Model: Ernst & Sumners, 1989

42

Kauffman & Lambropoulou

~
K
0

~
K
1

~
K
2

~
K
3

~
K
4

Figure 28 - Processive Recombination with S = [1/3]. Lets see what the form of the processive recombination is for an arbitrary sequence of recombinations. We start with O = [a1 , a2 , , ar1 , ar ] I = [b , b , , b , b ].

39 and semantics. Cognition gives rise to the possibility of design, measurement, communication, language, physics and technology. In this paper we have covered a wide ground of ideas related to the foundations of mathematics and its relationship with biology and with physics. There is much more to explore in these domains. The result of our exploration has been the articulation of a mathematical region that lies in the crack between set theory and its notational foundations. We have articulated the concepts of container <> and extainer >< and shown how the formal algebras generated by these forms encompass signicant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalism for protein folding and the Temperley Lieb algebra at the foundations of topological invariants of knots and links. It is the mathematicians duty to point out formal domains that apply to a multiplicity of contexts. In this case we suggest that it is just possible that there are deeper connections among these apparently diverse contexts that are only hinted at in the steps taken so far. The common formalism can act as compass and guide for further exploration.

Summary:

References
[1] R. J. Baxter, Exactly Solved Models in Statistical Mechanics, Academic Press, 1982. [2] H.P. Barendregt, The Lambda Calculus Its Syntax and Semantics,North Holland, 1981 and 1985.