Bio-Electronics

* See also Era_Computers
* See also The_Thinker
* See also Rapture_Computers
* See also Era_Electronics
* See also McClendon
* See also Bioluminescence
* See also Technologies in Rapture
* See also Computer_Oddities
* See also Historic_Tech_Timeline
Need More Diagrams to illustrate for this wall of text
Bio-Electronics did not exist when Rapture was built, and didn't come about until ADAM-Tech had grown sufficiently. So WW2 Era Electronics with only some fewer augmentations were available in the Construction. That still included tubes, including CRTs and TV imaging tubes for remote control operations. Computers are minor factor at that point as they are little more than huge calculators.
Another Kind of "Bio" Shock - An Early/Earlier Computer Revolution :
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Bio-Electronics ...
It is still not gonna be your 'smartphones' and 'tablets'. But even simple computer smarts/logic can solve problems that hampered certain mechanisms/processes ( like simple Automation ), or could replace far more complicated mechanical solutions ( and thus can lower costs and make some things cheaper/easier/more-possible to produce ).
That includes basic devices we have today ( which were Science Fiction in the 1950s/even 1960s ) which USE miniature Computers/Control-logic/Transistors for various appliances and tools : miniature TVs, TV Cameras, TV Monitors, digitized data, primitive computer terminals, complex automatic controls, etc ... Rapture existed back when Vacuum Tubes were STILL largely the mainstay of the Real World's electronics.
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Bio-Electronic Idea Summary :
The Possibility : Nerve cells can do similar logic operations to tubes/transistors/ICs. ADAM can genetically manipulate tissue/cells, so a result : organic computer components ( and miniaturized far from what was available 1940s - 1950s - even in the 1960s ). Note - Artificial Intelligence requires a huge amount of processing ability, so miniaturization, mass production ( masses of circuitry required for the complexity needed ... ) would move computers towards that goal. Real (living) nerve tissue can self-organize ( in useful ways), so that is another component for achieving the computing scale needed for 'The Thinker' 
(( Even if it was just a simulation of intelligence -- AND not being anything close to Sapience -- Which BTW, WE 60 years later still have Not gotten anywhere close to, in our Real World. )) 
You can still mix in more conventional technologies ( like copper wires and transistors ) to interface outside of this 'organic computer', and many things being controlled can still employ vacuum tubes and relays. 
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A Major Bio-Electronics Breakthrough Came :
Electron Microscopes ( used in medical research ) were in use ( we saw them repeatedly in the Solo games ) for various ADAM related research. Electron Microscopes employ a vacuum to contain the viewed subject, allowing scanning by an electron beam.
Vacuum is a Semi-Conductor ( as used in real Vacuum Tube Electronics ). Similar development had been started 100 years ago with glass Vacuum Tubes.
Thus an important element for the Bio-Electronic revolution in Rapture was the discovery of a Semi-Conducting effect seen on some ADAM test specimens ( observed while IN an Electron Microscope ). The potential electronic use was realized by McClendon, who was at the time attempting to improve miniaturization of his Electronic products ( transistors had been invented/produced on The Surface by that time, but were large, temperamental and expensive ).
McClendon's further research/development discovered that living nerve cells, if treated/modified properly, could act as Electronic Diodes and Transistors, Logic Gates -- and that this could be done at a VERY small scale. Additionally, they could be GROWN and guided into useful circuit patterns which each normally took many dozens of discrete (individual) conventional components.
This technology was what McClendon had been looking for.
To allow for reasonable technical developments for Rapture, the Story/Lore should be : that McClendon (and others) immediately investigated ADAM for its possibilities very soon after its discovery ( Which would also posit that it was not kept secret for any length of time by Tenenbaum ).
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Since I Don't Like "Wave of the Hand" Fiction : 
The timeframe/timeline for Rapture's Bio-Electronic Tech development needs to be started as early as possible, and with similar research to be going on with conventional electronics ( including Transistors ) and even well before that ( ie- McClendon ) during the War and before - possibly with experimentals which had not been realized because of various Surface World (historic) limitations.
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Why 'Sea Slug' Nerve Cells Are Used For The Neuristor Bio-Electronics :
Sea Slugs were extensively researched as part of scientists ADAM developments ( and many were collected which were wrong type ).   Chemicals to get the cells/tissue to assume certain shapes/geometries required for 'circuit building' had already been researched/developed.
http://www.sciencephoto.com/media/348066/view
Their Nerve cells are Larger in size ( easier to see/make modifications during research - also easier to interface more normal electronics to (need to interface/connect to electric circuitry ).
http://www.imec.be/ScientificReport/SR2009/HTML/2010/afbeeldingen/SR043F2.jpg
Simpler function, more robust than human cells.  Conditioning of them was researched as part of Sea Slug 'domestication' efforts.  Genetics simpler than higher lifeforms, simplifying the many genetic/physiological manipulations to make their Bio-Electronic use 'workable'.
http://www.sciencephoto.com/media/348086/view
Reacts in more predictable ways to ADAM chemistry manipulation ( the ADAM-containing secretion is thought to serve as a toxin stunning the Sea Slugs 'prey' in the Ocean ).  The 'Baking' operation requires forcing cells to absorb certain metallic chemicals to turn them into transistor-like circuitry.
http://www.sciencephoto.com/media/348076/view
Educational Film shown to Rapture students - 'Our Mr Sea Slug', with a narrator who sounds strangely like Orson Welles ...
http://www.bio.brandeis.edu/lismanlab/images/Dentate-CA3-circuitry.gif
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'ADAM-Effect' -- Use of ADAM in Rapture's Bio-Electronics Technology :
Uses the Original genetic patching-effect to allow cells to form to carry out their Analog/Digital circuitry process ( use of genetic/physiological "promoters" and "inhibitors" for the specific types of tissues used ).
Stem cells are un-formed, but will adopt genetically-guided specific forms for required tissue. The cell differentiation will largely be done before the main production process to 'culture' all the different types of cells involved. Specific genetic patterns create cells of types used to form or support the formation of the bio-electronic functional units. For this use the cells do not have to be Human.
First - to help control the nerve tissues employed, to hold it in an unformed/untriggered state until placed into the substrate. 
Second - to be carefully/specifically manipulated to grow into the structure and connections/interconnections/bindings required for the desired electrical/logical functioning. This include guided training/formation of those 'nerve' connections for certain types of logic. 
Third - is for very specific changes to the tissue needed to be ( structurally and chemically ) made to take place at specifically triggered times in the production process, to build up the composition which is frozen later ( a process that converts the living cells into inorganic circuitry ). That transformation can lead to the cells being 'unstable' at the end of the formation, but the living tissue is quickly destroyed in a conversion to the final form the circuitry takes - locking in its structure and function -- and then no longer being under any mutatable 'ADAM-effect'.
This would have to be done en masse to have practical costs. This would be Bioelectronic Automated Production Processes being equired for component replication for consumer products.
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How Plausible is Bio-Electronics ? :
It has to be asked : Is this any more complicated than the fabrication processes used to build Integrated Circuits in the Real World ?? If so, why not just simply use those ?? The Bio-Electronic technology (here detailed) physically would use fairly crude precision detail fabrication ( only fractions of millimeters ) versus modern Real World photo-lithographic fabrication ( micro-meters/nano-meters ) which took decades of time and money and the genius/work of many ( starting in 1958 ) to develop ( literally with far more people's development work/genius being involved than the whole population of Rapture ). 
The Biological aspect is the Rapture contexts Sci-Fi Shortcut -- Here assuming complex genetic intra-cellular manipulations were possible. Those are similar ( and perhaps simpler ) to what was needed for a Plasmid's physical Human body changes, and similar in intricacy to the Tonics manipulations of natural cell/tissue functions. 
As mentioned elsewhere, the Bio-Electronic circuitry is still fairly bulky ( compared to modern micro-electronics ), and is still required to be interfaced with 50s-era technology. But it gains in that the nerve cell mechanisms can each do logic functions otherwise requiring MANY discrete components, so it gains back a significant compaction/logic-density factor. With that, a breadbox sized computer can do what a 1950s large mainframe could do ( BTW, your smartphone today does far more processing than a 50's mainframe ). The tech was the equivalent or somewhat better than the transistorized/small-scale-integrated computers built for missiles developed in the Real World starting in the 60s. 
Why hasn't this kind of technology used in our Real World ? ( Before now, when there now is some basic Bio-Electronic technology actually being developed, which does 'leverage off' current micro-electronic technologies/methods ) ?? It is because the tools and 'material' and knowledge of the Rapture Story's GENETIC Manipulation in Rapture ( and used for the fictional Plasmids/Tonics ) do NOT exist in the Real World -- We even now are only now beginning to understanding the biological mechanisms involved with Stem-cell activation ... The Helical molecular structure of DNA itself was not known until 1953, and any significant manual manipulations of genes was decades off. Suchong mentions a 'gene sequencer' when talking about Tenenbaum's genius, but that (real) technology took til the mid 1970s to exist ( and that is just for READING DNA sequences, NOT for assembling/modifying nucleotide sequences ). Today they barely can change a simple cell's structure and function via DNA changes.
The overlap of Bio-Electronics from that other ADAM genetic technology -- making use of similar tools/materials/knowledge/skills/methods already helps ( in the MMORPGs fiction ) to shorten/accelerate the logic/computer-technology's development progress. The re-use of existing natural processes of nerve cells was fundamental for this, as even today, they still know very little about how nerves and particularly brain cells really work, and certainly NOT of how to recreate them genetically or otherwise. 
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Knowhow/Tools Useful for Developing this Bio-Electronic Technology :
Information discovered through Rapture's general ADAM research, which did fairly complex things genetically with cells, and methods to 'trigger' cell growth and gene activation.
Electron Microscope - used to see into cell structures, and the process to make sample preparations required for the Electron Microscope. This led to similar manipulations used in the 'Baking' and Mineralization Processes used to form the Bio-Electronic type tissues/components.
Cell Culturing - controlled cell growing and possibly 'cloning' of the types of cells used. If the different cells can't be 'cloned' then they need to be obtained from existing tissue sources. 
Ion Transistor - Ion-conducting Polymer ( Real World Thingee ) :
Many organic chemicals can be 'polymers' - chains of assembled simpler molecules. Conduction is with fairly high resistence.
Organic-based Electronic Ion Pumps used to stimulate nerve cells with a controlled release of neural-transmitters. In the Rapture-verse, something like this would be used for training cells for Rapture's Bio Electronics ( while they are still alive ). 
Used for Miniature Components able to put 'stimulation' with pinpoint accuracy ( putting tiny amounts of chemical in exact locations within the Bio-Electronic substratum being constructed ).
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What are the difficulties for this Technology -- Really ? ( and therefore making it improbable to work ) :
* Natural signal processing function still working AFTER the Process that changes living tissue into an inert form.
* Getting the internal formations/structures formed within cells ( particularly conductors and insulators ) -- WHERE you need them, and NOT being where you don't want them.
* Semi-conductors/conductors being formed from chemicals introduced, which the (circuit forming) living tissues might find increasingly toxic - various metal ions and high concentrations of the polymer chemicals that form the semiconductors, and similarly nonconductors of sufficient concentration ( to block appropriate voltage passage ).
* Cell structures being large enough to Conduct/Switch the currents/voltages required, and Semiconductors with large enough areas/volume to Control an adequate signal, and then with Insulation thick enough to function ( all particularly when 'organic' Semiconductors typically require higher voltages and external circuitry - and can only be so sensitive ).
* The Feedback mechanism to grow the cells in desired/right pattern to make connections in response to 'training' stimulus ( weak electric current cues ). This actually would have to make use of multiple support cell types, which are required to function (Correctly) long enough in the 'training', and then to be 'burned away' later in the fabrication process. 
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 Super Miniature Circuitry Done Another Way :
Rapture's Bio-Electronic technology would have to made WITHOUT the use of the advanced (modern) Micro-Photo Lithographic techniques ( optical masking done usually with ultra-violet reactive substances to block vapor/sputter depositing/doping/etching ) currently used to assemble small micro-electronic circuitry (ICs). Those belong to a VERY complicated massive set of advanced technologies, unlikely to be accomplished in Rapture - they took decades and innumerable engineers working for big companies ($$$) funding their development in the Real World (( This isn't Fantasy Infinite BS, where such things happened with the wave of a hand and on a writer's ignorant whim )). 
Rapture could Use to advantage living nerve cells, which have natural self-forming mechanisms ( with some clever guidance ), to do micro manipulations which were too-crude/impossible otherwise.
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Bio-Electronics - The Use of Biological Mechanisms to Form and Function as Electronic Circuitry :
Typical Nerve Cells - with cell bodies around 10 microns ( micro meters - 1,000,000th meter ) are actually bigger than today's common microelectronic component details ( ~10 nanometer - 100,000,000th of a meter ), but have parts ( the small filaments, axon and dendrite connections ) of that size and smaller, and functions magnitudes more complex than any single transistor/logic gate.
Smaller Nano mechanisms have been theorized ( even down to using individual atoms as mechanical lever/lock 'features' ), but have problematic construction issues. Whereas biological mechanisms already have much of their functionality already naturally existing ( ie- self forming, and redundant structurally ), saving a GREAT DEAL of work (time and money) to develop.
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Better Electronics Through Genetics (or NOT) :
The idea of these Real World modules are similar to the Bio-Electonic 'Stacks' ( edge wired substratum layers with external pin interface ), which would make up Rapture's Computer components, and plugged into a socket on a electronic chassis.
A whole mass of circuitry would be tied together internally, where their internal weak electrical (interconnected) signals don't need to be amplified ( just like modern computers ). 
