*** Appendix - Motifs which describe cellular regulation in bacteria: how flexible are they?

Bacteria exhibit a wide variety of motifs which regulate cell activity. Regulatory switches allow bacterial cells to make an all-or-nothing (on-off) response to internal or external signals. Some cellular switches (like door-bells) lack a memory; others (like light switches) remember their setting. Bistable switches in bacterial cells have a memory and exhibit a history dependence (known as hysteresis): their pattern of responding to variations in the strength of a signal depends on the initial setting of the switch, and they tend to react slowly to changes in the signal value. There is one pattern of responding when the signal increases in strength (a "going-up" pattern), and another when it decreases (a "coming-down" pattern). In each pattern, the switch tends to remain in its current setting until the signal reaches a certain level that makes it suddenly "flip" settings, over a narrow range. These two patterns make up what is called a hysteresis loop - a switching pattern commonly found in ferromagnetic materials. Bistable switches can be set to an "on" or "off" position indefinitely by an environmental stimulus encountered by the cell.

Certainly, the behaviour of a bistable switch can be described using Dennett's intentional stance. It remembers its setting, it resists changes and "tries" to "ignore" random noise within the cell that would cause it to flip continually backwards and forwards between on and off states. (This conservative trait is adaptive, as it cuts out disruptive interference.) Most impressively, it is apparently capable of flexibility: it can change from one pattern of responding (the "going-up" pattern) to another (the "going-down" pattern). Does this change of patterns qualify as flexible behaviour, according to our definition? I would argue that it does not. In fact, the switch is inflexible within a limited range of input signal values, as it resists changes to its setting. Although we can speak of the switch as remembering its old setting, it would be wrong to say that it changes its pattern as its setting fluctuates. We could more economically describe the "going-up" and "coming-down" patterns as part of a single pattern (the hysteresis loop) which is built into the chemistry of the switch. The value of the output ("on" or "off") can be defined a function of two variables: the strength of the current input signal and that of the previous input signal. Together, these two pieces of information tell us whether the signal is "going-up" or "coming-down". Hysteresis in bacterial cells is a time-lag phenomenon, rather than a true case of flexible behaviour.

Another motif in bacterial cells is the biphasic amplitude filter, in which a device amplifies an input signal only if it falls within a specific range. Mathematically, this can be described as invoking a function F to convert an input signal into a new output signal, if and only if the input signal falls within a certain range. A cellular process controlled by the filter can only be initiated by a particular set of circumstances in the cell's environment or within the cell itself. This is a very selective way of responding to environmental inputs, but it cannot be termed flexible, as there is no change in the pattern of response over time.

The same can be said for bandpass frequency filters, which allow bacterial cells to function in a noisy environment by filtering signals within a frequency-domain, extracting information from them and separating them into their component parts. Bandpass filters amplify a signal if and only if it oscillates at a particular frequency. Again, we cannot speak of flexible behaviour here, as the cell does not change its pattern of responding to signals over time.

Other motifs describe the way in which cellular processes, which have to be regulated with precision, are protected from disruptive background noise arising from protein translation. Mechanisms such as negative feedback, redundancy, biochemical cascades, checkpoints and delay elements, as well as frequency filters, serve to ensure that cells can maintain their normal routines. Other motifs actually exploit noise, either by harnessing it to drive an ordered process or using it to amplify a signal. However complex and sophisticated these mechanisms may be, they do not qualify as flexible under our definition.

Bacterial cells also have internal clocks and oscillators that control their growth and enable them to adapt to changes in their environment. Again, while these are highly adaptive, there is no appearance of a new pattern here: all that varies over time is the values of the output and input variables.