Similar modules to these REAL pictured ones could be done for more basic circuits ( but still would significantly improve typical circuit density ). They could be used (as an example) for standard AMPLIFIER circuits - they would be one modular component instead of an ungainly handful of discrete components. Modular units are easier to maintain/replace for repairs ( You don't have to be an electronics technician to fix as many things ).
Such standardized 'modules' would be something Rapture would be built using ( mass-produced, they would be cheaper - which if you hadn't noticed was a big thing with Ryan ). Figure that some tasks for New Rapture will be scrounging up such standard components to get things working again.
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"Slugnals" -- Signals between bits of Sea Slug brain used in the early experiments attempting to produce usable electronic functionality ( the original Research was for the physiological control of Plasmids ). It was pretty quickly determined that LIVING tissue just could NOT be stable, even when it could be 'trained' in more complex functions. A clue was taken from an early incident which originally got McClendon's attention - Tissue prepared to be viewed in an Electron Microscope ( which operated in a vacuum ) required preparation by Freezing the specimen, and having metal vapor deposited upon it. 
Suchong actually consulted with McClendon about Plasmid 'control' issues ( that is AFTER several rather messy incidents resulting in self-immolations and castrations ), this giving McClendon a more 'inside' access to developments he required for his subsequent Bio-Electronics work.
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The Electron Microscope ( Some are seen in Rapture ex- in the Inner Persephone Infirmary )
When invented ? Prototype Electron Microscope existed in 1931, and the Scanning Electron Microscope 1937.
A useful tool for the Bio-Electronics tech development ( for genetics, not so much for looking at genes which are too small, but more for looking at the results of genetic changes have made to cells/tissue - which ALL the ADAM technologies are based upon ).
I've contrived a story about how the Bio-electronics got started - someone noticing odd effects on prepared microscope materials ( usually vapor coated with gold to see surface features ) being looked at by an Electron Microscope ( Which is done with the specimen bombarded by Electrons in a vacuum chamber ). Word got to McClendon about some strange effects seen and HE was one who - could realize the potential of what was being seen.
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Neuristor  (Bio-Transistors) one of those Great Rapture Technological Feats :
The electronic Synapse & Axon - the making of.
Engineering the Technology was greatly short-cutted by utilizing existing biological mechanism (nerve cell structures) instead of creating it from scratch ( largely impossible genetically a).  (( Just about all genetic engineering done EVEN TODAY is still just recombining existing genetic material. ))
Made possible by ADAM manipulation of cell genetics to do a process of growing/forming the desired semi-natural nerve structure groupings of cells to do the complex electronic function required for the computing/logic ).    This would be outgrowth of Plasmid research, which modified human body structures ( which is much more complicated and harder to do In Situ ).  It would(should) initially have been based around Sea Slug nerve cells, which got ALOT of investigation in Rapture ( as you might expect ).
Real Nerve Cells interconnect potentially with hundreds of other cells with very small fibers ( features which could only be partially fabricated in the Real World 40 years later ).  Inducing natural nerve cells to form grids to facilitate useful logic interconnects was an early achievement ( child's-play compared to making Bees (or whatever) come out of your hands ).
This technology uses the natural 'learning' nerve feedback, shaping/training the arrays of cells while 'alive' to build/shape/force the desired interconnection 'logic' to process binary/analog input patterns in complex ways, which generate expected 'programmed' outputs ( thus computing the desired useful logic functions ).
Then there would be 'baking' process to fix the function permanently into a post-biological circuit, after 'doping'  conductive chemicals (like metal ions) so the cell structure will function electronically afterwards.   The 'baked' cell functions would then operate using normal transistor/electronic physics in a pattern similar to the original 'trained' living neuro-functioning cell.   Electronic signals going into the circuit are processed and appropriate electronic signals then come out of the circuit.
Finding a way to translate/convert the natural cell into working electronics was the 'trick' and once that was found all kinds of opportunities became possible.  ADAM modified the cell's genetics to form useful interconnections and train easily, and to then be triggered to start absorbing various chemicals which on 'baking' would make the 'fixed' cell function electronically.   The natural cell's inbuilt/original 'learning' mechanism was not needed, so THAT complexity could be ignored/lost (a simplification).
Attempts to use continuously 'living' cells as components failed because they continue to change (and even die eventually) and were not easily/practically able to be connected to standard electronic circuits.
Pre-Planar process transistor electronics are used to interface with this hardened Bio-Electronic circuitry.
These circuits usually have alot of excess cells involved because of the fundamental way Neuro-Nets operate. But because they are small ( ie- 10 microns,  10000 per square millimeter ), all those extra cells don't take up that much space ( thousands of functioning 'gates' in the space of a typical discrete transistor of that time ).  Each cell potentially can also perform the function of hundreds of transistors.
Simple vision functions takes millions of cells and a structuring of different patterns of NeuristorsNeuristor - https://www.thefreedictionary.com/neuristor mimicking a real brain's overall structure, with a progression of different functions ( optical feature processing, pattern detection/interpretation, situational conclusion ).  
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An important second generation of development used the production(growing) of reusable 'molds' which once formed (trained correctly) and 'baked' could be used in a process to stamp out/replicate various circuitry patterns.  This facilitated faster and easier (cheaper) mass production of certain useful logic patterns ( ex- computer memory which utilized millions of replications of the same simple circuit ).
( Ex- "R-34 Wire Cluster" which on having a simple Neurister feed back mechanism added became 9000% more reliable ).
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Brain Boost (ADAM Tonic) greatly accelerated the development of this technology ( one of those meta level collaboration accelerations of technology ).   It took just a few Manic researchers, who couldn't sleep, who delved into all kinds of odd things (some of which turned up some astounding Tech).    Hmm, Brain Boost (or a derivative) could help accelerate the learning process employed to 'Train' the Neurister nerve cells, Later, the resulting Computer Tech sped up cell training by magnitudes -- lowering costs to develop this technology for Consumer Products ( the Business of Rapture is Business -- after all ).   Voila (behold!), even more money for further tech developments, and enabling more complex uses ...
The Thinker's system employed third generation neuro-electronics and the independent work with N-Gram Big Daddy Conditioning combined to create that Artificial Intelligence.   NOTE- Porter's memories of his wife 'made her' real to him, so that N-Grams recorded/taken from HIM were utilized to create that artificial personality  (in effect he saw what he remembered).
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Interesting sidebar - use of human tissues in this Research - Ethics in Rapture - cutting open the brains of "Experimental Subjects", and extracting tissues to be use for this electronic stuff ( to make money - not just to 'save lives', as much Medical research purports to do ).  BRAIN DONORS !!! As in Persephone - If you sign the Waiver and sign up for the 'Experimental' Program ( and it spells out reasonably honestly what is involved and what the risks are ).   Alot of the BioShock Players probably don't know that this was actually common practice in the US in the 1040s and 1950s - use of prison/jail inmates for various VOLUNTARY experimentation.
But then, alot of the research was based on the less 'legally entwined' Sea Slug tissues, which were simpler and more robust than human tissues.
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Idea - If The Thinker could mimic Porter, then have it mimic Ryan ( in a new plot "Twist", Ryan arranges it to make believe he's alive - but is really 'The Thinker'. But then ( 'wheels within wheels'https://www.merriam-webster.com/dictionary/wheels%20within%20wheels ), actually HE IS still alive  ( not great, but better than the stupid/lame/illogical suicide part of the story 'Twist' we got fed ).
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Tictactoe.jpg|Early computer game - an actual achievement for THAT time
File:Onetuberadio.jpg|One tube (inexpensive) radio mechanism - Rapture was quite a bit past this
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Small on the Inside - Circuitry : 
The Bio-Electronic circuits have the same problem that modern computers have -- inside, within their micro/dinky 'integrated' circuitry, they can do things very fast, but they then have to interface outwards to less sophisticated technologies, which are not as fast and generally are very large and clumsy. SO the problem is : to try to do as MUCH as possible while INSIDE the Bio-Electronics before having to transition outward ( thus with less constant in/out data flow to slow things down, and passing of control instructions inward ).
A similar advantage is that the size of the circuitry means that very small currents and voltages are involved, which then has to transition (amplify) to much higher currents and voltages externally to work/interact with other electrical machinery.
This also means that the Bio-Electronic circuitry is susceptible to electromagnetic interference and to damage from over-currents, so that the circuitry needs adequate protections in its various use environments.
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Fine Wire required For the Bio-Electronic Circuits :
Wollaston Wire ( less than .01 mm thick ) platinum wire first made in early 1800s ( human hair typically .05mm ) Gold can be similarly used. Wire Surface Etched with micropores so that the cell-to-wire physical connections are facilitated. 
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Good as Gold :
"One gold coin can provide enough gold wire/thread for thousands of bio-electronic circuits" - McClendon
Note To Players - Those corpses you bring back for 'salvage' - you might want to have a pair of pliers handy for any gold teeth ...
Small very thin wires (out of pure gold) can be created -- using a metalworking technology (real world) thousands of years old.
Handy in making Vacuum Tubes also ( and gold is used in plating for all kinds of electrical equipment ).
Would Rapture Dollars be Gold ? The coins get pretty small even when Gold was $35 an ounce ( denominations had been $2.50, $5, $10 & $20 Dollar in the 30s, when it was ~$20 and ounce ).
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Glass - A Well Understood Insulator Material to be Utilized for Bio-Electronics :
Miniature Glass fabrication was an important part of Rapture's Bio-Electronic technology. 
First to produce thin flat glass ( something like microscope slide glass ) used as the 'board' material for Bio-Electronic circuits (it needed to be a good insulator). The shaped glass is smoothed/polished. 
Melted dimples and etched/scratched lines are added on the glass ( use to contain/support the various circuit materials ). Various materials Biological and mineral are deposited in these gaps.
Scraping the glass flat in final stages, leave only the indented areas filled and the surface flat enough for 2 surfaces to be joined with no significant gap ( and to bring materials on each surface together for circuit continuity ). 
Being able to do these processes repeatedly/consistently for some more complex circuits, which had to be built up in stages and then scraped/polished/cleaned for the next build stage ( The 'training' stages have temporary materials added to facilitate them, and these get removed afterwards ).
In some cases, vapor depositing of conductive metals ( over the whole surface ) would be used which would fill the space indented in the glass, and then on polishing leave the metal ONLY in the indents ( making circuit traces ). Glass of course beings a very good insulator as a substrata for the electrical circuits being built.
The techniques use could be automated ( not done manually ), which would allow production prices/difficulties to be lowered/lessened significantly.
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The idea of Programmable Logic ( used in so many devices these days ) assists in creating complex control circuitry which would be far more difficult (and expensive) if done wholly using discrete analog or mechanical circuitry. You still need conventional (era) electronics ( transistor or tube and relays ) for the needed power actuators for various devices ( motors/solenoids/pumps/etc ... ) and to generate/feed IN the sensor data the circuitry's functioning requires.
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Micro Details : 
Early Bio-Electronic glass substrata had been stamped to hold the 'biological material' within a well pre-designed pattern (similar technology for fine details were already being done as small - like ordinary Phonograph Record grooves being stamped in plastic with as many as 9 grooves per millimeter ...) Useful when the circuits design called for a regular patterns (grids/arrays). Micro-Pantograph mechanisms can be used to 'carve' the master Stamp Molds (in metal) for such patterned circuitry ( used then to stamp glass ). Precisely photo etching numerous circuits that way would be far too costly for the uses they would be put to ( archaic modern computers requiring million of transistors - current ones BILLIONS ).
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An Interesting *TODAY* (REAL WORLD) Technology : 
Using '3D' Printers to lay out patterns of cultured nerve cells to rebuilt damage to " sensory and motor functions of complex nerves " ( to be embedded surgically into patients ). Previously I had heard talk of using similar 'printing' technology to assist in regenerating Liver tissue ( the Liver is a highly self-regenerative organ ) and for culturing skin ( extremely important for treating burn victims ).
This adds ideas for medical applications using ADAM's properties ( Medical uses most probably were the very first ADAM research done in Rapture before the "Firing Fireballs Out Of Arseholes" stuff happened).
XY Plotter type machines have been around since the 1950s, so that technology could potentially be allowed in Rapture. Scaled down with a micro-pantograph it might also be usable for some of the fine inscribing work/cell depositing used to make the Bio-Electronics.
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Bio-Mineralization Process :
Bio-Mineralization is the formation of inorganic materials in a biological environment, as it is found in the development of bones, teeth and shells. Certain bio-minerals are also often associated with "pathogeneses" of tissues.
Various Plasmids and Tonic can make use of this existing natural process to modify the human body to support the functions needed for the Plasmid/Tonic's abilities ( usually takes alot more than that 'game' insta-change type modification - which the MMORPG won't have ). Hence, there would be less in-game (MMORPG) 'instant' changes by 'Tonics' and 'Plasmids', and more realistic application ( done carefully by professionals and careful process ) over sufficient time for tissues to carry out their changes.
Employing a process to cause Bio-Mineralization would ALSO be fundamental in creating stable, rugged circuitry from living tissues. Conversion to a chemically inert form with desired electrical properties and patterns would be the goal.
Formations of 'plastic' ( repeating chained molecules ) and patterned crystalline structure ( utilizing biological minerals ) are natural processes. Manipulations to induce the desired modification at least is possible ( a big part of the complexity/difficulty would be placing the organic markers such mechanism use to guide their operation and proper formation ).
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Making Bio-Mineralization Technology (The Great Leap) :
Use is made of an existing biological mechanism, where an organisms cells build mineral structures ( example - building bone tissue by Osteoblasts ). Being an existing biological mechanism, it thus doesn't have to be created (genetically) from scratch ( BTW it would be largely impossible to reproduce such a complex biological result originally as done by trial-and-error via Evolution over millions of years of mutations of millions of organisms to form the required working genetic codes ). But genetic manipulation could be created by applying/modifying existing (natural) genetic patterns. 
The Bio-Electronic circuitry used in Rapture would use this process in converting living tissue into inorganic materials, which have better durability and stable properties ( conductance, semi-conduction and insulation ). Various minerals with the appropriate properties could be absorbed by cells and placed into crystalline and polymorphic formations required for particular electrical/electronic operation ( both inside and external to the cell ).
A simple important electronic component like a Diode ( used to force electrical currents to travel only one direction along a conductor path ) is achieved by intermixing two additional elements into the crystal structure of two adjacent regions of the base material ( such as the semiconductor Silicon ). Transistors are formed from three such adjacent 'regions'. Metallic elements can be organically manipulated and made to form strong-conductors/wires to transmit signals across a cell.
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Redundant Structure of the Bio-Electronic Mechanism :
Living tissue, because individual cells can die, usually have their function/logic done via the cooperation of multiple cells doing the same operation. The signals of several cells can be averaged together to carry out the function ( and while alive, tissue can have other cells take the place of the ones lost - If a particular cell dies, the others adjust to continue the intended function). This redundancy mechanism/behavior can be utilized in a technology where it is hard to manipulate single cells directly ( ie- try picking ONE cell up and placing it into a 'circuit' ... ). A group of cells though can be manipulated, and if of the right properties and are 'trained' in the same function, and can respond together the same way. Damage which potentially can happen while converting the living cells into inorganic circuitry may destroy/disrupt a few cells, but the rest could then continue to function properly. Finding how much redundancy is sufficient would part of the circuitry design process.
Consider that a 1 square millimeter area with a depth of one tenth of that can easily contain 10000 nerve cells. Individual functions with significant redundant could take only 100 cells. That is a significant size improvement for circuitry in Rapture's time, when transistors ( and other components ) were good fractions of an inch in all dimensions. 
The process used to 'grow' the complex circuitry ( including the irregular logic needed for certain functions ) can also be worked to force corrections while the circuitry is being formed -- to be patched/adjusted while it is still alive and growing ( while it is in a modifiable form -- A natural process of living Nerve cells ).
With certain simpler, regularly structured (but very numerous) circuits ( like a memory bank, where the simple basic 'bit' circuit is replicated many thousands of times in a grid ), some (likely) defects can be worked around via programming -- by using a customizing compiler to build around known defects existing in that one circuit ( ie- a few bad memory addresses, just like they do in the Real (modern) World for those long-underway space probes - which were subject to Space's harsh/destructive radiation -- potentially damaging the computer's memory electronics. ) 
Boorrrring ... ( A point though is : Clever Solutions are 'nothing new' to overcome difficulties and constraints. )
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What is the State of Bio-Electronic Technology in New Rapture ? :
As might be expected, with things disrupted/interrupted by 'The Chaos' following the %27civil war%27, alot of the things once produced in Rapture no longer are. Production of New Electronics would be one of the things disrupted.
Minervas Den ( and its annexes ) were largely intact, with living ( and still not all insane ) personnel and still having working production equipment, and the various designs/plans archived. Advanced circuitry was used for 'The Thinker' and by McClendon's robots. With that facility having been isolation, the capacity to produce much of the technology may have survived. 
Various Player Activities :
* Salvaging reusable components and modules ( and bits of wire, electrical/electronic parts and other things ) to supplant what few things can still be made.
* Repairing some of the old production machines/tools in Minervas Den ( replacements/repairs, maintenance ).
* Finding materials (like gold) needed for new production/repairs ( Ick. Gold Fillings salvaged from corpses - bet you never thought you'd be Pulling Teeth with Pliers from skulls in a game, did you ? Then again, that was one of the activities in Hensen's Muppet MMORPG wasn't it ?? ).
* Use of the facility to Repair parts/components/assemblies ( developing your Fabrication Skills )
* Research and recovery of technological information ( searching out/recovering data/knowledge/plans )
* Recovery of various Program archives and manuals.
* Maintaining various automatic systems still operating throughout Rapture, or switching them over to manual control when they fail. ( Repairs at the location where the critical equipment is, and their connecting wires/conduits ).
* Find and use Libraries containing Surface Information covering similar subjects
* Contacts arranged with "The Surface" to get things ( tools/materials/knowledge ) no longer available in Rapture ( The Ryan Loyalist faction still had contacts and various Smugglers can still obtains some things for the right price ).
* Recovery of some of the old NPC experts still alive ( and you are likely having 'to convince them' to cooperate ).
* Try your hand at programming. Some skill may be required.
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Micro Printing Processes for Bio-Electronics :
Though much larger detail than today's results of micro-lithography in making our Integrated Circuits ( which is down to Nano-Meters - millionths of milli-meters ), the size of printed details allowing a fraction of a millimeter is possible with available (1940s) printing/etching technology in Rapture ( which could be further refined/developed/specialized ). This would be useful in laying out the (to us) quite small physical patterns in materials required for Bio-Electronic circuitry.
"Printing" - Basic shapes of layers of materials laid down in fixed thin patterns, sometimes layered (building) ontop of other patterns ( done with sufficient alignment accuracy to 'match up' the layers ).
Deposited materials ( to some places and not others ) : 
* Chemicals which stimulate various cells to adhere at a position and grow into their desired form
* Metal-based Conductors, which act for signal transmissions in the finished circuits ( or external bonding sites with mechanical conductors like thin gold wire ).
* Insulators, laid down to block/guide electrical activity, built up structures (dams) which can be used to contain other applied materials ( impressed wells where a group of squee-geed-on nerve cell cultures can accumulate to eventually self-organize and connect into the inorganic circuitry ). The base Glass substrata is an Insulator.
* Masking, temporary materials deposited to facilitate etching/reactive conversion processes and chemical treatments ( protecting some spots and leaving others open to be etched/chemically modified. )
All of this 'printing' is much larger/cruder than what was done (even) decades ago when (Real World) Micro Electronics technology advanced. It would be still far smaller than the bulky electronics in Rapture's time era ( tubes/early transistors, crude circuit boards ). Alot of this 'Printing' is to serve as the physical receptacles and to lay out electrical connections/interconnections of the Bio-Electronics components, which CAN do alot in a very small space. Those components have to be organized, and formed/guided, and connected, to build the more complicated circuitry ( ie- what needed for "The Thinker's" simulated Intelligence, or for sensor signal processing and remote controlling of security devices the game shows ).
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Microglia - Support Cells
Microglia promote learning-dependent synapse formation through a brain-derived neurotrophic factor.
( Plain English : Part of the cell mechanism that allows brain cells to learn ).
So these would be one of the 'factors' introduced in the guiding Phases of the growth-building of Bio-Electronic applied cells. The Cells natural function when placed upon an organized structure and with various signal patterns applied would be used to form the desired electronic logic.
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Idea for A Bio-Electronic Manufacturing Mechanism : 
For the (glass) Substrata Etching used to form 'circuitry' guides for the living nerve tissue pattern's growth phase.
An 'Etch-a-Sketch' 'Etch-a-Sketch' - https://www.bing.com/images/search?q=etch%20a%20sketch%20 type mechanism : A 2-axis rotating indexing knobs working jackscrews using rotary relays, controlled by a 'card' driven indexing mechanism ( like a Jacquard Loom ( a 200+ year old control technology - maybe later would be computer-tape controlled ). Can also be used to 'drill' dimples/depressions in the flat surface where organic tissue is later paced.
'Pantograph' arm mechanism that scales the primary (driving) movement down to draw sub-millimeter features ( using a Diamond or Carborundum tipped tool, etching the glass substrate ). The line and 90 degree turn movements of an Etch-a-Sketch (toy) are reminiscent of many early circuit board formats.
Allows mass production manufacturing, when used for 'line' etching ( along with multi tooth 'comb' pattern cutters for parallel lines, and hot pattern stamping, and silkscreen masked depositing of materials ).
Diamond point tool ( nice - there might be a Bounty for Diamond jewelry you find out in the wilds of Rapture) is used (because of its hardness ) to scratch glass ( which will then need annealing later to moderate/smooth the weak fracture points on the thin glass ).
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Possible Organic Triggers for Bio-Electronic Circuitry Conversion and Training Processes :
A primary need for Bio-Electronic manufacturing is a complex sequence of precisely tailored cell interactions, sequentially/phase-controlled in the process to affect the cell structural formations.
It requires external signals which can be used on Genetically-altered cells (used in the Bio-Electronic and other technologies). This is done via the Cell's basic genetic (natural mechanism), or via a "Plasmid" ( some extra/added/modified genetic material introduced to a cell to manipulate its behavior ). Modified genetics would allow several cell-modification Phases to meet what is required for whatever needs to be accomplished. 
Various environmental stimulations would be used to trigger the different phases of the genes/mechanisms existing within the living nerve cells :
* Weak electrical potential on electrodes or regions of the sub-stratum the cell sits on - to stimulate a reaction.
* Chemicals introduced ( enzymes, proteins, neuro-transmitters, genetic triggers, etc ... )
* Temperature level ( accelerating certain chemical reactions, and sometimes slowing by lowering temperature )
* Light Wavelengths - activating specific genetically produced chemical reactions
* Hyper-Frequency module stimulation ( microwave vibration harmonics keyed to specific bio-molecules )
* Electro-magnetic polarization ( electro-magnetic vibrations tuned for certain molecules )
As mentioned previously, a complementary Bio-luminescent output from the cells could be engineered to activate as part of different phased modification steps, giving feedback indicators to an external process control mechanism ( when bits get glowey then you know you've done enough of whatever to achieve activation ... ).
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Living Cell Neural Computation :
Living Nerve Neurons and their support cells (Neuroglia) would be laid down/deposited in thin layers and induced to adapt to patterns of signals from an array of small input electrodes, use a learned/trained signal processing pattern, and then connected to feed into a set of output electrodes. These would supply expected (programmed output) response signals to the inputs. The cell's natural learning/self-correcting mechanism would be employed using repeated pattern stimulations (a training set) after which the cells are genetically Triggered to cease adapting. The goal is to have the cells recognize a generalized pattern from the given input data, and then generate the correct outputs to process sensor data, coordinate some machinery, or somesuch 'logic'. 
After one layer set of cells is trained and is 'frozen', an insulating separation layer is deposited and then another thin neuron-cell layer is deposited, to be subjected to a different set of input patterns, and be induced to respond correctly to that different logic. A whole mass of cells (ie- 100+ layers) then are to function as one unit, all processing the same set of inputs, but with each layer responding with a correct answer/response when appropriate. Those thin layer, each not much more than a few cells thick, would be assembled within a 1 inch square area and comprise something like 1 million neuron cells, which allows for significant interconnection redundancy, facilitating the many signal paths required for the desired Logic to be formed and operate.
The cells, using their natural electro-chemical mechanisms ( ion concentration, passing an electrical signal potential on to the next cell ), can only process in signal waves in cycle times of about 100th of a second, but because they can work massively in Parallel, they can actually do a great deal of data processing work simultaneously.
The resulting logic functions formed out of the cells can be modally divided up with specific inputs acting as subset-enabling signals (mode controls), as well as a large number of situational pattern inputs, all being used to do mass data processing on several hundred inputs ( example- optical/vision cognition/interpretation, or obstacle avoidance for movement ).
Gold electrodes used in this circuitry are thin, finer than human hairs, and would be coated with an insulator which the cells break down to make a signal connection ( you can't allow current simply flowing freely through the liquid medium the cells live in ). A weak positive signal (for inputs) or negative (marking outputs) or a neutral charge initially put on the electrodes would be used to guide the growth of the signal processing logic and formation of the cell dendrites and axons. Some Signal-carrying cells are mixed into the layers and are there to internally carry signals across the entire width of the cell matrix ( max approximately 1 inch square ).
Issue - Slow Speed of natural cells - which 'fire' less than a hundred times a seconds ( often just 'tens per second ) -- the offset of this is the ENTIRE thing runs in parallel and with sufficient intertwined logic it could dwarf the processing of an electronic computer whose linearly-run instruction logic runs 10000X faster ) -- again this would be used for very specific types of complex logic ( like pattern matching ), versus the basic computational arithmetic and if-then programming of more conventional computers.
Issue - The cells are living and have to be maintained (kept alive) in an organic way. During their 'lifetime', the living nerve cells in the mechanism are 'fed' by a plasma fluid containing oxygen and nutrients to sustained them. A substantial portion of the cells included are of types which act to support the functioning nerve neuron cells ( which perform the actual logic operations ). 
Issue - Circuitry Lifespan - the cell tissue eventually degrades and unless 'repaired' ( T-Cell applications ? ) it ceases to function, or worse malfunctions. This living circuitry then is really only applicable to uses which have a short expected lifespan after being created. Likewise, small changes (degradation) in the nerve interconnects can cause variable/inconsistent results, which increases as the cells age ( goes gradually senile ... ). Short term Recording of visual data might be one use which allows for less-than-exact data retention.
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IT IS POSSIBLE (an important idea) that such living circuitry might be used as implants to regulate and control some Plasmid/Tonic operations - adding a 'smart' component to facilitate things of greater complexity, when purely gene-based solutions are insufficient.
Also some life-extending genetic changes might be possible to help extend this product type's lifespan ( which in lacking, means you might have alot of broken/malfunctioning machines by the time of the MMORPG games setting ).
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This Live-Cell system might possibly be done with a step-wise 'static-alization' process ( killing the cells which are converted to inorganic electronics, layer by layer as each is built ) to create the final component. This would be a mechanism for producing complex 'irregular' logic that many AI applications require. The inorganic circuitry has the potential of being driven hundreds of times faster than the original living tissue, and is has a slower degradation rate than living tissue.
Patching : Extra steps are required to thermally/chemically 'bake' the cell tissue and cannot be done without direct access to the cell layer to apply the additional chemicals and mutation triggers required for the conversion. Also, frequently the cell "Learning" fails ( doesn't function as required ) and with the top layer still accessible - to be cleaned and restarted/rebuilt without having to discard the entire unit ( which may have several hundred 'layers' built up already ).
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Componentized Complexity :
Early CPUs (Real World "Central Processing Units") spanned entire large racks of circuitry. The miniaturization was developed decades later to put whole circuits on chips ( and a complete computer on one chip even later ) did not yet exist (AND WE SHOULD NOT EXPECT IT TO IN THE MMORPG time period).
A Rapture Bio-Electronic CPU would be spread across multiple substrate layers, interconnected via substrate edge spanning wires, with different functions present on various layers : register memory, input/output channels and buffers, different arithmetic units ( Adder/Multiplier/Divider/Shifter ), instruction decode logic ( which controls all the others ). If the unit was to be self-contained ( like a controller module ), then many RAM and ROM layers would be included. 
An advantage of having these on separate substrate layers was that they could be manufactured separately, and the defective ones eliminated before their assembly - versus a more complicated one-piece/fewer-piece candidate computer having to be scrapped whenever it tested-out as a failure/defective. Potentially later malfunctions/repairs with the layers being disassembled and a replacement inserted ( or the good layers reused ).
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A Different Circuitry - (Continuing) Living Nerve Tissue Used for Computer Bio-Electronics :
Living tissue, Short term memory, Self Organizing, Use of Stem Cell mechanism for recording and self-adjustment ( and wiping to rerecord ). Researchers would have investigated Ideas at least for attempted tech ... ( unfortunately turning it into something useful is the problem ).
Growing Your Own Brain (Sort Of) :
Training animals and then cutting their brains out isn't really practical. Assuming you can keep it alive, they just work the same as for the animal, except now piecemeal/separated from the specific external sensory inputs ( which are too complex to attach the artificial equivalents of - so no good functionally any more ). You still might make use of various specialized tissues, but that's not a 'brain' - just a functional sub-tissue component. And you would have to directly manipulate that 'part' of tissue " In Vitro " ( outside its normal biological context ) to make use it . Training would have to be done to grow/form/shape its logic functionality using the desired input patterns, and stimulate then to interpret and generate the appropriate the outputs. It is time consuming to do for complex interpretation functions even when automated.
An Important Limitation is : That being 'alive', it would eventually deteriorate and its function degenerate with time. So applications needed to be some relatively short term purposes ( assuming its even practical to 'grow' in the first place). For living tissue, there also needs to be sufficient support tissue and mechanisms to maintain its physiological living state ( overhead like oxygen/food/waste transport - which can be quite complex ). An external Flow of nutrients and oxygenation is required to keep the living tissue alive, and a cleaned environment kept free of bacteria.
The Brain Unit's core would need to be a small volume ( not much larger than a cubic inch ) so that Nerve cells are close enough to interlink sufficiently between themselves, so that their nerve-cell-based logic can interact. Biological Support machinery many time that size would have to exist to sustain it.
Electrical Inputs - hair fine wire electrodes which will inject inputs and take output signals from the living tissue. Grids with a (practical) spacing (something like 1/2 mm), using Gold wire/thread with some kind of bio-friendly coating for cell synapse adherence/interfacing - that is a general insulator except where the nerve fibers (Axons and Dendrites) make contact ( and do conversion between ion-based neuro-chemical potentials amplified into electrical signals ).
Thin layers of cells are deposited, forming a matrix to interact with the electrodes. This gets built up in many layers, with each layer passing through a formation phase when it is 'trained'. Then its function is frozen ( biochemically inhibiting synapse changes ) so that it won't be affected by processing the next added layer ( won't change from its already trained state ).
What kind of purpose could there be with a fairly limited lifespan ( and to justify the overhead expenses and difficulties ) ?? Such units might be kept 'frozen' ( to prevent deterioration ) for long periods before use.
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SPU - Slug Processing Unit ( A Nickname given by McClendon's Employees ) :
The basis of Rapture's later computers was a Bio-Electronic technology initially employing tissue from the brains and nerves of Sea Slugs (and some other species different from the ADAM Sea Slug) and humans. Such tissues, were genetically modified with ADAM to form regularized logic structures, and could be made to process data sufficiently to operate as sections of a programmable computer. Living nerve tissue is 'trained'/shaped (programmed) into a desired logic pattern ( employing the cells natural learning/forming process using ADAM-type un-formed Stem Cell methods ). Once the tissue is formed and has interconnected itself properly, then it is induced to absorb certain conductive chemicals and polymers, and is converted/stabilized into an inorganic/mineral form, retaining its 'trained' functional structure ( with the added elements now having the characteristics of electronic components ).
Internally, this 'brain'/nerve tissue works in an 'analog' mode to implement Binary Logic processing for processing digital/Binary data ( which humans can UNDERSTAND/design/train ). This circuitry then connects outside itself to 1950's era (early transistor) electronics (to tie together modules of similar circuitry, to interconnect multiple 'brains', and connect out to sensors, control terminals, magnetic storage devices, and other data/command sources).
'Squirmy Logic' (another nickname) - Logical Inferences Operations upon data : Needed for AI programming. High level 'intelligence' logic moves around with the data, and runs parallel/simultaneously in many parts of a larger interconnected computer system ( the Thinker isn't one computer, it is a network of many thousands of small computers all working in parallel together ). The primitive processors (individually) are not much-more/even-as intelligent than a slug, so earning their nickname, but massed together can create a far more capable system.
Functional units - many different functions : Searching and Managing memory, Communications connecting within and outside the Bio-Electronic module, Processing the Logic Inference Operations, Mathematical Operations, Managing Prioritized Workflow of a set of 'brains', Optical Interpretation, etc...
Non-Binary 'Fuzzy Logic' would also be handled (the nerve cells are actually better suited to processing this kind of calculation). In the end, whatever results are produced, they need to be converted into binary/digital form to be used for most real applications. Fuzzy intermediate values are not storable except for limited immediate use within the unit, so there would be alot of conversions back and forth within this style of computer. Such Logic can process 'temporal' flows looking for patterns in the inputs.
Task driven Inference engines - Data is retrieved/interpreted/combined and evaluated, conclusions are drawn/decided following the 'intelligence' logic. Those conclusion activate further processing, until the processing goal is met and final conclusion are produced. Information(data) and logic programming is distributed across the computer's system and Data/Instructions are routed to where needed.
One of the limitations of this technolology is the size of the normal (Real World) electronic components - all 'discrete' (many individual components) as integrated circuits had not been invented yet. Miniaturized individual transistors used to convert the Bio-electric signals to normal electronics were still bulky and made up a significant portion of the content of the many 4x4x4 inch computer modules. The "brain" circuitry made of nerve cells ( around 8000 inter-neuron nerve cells exists in a typical Sea Slug brain, each cell functioning in a way which conventionally might take upto 1000 transistors ) vastly increases the logic density ( each 'brain' doing the operations equivalent to a whole large rack of transistor-based circuit boards ). One advancement over contemporary computers was that each SPU could operate independently, and in parallel with numerous others (the Thinker was made of many thousands of such modules).
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A standard 'small' configuration was 32 'brain' sub-units each on their glass substrate layer, interconnected and stacked into one 'module'. Different brain layers had different functions - Input, Output, Processing, Control, Communication, Memory, Memory Access, Data Registers. Such a processing module was paired with one or more memory modules, where data and/or programming instructions were maintained.
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Organizing the Circuitry of Bio-Electronics :
The ability to fabricate electronics with small details would be very limited in the technology era of BioShock (late 40s-50s), and we shouldn't expect the people in Rapture to easily/automatically come up with what we have now (or even 40 years ago).
What you would have would be the crude shaping of circuit materials only with detail fineness of fractions of millimeters ( instead of "microns", 1/1000ths of a millimeter common today ). These details being laid out to form Rapture's sort of "integrated circuits" are utilized to make the basic signal paths ( with printings conductive/insulator materials ) and spaces in which the biological material will be deposited ( in proximity to the signal paths ) and formed. 
Within this conventional framework which supplies power and electronic signals, the biological components would be situated and connected. They perform the switching and electronic interactions. Their more complicated functions must be formed and link up to a conventional electrical framework by themselves - effectively growing onto the circuitry. This would be to a great extent guided, but the materials making up these bioliogical components are too small to be manually fabricated.
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Things that would Need to be Genetically Engineered to Make the Nerve Cells Behave :
* Genetic Triggers which would activate the different phases (behaviors) of the cells building the Biological Electonic structures ( when subjected to certain chemical trigger agents ). This might be several different triggers applicable to multiple types of cells. 
* Stimulate Growth of a cells connection to a positively charged signal line ( or to a negatively charged one ) - inducing specific line ties with signals during growth causes specific (desired) connections to be created. 
* Formation of Good Bonding points between cells and to inert signal lines.
* Reinforced electrical conductivity ( absorption of metals and formation of biological conductors ) and sufficient insulation of cell structures.
* Creation of Functioning Diodes to control the direction of signal data and power feeds to cells
* Amplifier - a nerve cell structure taking in a small signal and outputting a much stronger signal ( it is actually a natural function of the nerve cells )
* Threshold detectors - there are many stray signals surrounding natural nerve cells and there is a way for them to ignore these.
* Shaping the cell structure to operate with the electrical properties when 'mineralized' ( after the 'baking' process ).
* Support cells which interact correctly with the operational cells and which get 'nullified' when the cells are eventually 'baked'. Separating the formation process from the final state of the Nerve tissue.
* Feedback markers (fluorescent) which can be used to inspect the circuitry to help determine completeness of formation processing, and to highlight defects ( for culling rejects ).
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Minimal Instruction Set Computer (most early computers used these, and the following is more advanced than most of those) :
:Transfer Instructions: JUMP, CALL, RET, JZ, JCZ
:Memory Instructions: LOAD, STORE, LOADP, STOREP, LIT
:ALU Instructions: COM, XOR, AND, ADD, SHL, SHR, ADDNZ ?? DIV OR
:Register Instructions: LOADA, STOREA, DUP, DROP, OVER, NOP
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Advantages of Nerve Cells Over Tubes/Transistors :
Multiple cells can be used grouped together to produce complex input-logic-output operations in this technology ( It is what Nerve cells do naturally, allowing the system to be better immune to 'noise' ).
When group of cells get the same inputs which they average together to give a 'consensus' output. This is actually advantageous in the Bio-Electronic production process where manipulating/placing individual cells (which are quite small) is rather a difficult task, and where the formation of the final circuitry may not work consistently for any single cell (so you have a gang of cells doing the same operation, and if a few don't 'work' the whole can still operate as needed) ... 
Thus the Nerve Tissue's natural system ( with minimal genetic changes required ) of being trained to process signals as a group is employed.
There are also additional cell types which support the operation and growth of the primary Nerve cells, which would be placed into the cell groupings. These cells could be destroyed for the final circuitry ( no longer needed for the formation phase ), or be made to function as connections and insulators between the primary cells as they are converted to a non-living form.
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ADAM Facilitates Bio-Electronics :
ADAM technology allowed tissue cells to be genetically manipulated in shape and function and internal composition. A nerve cell's growth of its natural filaments (connecting between cells) and internal structures could be made use of, instead of attempting to genetically produce such features via new genetic code ( task of great difficulty for even minor additions/changes - even with today's Real World methods ).
By super-structurally guiding Nerve cell formation/growth (shape/connections) and a phased process of 'cell' formation - absorption of metal ions/insulators/doping components to form into operable electronic circuitry, very small electrical circuits could be mass fabricated inexpensively ( or even possible - when the next best alternative are single-transistor discrete components of that era ).
Non-organic signal lines made from conductive chemicals pre-deposited within scribed lines in the Glass sub-strata define placement and interconnects. A pattern of nerve cells laid out/guided on that substrate would then go thru a fabrication process which grew/formed and then fixed their structure by killing the living tissue. Thus leaving stable mineral/inorganic tracings/interleaved masses behind, possessing an appropriate structure/composition to function electronically.
This technology makes use of a glass/fused quartz substrate which would be pre-etched/stamped/fused/annealed ( a well understood existing technology ) and is a good electrical insulator and chemically inactive. The thin glass ( similar to microscope slide cover slip glass .25mm - .50mm thick ) allows close stacking within a "module", and pairing substrates giving 2 working facing surfaces for the circuits ( Ex- needed for 2 perpendicular sets of parallel control/signal lines with sufficient electrical separation ). These surfaces can carry additional signal lines connecting back to a particular edge if needed, and be used for power distribution - including (if required) conductor traces thru holes penetrating the glass substrate.
Standard large socket-based packaging (4 by 4 by 4 inch Modules) can incorporate small gold wires/threads to connect the edges of the numerous stacked Glass Substrates (upto 75 layers in 4 inches), and externally interconnect to conventional transistor amplifiers and interface circuitry and the modules's plug interface. The modules are then rack assembled into much larger arrays for the full computer ( typically made up of a CPU module, plus several Memory modules and a 'smart' communications module ).
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The Nerve Cell Binary Grid Memory 'The Thinker' is Based On :
Computers need to hold digital 'Data' to operate_upon/manipulate/input/output. For Computer digital 'Memory', a grid array pattern is used to access addressable(via a numeric index) memory cells ('bits' to 'bytes' to 'words' of memory accessed as a contiguous numerically addressable data block). This Memory is read from and written to the calculating parts of the Computer.
The 'Memory' modules most commonly used (standardized for mass production - being a common component which a computer needs ALOT of) for The Thinker would have a 2-Dimensional bit grid of 64 by 64 'cells' ( each cell is about a square millimeter in size ) stacked 24 or 32 layers deep ( typical bits per word size ). Each memory bit 'cell' would be grown in a dimple/well in the glass substrate where the biological tissue was placed (a suspension of several/multiple genetically altered nerve and 'assistor' cells), and thru a production process gets formed via RNA manipulation and the use of various environmental triggers. This then is combined with previously done non-biological formation of the substrate ( which includes circuit line tracings, running thru etched channels ).
A X-Y mesh of control signal lines (etched in a grid pattern across the substrate) running thru each cell, electrically allows individual "random" cell addressing/access (read and write). Bio-circuitry multiplexes and de-multiplexes the XY grid control lines. Each substrate's outputs only a single cell memory at a time ( to minimizing the module's total circuit complexity ). Each substrate layer thus is 64 x 64 = 4096 memory bits (( A very small amount compared to the memory used by today's computers. ))
A small holding current continuously running through various signal lines maintain each cell's bit data-state (different from Magnetic Core Memory which can retain its state when the power is completely turned off).
A process of Controlled growth creates the 'bits' storage circuitry -- living Nerve cells connect to the control lines pre-imbedded in the glass ( guided by electrical activity and chemical genetic switches triggering the growth ). The tissue cell's final 'fixed' structure acts as a capacitive circuit, charging up when 'written' and discharging when 'read', the XY control lines are used to select/set/reset each cell. 
Simple Memory circuitry is repeated and made regular in a grid structure, but it must have no flaws (no bad 'bits'). It was found that by using multiple nerve cells for each bit, the redundancy sufficiently eliminated defects ( it also eliminated the difficulty of trying to place one active nerve cell in each 'bit' dimple ). Another successful defect-handling method was adding a few redundant rows/columns (ie- 67 x 67 vs 64x64) on each substrate's grid pattern, and in production after testing by connecting-up only the row/line sets of 'bits' that worked fully. This made the 'yield' rates for production much higher and the units cheaper (with less useless defective components to throw away).
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Optical grid sensors (as used for robotic 'eyes') were fabricated in a similar 2D 'grid' pattern, by adding a light sensitive material (slug eye juice ?) into each pixel bit (cell) of the 'eyes' retina grid ( made to a multiple of greater than 64x64 dimensions to create sufficient visual resolution ). This revolutionized small TV cameras (needed especially for robotics). Optical interpretation functions are one thing nerve cells do much better than transistors.
This might be a particular use for direct tissue utilization - maybe not for a TV like image, but for a simpler sensor that is still usable for certain robotics applications. Making use of the existing structures in an organism's visual processing physiology is alot easier (or actually possible) than cobbling together an equivalent mechanism from scatch.
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More complex 'grid' processing circuits were built, as each glass substrata grid dimple could hold dozens of specialized nerve cells ( or be made more complex to hold even more data 'bits'/sub-processors/logic ) which could form micro-brains capable of performing local complex grid-oriented functions (ie- various kinds of optical processing for Robotics, sound signal processing, map solving, encryption/decryption).
Smaller grids of this kind of 'memory' was used on the SPUs (Slug Processor Units) as data holding 'registers' for the CPU logic to use in its processing. Typically there are at least two data registers as calculating inputs, one for output, an instruction register to select/control the functions performed, a program pointer register used to traverse the program memory, and internal state registers (latches) to facilitate synchonization and timing. Additional 'registers' hold intermediate values in longer calculations, and registers to address data in Memory.
Specialized Memory Control Modules were used to interconnect a SPU (or Communication Module) with multiple Memory units, to tie them together and greatly increase the memory locally connected to a SPU ( some tasks just manipulate alot more data than others ). This modules function is analogous to a 'Mother Board'.
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ROM (read Only memory) would use similar structural grid features, but would be much simpler (and smaller/denser) as it had a fixed pre-set data content (no write/refresh)/ It would be used for programs and their data, which rarely would be changed once perfected. The Bootstrap loader in ROM for a computer would have a small program that would run and fetch the main programs into the system on reboot/re-powerup. 
Special processors like communication ports/switches would have their entire (small) program static in ROM ( a logical thing since they were the path the main computer's programs got loaded into the 'computer' when it was rebooted/repowered - from disk/tape/network). Another use for ROMs is to generate the control signal sequences within a CPU to execute complex program code instructions (microcoding), which can allow customizing instruction sets to match varying hardware components ( the mix and match you can do with different combinations of the component substrate 'disks' ). Some variations of such circuitry allow re-altering (Programming) the PROMs data ( as an infrequent and usually slow special process ), instead of fixing its data only initially during manufacture.
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An advantage of these biological-based memory cells is that they can perform complex functions 
within each cell, which would otherwise take quite a bit of logic made up of many transistors. One such 'logic' function is Content Addressable Memory (CAM), which is used for simultaneously (quickly) searching a bunch of memory entries to match a key pattern. Very useful for certain data search operations ( which a distributed (parallel) computer 'mind' (AI) would make great use of ), or track the matchup of a multi-processor Data ID index to a local memory address. 
The nerve cells also are quite small, so that thousands could be placed in a few square inches ( 'miniature' Transistors were not so miniature at that time, and the same space could only hold about a dozen transistors ). One problem is that biological-based circuitry processes use very tiny amounts of electrical current. This requires any signal coming in or going out of the Bio-Electronics to be amplified/regulated to interface to normal circuitry. This gets done with a few conventional transistor components. Thus it is preferred (as much as possible) for the computer processing to be done WITHIN the Bio-Electronic circuitry, before 'going outside' ( to avoid having to employ alot of bulky ordinary electronics ).
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Natural Architecture of Nerve Cells :
A single large nerve cell is 1/100th mm (10 microns) across (that's is its body and not all the filaments (dendrites/axon) fanning out from it, which can reach quite far - many millimeters/centimeters - to reach/connect-with adjacent cells. One nerve cell can have thousands of connections to nearby cells. It can have internal operations done upon its inputs more complicated than simple logic ( things like multiple SUM/AND/OR/NOT and Threshold operations ). When used in Neural Nets, the signals are no longer binary and can do much more complex operations within a single cell such as summing varying weights of many positive and negative inputs in combination to generate a 'conclusion' within a network of similar cells, and that to send on to others.
There would be uses for these naturally complex structures/functions (natural Neural Nets). Some of these Nerve Tissues have a well defined/specific structure which might be selectively employed ( ie- many of the Fly-bots abilities are not that far from a Mosquito's behavior, which if not used directly can be genetically mimic'd ( copied instead of created ) to do processing similar to the animal's brain ).
Ant brain : 1/8th of a mm (120 microns) - 250000 neurons total. Mosquito brain even smaller.
Sea Slug : ~8000 large neuron in a nerve cluster (18000 neuron its entire nervous system) 
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Parallelism :
This Bio-Electronic computer technology is quite a bit slower ( in switching speed and transmission of data ) than the modern Semi-conductor based Integrated Circuit technology our modern computers use ( though still alot faster than native (living) nerve tissue is ). The Rapture systems, to achieve The Thinker, would use massive parallelism of many smaller computers tied together. It would employ numerous generic processors which could be assigned processing tasks "on-the-fly" with programs sent to them, and then those assigned task's data being pulled from somewhere else in the computer network. Results then get sent on elsewhere, and that processor is freed for another task ( this is something we have barely started to do in today's computers ). So a great deal of this system makes up the communications allowing the data to flow around within it.
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Connectivity - Much of a Computer is All Those Little (Long) Wires Connecting Everything :
Each Bio-Electronic module has a 'plug' connection of many dozens of 'pins', which were to be wired to adjacent modules, or to power, or to longer-ranged communication lines. Like our current-day computers, 'parallel' (many-wire) signal connections don't work too well over distance, so instead, 'Serial' type communications ( which are potentially slower but are much simpler electrically/electronically ) are used to tie "The Thinker" together.
Specialized Communication modules were usually paired with each SPU (CPU) to handle short and long distance interconnections, and routings of data/programs between parts of the computer and outside.
The racks in which the modules are mounted have a network of communication lines, which the modules use to route messages. Local lines connect to other modules in their immediate rack segment, others span the entire rack, and others are Trunk connections which link one rack to others ( and some relay connections across Rapture ). 
Some of the communications lines function like telephone party-lines, with their use being shared, with one module sending at a time after waiting for the line to be clear/non-used. Other 'Comm' Modules may be listening to see if a message is addressed to them. The logic 'smarts' to do this 'listening' and 'waiting to send' is on the Communications Module (CM), and has temporary data memory used to Hold messages being received or waiting to be sent. This offloads much processing from the computer SPU/CPU, and allows some efficient dedicated logic to do the simple request/fetch/send/addressing/listening functions.
On this extended network of computers, some intermediate 'operator' Communications Units (CU) transfer connections to/between Trunk lines, route long distance requests for data/program task instructions, copies of requested data, and processing results/status's. Memory buffers can hold messages for a period while the route required is currently busy. The standard Memory Manager Module (MMM) has a full set of communication processing capabilities to pull or push requested data through the communication network - acting for its local SPU(CPU). 
"Crossbar" switches are used to make simultaneous cross-connections between a limited number of local lines. Further connections must use buffered message-relaying units to work through oft-busy Trunk lines. All relay units have local memory to cache a copy of the message being sent, so they can wait to forward the message when the required routing's line clears. Simple protocols control streams of data transferred buffer by buffer.
Data inter-communications might be slow by today's standards, but the massive parallelism makes up for much of that. So like any computer, even back to the very first, there is a mass of wire connections back behind the 'works'. Another advantage in "The Thinkers" architecture is that there are many redundant routes for any data to get where it needs to go (a handy thing when maintenance standards get lax, or part replacement is problematic and falls behind).
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Local 'Standby' Backup Batteries for 'Memory' :
Since the Bio-Electronic (and the older tech system's) memory type is not 'persistent' (like Magnetic Core memory can be), and its data gets lost if the power is cut off. So certain critical parts of a computer could/should be protected during an inevitable power failure. The program and data state could/should be preserved until the main power was restored. The standby power consumption was low enough that the batteries could sustain the memory for weeks. Needless to say, in general, any significant data was normally moved to 'persistent' storage (magnetic disks/tapes) as soon as possible (and even those units had to have a system to not 'crash' in case of power failure).
Periodic 'Sync'ing of a project data seems it should be a normal and routinely done operation.
Rebooting The Thinker (or parts of it) seems would be a frequent occurrence.
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 RSAM (A Programming Technical Innovation) : 
Rapture Sequential Access Method (a basic database management system) : 
Locally developed version of an ISAM/VSAM type database programming data structure ( important for organizing data on 'Files' and 'Tapes' and across Networks ). Its a 'library' of functionality used by other programs. ( IBM released their equivalent in 1964 - so we can push it a little bit ).
One of those programming projects that a single person could successfully develop (program), which would be an important aspect for such useful things in Rapture, given the idea and the hardware capable of doing the processing (its is something simple enough which could be written in assembly/machine code). 
A variant/expansion of this would be used for the 'distributed' nature of the later computer systems ( tracking/finding/retrieving data across a bunch of computers ).
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How to Build a 64Kb(bit) ROM Memory Using Bio-Electronics :
ROM memory (Read Only Memory) is used to hold static programs and static (unchanging) data ( and keeps its data when the power is turned off ). It is very useful for machines which don't need to be powered-up all the time to retain their programs, and to NOT have to wait to be reprogrammed after being turned on ( or which glitch alot and have to be rebooted constantly). Additional Read/Write type memory is required for the temporary data used by the programs ( and can be a much smaller amount depending on the functionality required ).
One biological method is : To create a number of Neural Net networks, each existing for a single bit output (for 1 bit of the machines 'word' memory width), and then group as many of those separate 'bits' circuits as you need to provide the computers memory 'words' ( a set of 'bits' sharing the same address input which simultaneously/in-parallel outputs the bytes/words of data the computer needs ). A typical 'word' length for computers was 8-bit(byte)/16-bits/24-bits/whatever ( many odd sizes in those early days ). Each bit's memory values are independent of all the other bits. 
64K (65536) = 16 input lines for memory address (to access 2^16 separate values) uses 16 parallel on-off address input values to stimulate the circuitry -- to make an 'address' request for the data stored for that memory address. The actual storage is done by many more thousands of interconnections between the 'memory' cells. When the signals flow through all the cells cumulative output (amplitude) is measured which is then interpreted as and on-off value, which then is converted to a 1 or 0 digital value use by the computer.
Training the ROM values (setting the data into the device) - makes use of nerve cell structure and function to form a circuit, which through neural cell-type interaction returns the correct 1 bit value when the whole circuit is stimulated by any specific address combination (0 - 65535) of those 16 inputs signal lines. ( It is something like retrieving a memory in YOUR brain where a pattern of signals causes groups of cells to match a pattern of association, and then results in another pattern being retrieved ).
About 90000 nerve cells (each having thousands of connections to other cells) should be sufficient to form the Neural Net for 64K bits of memory. That number of human nerve cells (in Reality) can fit into a drop of water. 
Positive and Negative input signals ( originating from the 16 memory address inputs - a '1' or '0' signal on the address lines ) travels across the bit's circuit ( the interconnected nerve cells ), act by combining/canceling and summing within layers of nerve cells resolving into a single stable output.
The circuit's "baking" ( the process of killing and mineralizing the cells, but keeping the data flow logic patterns ) would be done once the circuit has been 'trained' correctly ( that is it answers correctly/consistently to each of those 64K different 16 bit patterns of its address signal inputs ). The mediocre yield (Pass/Success rate) for this manufacturing process also makes it prudent to make the circuit as simple as possible (ie- for 1 bit, or smaller than 64K if allowable ). The 'baking' conversion also speeds up operation into a purely electrical mechanism, versus the chemical interaction of living nerve cells which generally activate only around 100 times a second ( far too slow for any significant calculations ).
An advantage of doing the memory 'bits' as separate circuits is that they sometimes train incorrectly in their data pattern (Fail) and must be thrown away. SO each bit would be trained separately (a circuit 1/16th the size), with a test process rejecting and throwing out the defective 'bit' circuits -- thus not wasting the manufacture done for each of the other bits ( which would be necessary if they were all in one big circuit ). The grouped memory circuit of 8/16/24/32 bits sub-circuits containing the desired data then would be assembled for use as ROM in the computer.
Sometimes, simpler computers need only a little data memory for their program, and at the cost of running slower, can access memory serially, and making use of a single 'bit' circuit. 64 Kbits = 8K bytes, which is more than enough for some computer 'controller' automatic program operations. Circuits of 32 Kbits or 16 Kbits are easier to make (versus 64k), if that is all the memory size that computer needed.
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Electronic Indicators :
Bioluminescent (based on another area of research) indicator on various bio-modules indicate/enunciate basic functioning (green) and problem states ( Ohhh Noooos!! Its flashing RED -- the Bio-circuitry is ANGRY !!! ) Probably you won't have to pull vacuum tubes every 15 minutes like those WW2 era computers ( the tube quality eventually went up later, and they didn't have to do that much maintenance anymore ).
Blinkey Lights are likewise acceptable ( The expected public image of a 'computer' is an array of blinkey lights, as well as a tape drive thingee spinning ). 
All those little lights on the components look so pretty ... ( and are EASY game special effects, which make it look more animated - like something is happening, even if they are blinking randomly ). Pretty glowey effects can only be a Plus.
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Organic Transistors (Probably Not Hummus-based Though):
* Organic refers to organic-based chemistry, not necessarily being 'alive'. Most Organic Transistors are polymers/plastics which have semi-conducting properties.
* These usually operate at higher voltages ( ~40 volt - since vacuum tubes often required 100v, this is still an improvement over common 1950s electronics ).
* Organic Transistor are usually slower switching than Germanium and Silicon, but beat Tube switching speeds by a long ways.
* ?? Potential use of ADAM genetics to manipulate E Coli bacteria to generate required chemicals/crystals/structures (for components less complex than the 'nerve' structured logic), as well as assisting in the methods of generating the viruses use in all the ADAM tech to insert RNA into cells that need to be genetically modified.
* Existing cells like Nerve tissue act as pattern builders. The final operational circuitry do NOT use the original signaling mechanisms of the living cells (which are based on internal changes of ion electrical potentials and changing permeability of various membranes, and which can 'switch' at most only a few hundred times per second). The Converted circuitry works more like conventional electronics with electrical conductors and switches using semi-conducting effects ( and which will switch more in the order of a million times a second ). The cells are induced to interconnect and act as components.
* Interfacing with the 'Nerve' cell circuitry - There needs to be a transition to conventional electronics going out to the 'world'. Amplifiers are needed for the tiny currents the modified nerve cells would switch and signal. These amplifiers would first be be organic 'pre-stages'/boosters, which are then connected to conventional (miniature) electronic Transistors for the external pin interface. 
Integrated Circuits still are too far off for Rapture to have, as of 1958, and I WON'T do a "wave my hand" TVTRopes Linky and say Rapture came up with ICs themselves ( having quaint mixed technologies is one of the elements of BioShock ). The Transistor was invented 1947, and the improved 'bipolar junction' transistor by 1950. So those technologies (and the understanding of them) would likely be available within a few years in Rapture (Ryan still had a substantial Surface Organization capable of obtaining information about such things and having them brought to Rapture)..
* The Living Nerve Cell's genetics would be used/controlled to cause the formation of the required chemicals with the cell ( absorbing and placing required chemicals/molecules, building layers/structure ) so that when it was heat treated (baked), and the living components were eliminated, the Transistor circuitry would remain and function as required. Note that Cell structures would be hundreds of times smaller than that times discrete transistors and could perform complex operations more like later ICs could ( the cells could act as more than just and on-off switch ).
* Doping semiconductors and forming transistors using Active Transport ( a cellular biological mechanism ) inside growing cells to form/convert the micro-scaled electronics semiconductors required.
* Genetic switches (RNA/DNA) which control phased behaviors of the cells ( there would be several phases involved in forming the required circuitry structures ).
* While the cells are 'growing' they have to be given oxygen and nutrients - often requiring secondary tissues to do/help those functions, which can later be disposed of when the cells are 'baked'.
* The shaping of the cells and having them interconnect would also be part of the circuits functioning. The growth would be guided externally to interconnect as the logic/function requires, growth triggers and guiding stimulus would be part of the genetic programming of the cells.
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Magneto-Fluid Circuitry ( Another losing technology which McClendon investigated ):
“Our platform uses a rotating magnetic field that enables parallel manipulation of arbitrary numbers of ferro-fluid droplets on permalloy tracks.” ( actual technical description from a today current company ) - Sounds a little like a variation on the Pneumatic/Fluidic computer circuitry which people have attempted to develop over the years (they are fairly SLOW compared to electronics because they have a physically moving mechanical component acting like the signal electrons). 
The 'rotating magnetic field' drives 'droplets' directionally through stepped pockets along the 'tracks'. The presence of a droplet in a pocket then (magnetically) affects other droplets moving nearby, acting like a transistor/valve to control flow along a 'track'. Circular paths can act as a data storage points - where external inputs feed in signals which control parts of the overall circuit.
Logic can be built from mechanisms like this, but is generally too slow for 'computers' ( Maybe matching 'in speed' the primitive First Generation computers which used electric Relays - their limited cycling of less than 10 times a second). 
More useful as : For controlling the flow of fluids used in chemical (including medical) Testing where samples are split up, and many different reagents are applied in different test reactions - mixed in a standard multi-step test sequence. Modern technology uses thin plastic slide plates containing the 'track' paths, which can be pretty much 'printed' cheaply (enough), and are disposable ( ie- avoiding contaminated medical samples, and usually difficult reuse 'cleaning' ... ). For Rapture's era they would not be plausible. So this would be some filler Assets stuff for some project that never went anywhere.
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Neural Net Training - Natures Way Is The Thing ... :
The Bio-Electronic circuits when used are no longer 'alive', but ARE alive while they are grown into the useful patterns the various circuits need (a VERY useful attribute). Extra nerve cells, which induce the training changes into the primary cells for the circuit, are actually more complex in their training manipulations, and go away (become irrelevant) when the circuits are 'baked' into their final state. Similarly, the incidental production (process) mechanisms used while the cells are alive are removed, no longer being needed and having fulfilled their function.
Many of the cells themselves are fairly large nerve cells from Sea Slugs ( something required to operate as "transistors" with enough current/power to interface with normal Transistors ). Their formation is guided by their inherent growing cell process ( existing in their largely natural DNA ). That is then guided by external stimulations to have them extend their signal connections to other cells in the intended circuit, and to the external signal lines on the glass substrate. A repeated set of patterns in a 'learning' process guides this growth until the desired logic pattern is achieved. Then the cells are 'doped' in another process, with the metal ions required to make them function after the cells are killed and 'frozen' into their functional patterns.
Early tests where the cells were left alive did not work, as the cells continued to grow and change their patterns finally reducing them to uselessness. The 'baking' process stops/freezes the circuitry, preventing any further change from occurring. This also locks the cell bodies into a limited functioning, with only a fraction of the capability which living cells have. Some research was done into Suppressant chemicals to stop living cells from changing, but they too proved ineffective. With living cells, there also would be the matter of feeding nutrients and supplying the cells with oxygen through a 'blood', which required excessive complexities and difficulties and a careful restraining/conditioning of the environment which the living tissue could survive in. Some of this 'blood' process IS used while the cells are grown, when conditions can be closely controlled/regulated, but the need ends when the cells are subsequently 'baked'.
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Nerve Cell Basics :
The nerve cells themselves internally react to positive and negative signals and perform logic operations based on specific ratios of the signals coming from a large number of intercellular contacts ( making each cell the equivalent of many transistors ). They also can be structured to do progressive stages of this operation, making possible fairly complex logic functionality within the one cell. There actually are several types of cells involved in making this process happen. Quite complex 'generalization' functions on 'noisy' data can be created which can detect patterns in sets of many inputs and synthesize and output ( a 'conclusion' or interpretation of the inputs ).
The training method for the final circuit logic patterns is done by using the living nerve cell's inbuilt reaction/memory/pattern connection forming process where they are first stimulated to interconnect to send signals between cells. Some inter-cell connection spots are positive, adding in to make the cell 'fire' its outputs, and other connections add negative which suppresses the cells 'firing'. 
This all is employed in a feedback learning system used to shape groups of many interconnected cells 'firing' operation. Electrical charges are injected into a set of input points, the stimulated nerve firings pass from cell to cell. A Signal is sensed/detected at the set of output points. If those outputs are not as strong or weak as the pattern expects ( for the correct 0/1 outputs - what the circuit is being trained for ), a 'corrective' negative signal is induced to various intermediate cells, causing them to shrink/reducing the paths causing the incorrect result. ( Note - this IS the way real nerve cells operate and this fictional technology is making use of a natural mechanism ). There are usually many patterns the cell must respond correctly to, and the adjustments are made slowly and repeated until all the pattern's output results are virtually 100% correct. At this point the cells structure and state would be frozen ( to be converted to an inorganic electrical form ).
Cells are interconnected in multiple layers, which allows for complex logic pattern processing to be done. Even so, there is a limitation to complexity, and the final computers processing needs to be broken up into many separate functional 'sets' doing different dissimilar functions. These are combined and interconnected using conventional wires to form the complete circuitry.
A major advantage is all the 'cells' in the Neural Net operate simultaneously ( with a wave of data processing passing thru the layers ), resulting in a huge increase in processing capacity, versus binary systems which work sequentially (like when the same function is executed using instructions on a General Purpose Computer).
The training is somewhat tedious to do, and the 'teaching' mechanism would be automated using another specialized computer - one able to read the output and intermediate signals (the internal state of the cells) and decide on proper adjustments to form the required logic is operating. Sets of Training Data is applied repeatedly and iterations of corrections are made smaller to tune the processing 'weights' to correct the logic ( This is a natural function inherent in the Nerve cells ).
It is possible that individual cells just don't 'learn' their function correctly, but there are a redundant number of cells used in each 'processing set' to accommodate that shortcoming. Normally, sufficient cells will be shaped correctly to achieve the desired logic results. It follows the natural biological nerve mechanism of redundancy. 
After the tedious methods of Neural Net training of an individual circuit (where often a workable pattern never 'gels' and the whole process has to be started over (thrown out) - increased failure with the more complexity of the logic). Someone had a bright idea that the pattern of input weights developed successfully once, could be successfully replicated into another blank circuit with alot less effort. A master-copy circuit would be trained, and when successful was then copied into many (hundreds) more blank circuits. Testing is done and failing circuits are discarded, and those that pass (the yield) proceed on to become circuits. Logic in many cases can be done piecemeal (like part of a CPU) and combined/wired together later. The simpler circuits have a much higher 'yield' than trying to do everything in one large circuit.
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Other Biological Mechanisms (Bacteria/Virus) Could/Would Be Used :
To provide the needed logic/electrical functions, it is harder/impossible to simply FORCE/modify any single type of living cell to do so. As much as possible, existing NATURAL cell processes would be employed -- using existing (natural) genetics. That versus somehow creating them NEW from scratch ( through DNA gene changes or RNA manipulation ) -- which is practically impossible ( certainly in Rapture's time ). Even the simplest, most fundamental things will be difficult modifications of existing cellular chemical mechanisms. The genetics used would be borrowed from different tissues and different organisms, but that way is 10000 times simpler than creating them NEW (Even today, the simplest artificial bacterium genes created are exact copies from natural bacterium, and they get inserted into cells with more than 99 % of their original DNA remaining intact).
The conversion to the final 'mineral' (non-living) circuit form requires the cells to absorb large amounts of chemicals not normally associated with a living nerve cell. One or more of the conversion process 'phases' activates the cell to start absorbing and internally organizing these materials ( which further allow/facilitate forcing in other chemicals ). Some, like the organic semiconductors which are polymers, are not as toxic as others, like metals, which the cells have to endure/survive long enough to absorb sufficient quantities to function electrically.
Some chemical post-treatments can be used to add additional materials ( so the cellular forms can also be some fixative pattern system the added materials bind to ).
The glass substrate offers structure for the final electrical functioning of the circuits ( as an insulator, and for being easily cut into (fine) channels filled with conductors to act as 'wires' ). It is also the thin platform/surface on which to separate/guide/organize the interconnections/growth of the desired biological circuitry ( which will eventually be biologically inert ). Glass is a well understood material to be worked with. Layers of glass can be stacked like cards, and interconnected on their edges allow larger circuits to be built up. 
Light Sensitivity genetically added to cells to be used as a trigger for some of the phased nerve formation effects required to build the circuitry. Intensity to signal completion within a threshold ( detectable by the processing machinery ) - including detecting completeness across the entire circuit ( like large memory arrays ).
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Circuit Composition :
Plasticizing the nerve tissue to form different structures from that of the original source tissue (ie- use the brain structure from Sea Slugs or human (or other) brain tissue, but flatten (2D) it out physically to facilitate connecting external signal lines into it ...). The Bio-Electronic computers had many specific uses for this stuff, and would combine a variety of different functions. 
The complexity of the functions would also require building subassemblies instead of attempting to build everything in one piece. Hence the thin glass plates type circuit construction.
Building the different functional parts would be done separately ( as components on their own glass substrate ), and then be assembled. The appropriate component substrates would be wired together into the needed arrangement. ( This facilitates rejecting failed components BEFORE assembling them into the more complex full system ).
Gold wires are used 'on the outside' to interconnect this circuitry. Gold is a good conductor, is relatively inert, is infinitely malleable and can be made into very small/fine wires ( handy when you have groups of 32 wires only a millimeter apart in a digital data-buss path, which have to connect between glass substrates ). Gold also nicely resists the heat used to 'bake' the circuitry.
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Bio-Electronic Circuit 'Training' :
This 'training' is getting the nerve cells to interconnect in specific ways to become circuit paths for the intended circuitry & it's logic. There would be the process of combining nerve cells of different complementary types to form/built a desired circuit function. 
One basic natural function of these nerve cells is to automatically grow and interconnect ( as they do naturally in their development stages) when activated by various brain/physiological chemicals. Those chemicals ( or series of them ) can be applied manually to the cells being shaped so to cause them to adapt to their environment situation ( and connect with each other as they do in nature ).
Different nerve cell types exist. These different nerve cells have different natural functions - various Logic functions, long interconnections, supporting other cells while they are living ( Minor genetic modifications MIGHT be made to the cells to alter those functions somewhat, but there is already is a wide variety in the human nerve system and other organisms ).
Additional cells would be added/applied in the 'build' process, applied and matching up to what had been previously combined and assembled/shaped. This would be a stepwise phased process of circuit formation, letting the natural properties of the cells do most of the work. The 'training' was largely 'guiding' that formation.
The more types of nerve cells having their behaviors/properties mapped out, the more building of different circuit blocks would be available by combining them. The chemicals to manipulate them would also obviously have to be determined. ( McClendon had done research for Plasmid activation as a start, and then kept advancing the technology and simplifying and improving the processes making Bio-Electronic devices. )
Simple Circuits can be produced by using a simple mix of nerve cell types. The more complex the desired pattern, the harder it is to get a mix of cells to interact to connect properly ( have a higher failure rate ). Past a certain point, the mix results are just too chaotic and are not able to consistently create the desired circuit pattern ( poor production yield ). (( Quite Complex circuitry would be needed for 'computers'. )) This problem can be overcome by more complex steps of production, but even that has limitations.
An early major advancement was : using pre-laid-out Physical Structures on the substratumsubstratum - thin glass ( non-conducting ) plates the cell circuits were built upon. to isolate into small 'pockets' where the cell mix would be placed within. This localized the 'training' interaction between the cells. Each of these pockets would have a sub-circuit form in it - so now allowing a simpler controllable process bilding with the cell mixes. Lines/grids of these pockets pre-laidout ( etched ) on the sub-stratum, allowing 'simpler' cell mix formations to develop en masse in physical isolation. Later, a physical link would be added ( signal line conductors, gold wire contacts ) to interconnect the inividual pockets to form the complex circuity.
Example : large Digital Memory grids ( for 'computer' memory ) with signal line address decoders built into the circuit.
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Bioluminescent Display on a Bio-Module's Grid Facing :
* Activity and fault indicators (for diagnostics - including while being constructed/assembled)
* Nifty looking lights (all that classic blinkyness that represents a old-school 'computer' for many people - except tiny - fits in your hand ...)
* The same kind of regular square 'grid' structure used for Memory and Registers can be employed to emulate the scan lines a TV tube has, where the pixels are just stored values on the grid with a Bioluminescent component to generate a corresponding light dot of appropriate density and intensity.
* Light sensitive cell structures likewise could be used in a 'grid' to make a miniature camera 'eye' component that could stream serialized image data elsewhere (or as input for visual interpretation for a robot). Add some additional 'smart logic to pre-process the visual data (like YOUR eye does) all in parallel. ( "Got to get some speed back on these overgrown adding machines somehow" - McClendon ) 
* An important use is 'opto-isolation', where the computer signals are completely isolated from high voltage or noisy circuitry. A small Bioluminescent component separated from a detecting 'eye' component (light sensitive bio-circuitry), light transmitted through an optically clear and sufficient electrical insulator. An electrical control signal turned into light travels thru a good insulator and is turned back into a signal to be used by further logic - there is no direct electrical connection.
* Mix of old versus new technology -- the Bioluminescence would be something built/replaced later after the initial construction using the mid-40s technology ( and Ryan Industries experimentals/advances )
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Bioluminescence, Sea Slug Eyes and Glass Substrate :
Glass substrate was originally used because it was a well understood material which could be made consistently thin ( ever see microscope slide cover glass ? ), and is a good electrical insulator, chemically nonreactive (mostly), can withstand the temperatures needed for the 'baking' processes of the Bio-Electronic circuits ( the processes that converts from living organic matter into stable functional mineral circuitry. )
It also transmits light, which potentially means that multi-substrate circuits ( multiple layers of glass used to expand 3D and pack into a small space ) could send signals photo-optically between the layers ( probably useful when the gold wire method doesn't offer a sufficiently high number of signal conductors ).
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Another use for Bioluminescence would be in the training/production process of Bio-Electronics - to signal completion of cell transitions, optical feedback to the machines doing the training ( It is very repetitive and prebuilt data training sets are fixed for the required training to be done ). Having Bioluminescent organelles within the nerve cell emitting light when the nerve cell 'fires' would bypass having to temporarily wire to that cell to pickup that feedback event. Such a training process is NOT deterministic, and often requires retries, and 'relaxations' (reversions) are required to coax the cells into their needed 'logic' structure and desired function. This can be programmed into a simple computer to assist in detecting feedback and in managing the 'training' process. 
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Display indicators (LCD-like mini-displays) would be an obvious use.
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Natural Nerve Function - Amplifier :
Nerve Cells act as amplifiers for the signals they take in as inputs. There function is something that takes multiple components in normal electronics (bulky tubes or expensive transistors at BioShock's time period). With various signals (some quite small) moving around in the Bio-Electronics, and having to be transmitted out through more conventional circuity, this ability for such amplifiers is very useful -- fundamental to the whole Bio-Electronic technology that was ( I have made in the MMORPG ) developed in Rapture.
Natural Function - Logic :
Natural Function - Interconnection :
Natural Function - Learning : Self Modification
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Data Media :
Punchcards ( NOTE - you see them in Minervas Den - Those Punchcards were somewhat oversized to allow the players to read text on them ). It is kind of 'a throwback' to fiction showing Cards popping out of a computer instead of a printout on a printer ( or even a ticker tape) which was the normal method of output. Cards were generally used for data inputs (or for storing programs ). 
"Retrieval Number" - an index to a chunk of data/task/program somewhere in the system
Paper Tape - there were alot of those about, used for smaller transfers than would be used via magnetic tapes. It was a simpler mechanical system for smaller computer's program loading or for data. It could also serve as an output text stream ( simpler than a cardpunch or printer ). 
Microfilm system - microfilm blueprint embedded in a punchcard and the punches used to sort/find the microfilm image you need ( I've seen real systems like this used - kinda useful when you have hundreds of thousands of blueprints filed ). Such card sorting/collating machines were used before computers even existed. The same microfilm also might be used to archive punchcard data/printouts in a more compact form, though it is costly.
Magnetic Tapes - We saw some tape drives in Minervas Den which require manual operations to load/unload/store/retrieve the tapes. Usually there would be a large rack of tapes ( hundreds/thousands 'hanging' edgewise in horizontal rows ).
WE didn't see Data Storage 'Disk Systems', as it was a bit too early for that technology. 
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Computer Circuitry Creation - Macro Process :
* Select specific options for the desired Module functionality ( define the process and layout of the circuitry, data images (ROM) required, planned interconnects, memory and processing capacity )
** Determine set of 'layer' components making up the module ( typically 32 to 75 layers will be 'stacked' )
** Includes 'layer' patterns for dual-surface facings and even a third 'printed' layer (overlay)
** Discrete components required, physical packaging, plug hardware
** Collect/Create the Training Data which is used to guide the growth of the 'circuitry' through its production phases
* Setup for a Batch size for this one functional component type ( with MANY extras being made to handle/replace the inevitable defectives ). 'Mass production' techniques are used to lower the overhead costs for what is produced ( ie- 500 4Kb random access Memory arrays made as a group 'run', and the 'yield' rates vary ). Extras are 'basic' components which will eventually be used.
* Appropriate cultures of the needed biological materials are grown/made ready for the types and patterns of circuitry desired. Genetic manipulation and control allows pre-application of the needed cells with the desired characteristics. Included are many 'support' cells which function as part of the production processes, and then are eliminated/nullified for the final product.
* Combinations of cells which work together are mixed for application to the inert hardware (ie- the substrata)
Interesting Concept - that 'smart' machines employing Bio-Electronic computational logic can be used to ASSIST in the production process of other Bio-Electronic items
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Bio-Electronic Module Assembly and Packaging : 
Component Assembly (multiple 'Disk' layers are to be stacked and interconnected )
* Stacked Sequence of all required functional components ( Memory, CPU-sub-functions, Comm, Plug Interface )
* Assemble multiple planes (disks) by stacking the glass substrates
* Add heat sinks in between layers (copper metal foil)
* 'Buss' Layer interconnects via gold wire channel on substrate edges making contact with existing 'tie points'
* Test (computer rig) Full module circuitry functioning - Faulty units identified - with 'tear down' done to recover non-faulty parts
External Connections and Encasement
Circuit board connections to amps, discrete components ( actual miniature transistors ) and external wires (to module plugs)
* Test external connections functioning
* Placement within module case (metal shell), with physical fastenings
* Retest (yet again)
* Potting (inert filler) material added to encase/protect/act as heatsink
* Add Labeling defining programmed function of 'module', storage til deployed 
* Module assembly complete
Final Operational Test - failures torn down to recover useful parts, defects recorded for process improvement
Inventory Control ...
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Structural Construction of Bio-Electronic Logic 'Disks' (Substrate Units) :
Phase 1 - Form the basic inert structural substrate elements ( basically being thin glass slides )
* Glass substrate prep - each of 2 substrate facings is done separately ( ie- one has X lines other has perpendicular Y lines - separated so they don't make contact ). Pre-Annealing the glass. Cleaning, etc...
* Embossing patterns in heat softened glass blanks ( pressed with heated metal circuit pattern dies, and then careful cooling and annealing ) 
* Etching/linear scratching the glass ( to form channels, dimples, wells ). Re-annealing ( to eliminate glass imperfections and halt 'scratch cracking' ).
* Chemical deposit ( forming wire Signal/Power Lines placed in the etched channels )
* Placement of fine (thin) gold wire where appropriate ( some are temporary tie points for growth/formation process signals - removed later )
* Pre-bake ( solidifies the applied chemical conductors and removes any 'tissue' contaminants )
* Surface cleaning ( removing residues/dissolvable byproducts - flush to glass leaving materials in the indents )
* May Repeat above for some more complex circuits ( additional 'scratching' (micro pantograph) can cut/trim some conductors as per required design ). Additional indentations in glass substrate added for use of subsequent phases.
Phase 2 - Addition of Control Lines (first use of 'biologicals' )
* Print on the working layer on one substrate with the wells for the cells and the channels through which the nutrients will flow to keep the organic material alive during the production process.
* Signal Line Decoder pre-building/training ( employing the previous phase's signal lines, to build the basic wire controls used for fixed function grids ). Also added are amplifier stages for inputs and outputs. These control circuit structures are required to build/train later Phases. Most Often being built as a fairly regular (simple) trained incremental pattern used for Address control -- using parallel Address inputs to control a longer series of individually addressable signal lines ( ie- 6 Address Lines (2^6) are multiplexed into 64 or more grid lines). May be done in 'stages' to simplify the required function of the nerve cell mechanism, ie- 4 parallel sets of 4-bit decoders ( cells taking 4 on/off inputs to decide if they are to activate their output - the control line ).
* Preparation of 'Soup' ( active biological 'logic' materials ) :
Includes mix of many Secondary "Glial" cells ( different support Nerve cell types ) and added the engineered "e Coli"(bacteria used to insert genetic mods) , all used to facilitate the nerve growth process and to carry out the 'training' feedback/adjustments ( Note- this is employing a natural nerve function/behavior to cause the desired formation ).
* Apply/placement of living biologicals into specifically placed wells in the glass (squeegee method) of 'soup' (mix of cells with sufficient redundancy calculated for the required circuitry) 
* Glass plate assembly (2 facing sides directly in contact, so biological element can grow to contact the existing signal lines on the 2 substrates)
* Flow of nutrient/aeration is established using nutrient channels which 'feed' the living cells... 
* Stabilization/acclimatization of 'cells' ( which are in their pre-growth/formation stage )
* Injection of control viral RNA/trigger proteins/chemicals for activating the desired phased cell manipulations/behaviors
* Apply sequences of chemical steroids/triggers of growth phases ( for extension/spreading of dendrites, axons, unformed synapse - the parts of the cells that interconnect with other cells )
* Apply weak electrical currents in phased 'turns' onto the signal line 'wires' and control points as signal triggers/guidance/targets, inducing the desired logic cell growth patterns ( grow/form the cell's natural filaments to connect to the specific signal lines ).
Training (run by a computer driven rig - application of Neuroplasticity) :
* Chemical triggers for the learning phase activity of the cells, Chemical introduced to activate cell behaviors, which includes growing into connection patterns.
* Control Line current stimulus/induced patterns are applied ( the 'biologicals' elements 'grow' as genetically programmed (designed) in response, and develop/reinforce strong/weak connections by the way they are stimulated ). There are positive and negative (inhibitory) cells (Gogli/Purkinje Interneurons) in the mix required to implement the logic.
* Signal-outputs are measured ( by the 'Training Rig' machine, reading real and temporary outputs ) and corrections being 'factored in' to shape the desired logic function are issued ( utilizing the already functional Signal Line decoding addresses, signal injectors, and signal amplifiers - cells which were previously converted into inorganic transistors/circuitry. )
* Application of correction trigger(s) to cells -- which change Nerve Synapse strengths and guide dendrite growth. ( Use of nerve cells natural correction process ).
* Repeat (rig training) til the 'living' nerve circuit logic works as required within operating specs ( Nerve Cells 'fire' (generate output ) when an appropriate pattern of inputs are active diagram ) Often is created as redundant overkill, because the later 'conversion' discards the 'ion' mechanism for an electronic equivalent ( utilizing the 'doped' tissues now acting as insulators/conductors/resistors/diodes/transistors/capacitors ), which has to adopt the 'grown' pattern of logic and continue operating electronically. Even with low yields (high failure rates), the advantages of such circuits would make them highly useful/profitable.
Thermal Conversion : 
* Using Genetic triggering of mineral absorption - with change of nutrient solutions being circulated, causing mineral/chemical buildup inside cells
* High temperature 'Bake' - destroys living components of cells (making them inert/unchanging/removeable) leaving mineral and organic polymer conductors, semi-conductors and insulators ( with a structure the cells were engineered/coerced into growing ).
* Test of resulting electronic functionality ( run by a computer-driven rig ), to discover any defects in operations.
* Wired corrections - adjusted for making use of pre-planned redundancies ( a few extras and the design to allow it ), and physically late wiring to the correctly working circuitry, and leaving any faulty 'circuitry' unconnected. ( This was actually done on complex real world chips like 'memory' where extra rows for functionality were built and allowed enough working 'rows' to match the chips specifications - 9 rows with 8 needed for a 'byte' and possible use of chips with all 9 perfect for Parity functional extra value ).
* Possibly repeat above process stage for any additional specialized circuitry (additional basic wiring) 
Phase 3 : Build Primary Function Logic ( Aggregate more Biological Circuitry upon the now inert Data Connection Circuitry ) :
Further circuit formations build upon the basic circuitry using a similar process to the above build phase.
The Data Connection Circuitry can further facilitate other circuitry formation being used as stimulus as well as process feedback.
* Addition of 'bits' cells to be grown AFTER the grid circuitry is operational - grid signal lines are required for 'bit' logic training/'programming' - Example in a 'grid' there is a dimple at every intersection of the X and Y control lines where function are done when the control lines activate
* Repeat - if there is more logic which is dependent on the basic logic preexisting, and subsequently needs to be formed and trained. Some sensor types have sensitive structures which need to be built in a final phase (if done earlier the circuitry would be destroyed by a subsequent process ).
* Complex Circuitry :
** ROM data value (static) array programming ( fixed memory containing a program/data )
** RAM Memory Array
** Irregular logic formation ( Arithmetic and logic functions of the CPU - a fixed pattern )
** Complex logic training ( ie- "Neural Nets" which take extensive 'living' training operations )
Phase 4 : Full test of the circuits electrical function and environmental tolerance (soak test)
Computer test rig repeatedly runs through simulated inputs/expected outputs. The actual logic runs, demonstrating it processes the correct results. Faulty units are discarded ( some may have clever 'partial' usages, and others redundancies which can have 'correct'/valid subsections selected, with failed sections disabled ). Repetition proves that circuit logic works reliably. May be repeated under different temperature conditions to meet requirements of the final product.
Functional Component 'Disk'/'Plate' complete - put into storage for application to final product.
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Make batches of all the other 'disks' flavors to make all the required components for the final product - Microcontrollers require a CPU, RAM and ROM memory, and interfacing to the controlled devices ( sensors, communications and/or machinery servos, signal relays ).
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Need to discuss HOW this is supposed to be done efficiently to warrant mass production lowered costs (all the stuff for 'The Thinker' without bankrupting all of Rapture, and to have similar 'smart' logic for various consumer items).
Old things still work fine - does adding something of this sort offer improvements or cost savings or new capabilities - DOING it because it merely is NEW is not valid in the real world ( and Rapture IS a bit small for custom fad items to produce profit, or even pay for their creation ).
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Development of Bio-Electronics In Rapture :
Time frame ? : It would be AFTER ADAM genetic research is fully going - and better if not too long after when The THINKER is supposed to have been made to exist -- while Rapture was still 'normal' - BEFORE the collapse ( Kashmir, and Porter being locked up for sedition long before Ryan's death ). 
The main player, McClendon, should be connected somehow to the ADAM technologies to have him develop/realize an interest. Electronics has to somehow take a jump past what existed in the Real World in those decades to do ANYTHING like what the game shows computer-wise.
A progression of discovery and development ( These are NOT 'baby steps', but each difficult achievements ) :
* Discovery of the 'converted' cell Semi-Conductor effect, realized while Electron Microscoping ADAM type 'genetic' research ( need some name of the guy ... "John Fremont" ?? ) McClendon ( who is an electronic genius ) hears about it and investigates. Evidence of Semi-Conductor properties is noticed ... 
* Diode Effect ( Used to facilitate one way signals/currents in electronics ) Miniaturization is the goal and he's been watching technical progress on the Surface.
* The Amplifier/Amplification Effect is found when McClendon starts playing with the modified tissue ( a goal required with vacuum tubes/transistors to make proper/useful electronics )
* Logic Switch Operation ( flow of logic (output) controlled by inputs put through AND/OR/XOR/NOT functions - required for 'Digital' electronics. )
New Mass Component Development project is funded ( includes some genetic cell growth manipulations )
* The Trained Summation Effect ( Neural Fuzzy Logic ) - Nerve cells grown/formed-for analog signal strength threshold filters ( via guided neural net function )
* Negation Effect ( different/combination of cells that create a reversed input - a natural function ) multi cell interactions
* Bio patterned learning ( ratio of cells, placement, stimulation with chemicals, electric currents ) - natural affinity so self organize/interconnect
* Simple control circuits ( components which do feedback regulation - a commercial product )
* Complex - digital circuitry ( more smarts built in to the components - more miniaturization )
* More Complex - array circuits, multi strata circuits, mass logic produced ( useful for computer systems )
* Calculator - Miniature Calculator Produced as Commercial product ( first to do Square Root )
* First Simple Computer - Von NeumannVon Neumann Architecture - Used in 99.99% of modern computers today architecture allowing digital programming 
* Massive Logic - large memory arrays, video functions, mainframe capabilities
* Full Computers, real-time/networked computers, robot controllers ( "computer in a breadbox" miniaturization )
* The Thinker - mass production of complex components - Voice recognition/voice generation
* Real AI ? Nope. Sorry. Not even achieved yet in Our World, even 60 years later. ( But mimicking something like it could be possible. )
Perhaps, rather than being a drunk and a confused businessman, McClendon ( who drove most/many of the above developments ) had 'burned himself out' while making these significant technological developments - not just 'lab' discoveries, but converting them into WORKING PRODUCTS ( engineering and beyond ). Perhaps, like Edison, he worked 18 hours a day for years, until he imploded about the time Rapture was falling apart.
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Bio-Electronic Term : "Meta-logical" ( The "Distributed Solver Methodology" of The Thinker's AI ?? ) :
Sounds a little better than 'Squirmy-logic' or "Mr Binary's Magic Logic" ( for the advertisements ). Or "Porter's ProblemSolver"
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Frozen Brain or Somesuch :
Freezing living cells to cryogenic temperatures - superconductors ( mentioned in docs at McClendon as a future possibility ) - Unrealized. Cryogenics is fraught with complications/difficulties, and even today is hardly used ( Hint - Superconductor effects usually take place within a few degrees of Absolute Zero (-273 F). With Numerous Difficulties, even in OUR Times. ) 
NOTE - The Real World of 'Quantum' experimentation requires similarly cold operational environments within some few THOUSANDTHS OF A DEGREE from Absolute Zero (0 degrees Kelvin scale), which even Today takes HORRENDOUSLY complex/tempermental/EXPENSIVE lab machinery to achieve ( Making it patently ABSURD for 'Stone Age' Luterces/Fink/Suchong to be doing any such things. It is just so much (Wave Of The Hand Fantasy Storytelling - as loosely based in Reality as a Diarrhetic Wildebeast's stool sample ).
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Natural Redundancy In Physiology :
In nature, nervous systems are based on redundancy of the cells involved ( and an adaptive ability to handle frequent individual cell death and damage ). My proposed Bio-Engineered electronics would use living cells which can self-organize while being guided in their formation - to be trained in the desired logical function, before they are 'frozen' ( 'mineralized' to form the final unchanging circuitry) . 
Precise placement of individual cells is NOT impossible, but IS tedious and impractical. Physiological cell growth/adaption/interactions naturally take place in an environment of multiple cells, including between several types of cells which complement each other. Mixtures of appropriate cell types would be deposited into the glass substratum en masse, with reliance on their largely natural process of interaction and interconnection then taking place. The cells would form to work as a group, as they do naturally. With further manipulation (training) they would produce/form into the specific (desired) logic structures for the electronic circuitry.
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Short-term Memory Function of Nerve Cells - For Computers :
Natural Brain memory use has internal feedback from the nerve cell to propagate the same temporary state, which is then retained and kept available for output signaling.
A Bio-Electronic mechanism would be similarly used (the feedback function), except it would be made compatible for the chemical changes the static Bio-Electronic circuitry requires.
The Bio-Electronic memory function is carried out using natural cell patterns which requires a combinations of several related cell types ( to join to form a feedback circuit ).
The needed structures/forms/patterns are imposed using a physical substrate to generally shape the circuits interactions ( into a more 'digital' pattern versus the more complex interconnections in a brain ). Interface points of each memory 'bit' connect to the on-stratum signal lines, which are then eventually fed out to external wiring.
The cells involved are 'trained' to match the required function -- to be a digital memory 'bit', which is then grouped in a grid of many bits built to form the data storage a digital computer requires. 
ROM (Read Only Memory), a separate type of memory, has permanently set data pattern. It is simpler, and doesn't need the mechanism to change data state. Its data state gets 'set' once permanently as part of its 'training' process - set into the desired data content ( to contain program or program data ).
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Using Natural-type Brain Logic ?? :
Nerves cells in a brain are self-modifying ( it is something they need to be alive to do ). They can form VERY complex patterns which they need to grow into ( genetic based structure then formed and modified through the organism's existence ).
Logic (for computers or other) could be done potentially as (analog) self-modifying 'neural nets', but those are VERY hard to program (train) for anything useful (hard even today). That difficulty increases geometrically with the desired functional complexity ( like being complex enough for just a SIMPLE computer ). That makes anything further (like The THINKER) pure magical fantasy ( which Rapture IS NOT supposed to be ).
The Thinker, even with fake-intelligence, needs logic programming far beyond the complexity of 'natural' logic mechanisms. If it was a human brain in a jar at its core (as natural tissue), being from some person who had lived a real life (to form its intelligence), only THAT might explain how it came to exist.
BTW, That 'alive' aspect is a quite difficult (as in horrendous) problem in itself. The mechanism to keep living tissue alive, stable and functioning is more a laboratory trick and not something you could have for a workaday machine. 
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INSTEAD, What the Rapture Bio-Electronics does is : Use nerve cells to make SMALL components, which then operate in a forced ( well-understood even in 1950s ) Digital manner -- Laid-out/following ordinary well-understood DIGITAL interconnections/circuitry patterns ( which our modern-world computers all use today ).
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Fine Wire Required For the Bio-Electronic Circuits :
"Wollaston Wire" (less than .01 mm thick) platinum wire first made in early 1800s ( human hair typically .05mm ) Gold can be similarly used. Surface Etched with micropores so that the cell-to-wire physical connections are facilitated. 
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Amplifier Bio-Engineered :
Nerve Cells do this function naturally ( Dendrite inputs triggering Axon output )
External signal lines coming out of Bio-Electronics have to have sufficient current and voltage to connect into conventional electronics - where further transistorized/tube amplification can be done. So the amplification of typical nerve cell signals IS NEEDED.
Internal signals ( like within/across a 'computer' block of connected Bio-Electronic sub-stratums ) also require some amplification.
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 "Yield Rate" (In Manufacturing) :
A term for the PASS (success) Rate of manufactured Components to be used in Products. Most components are thoroughly tested BEFORE being incorporated into more complex assemblies - modules/sub-assemblies ( Better to find defects early and before doing work that later may have to be discarded).
A low Yield Rate means you have to start the manufacture process by making lots MORE of the item, expecting that you will find/test them and have to discard/reject some number that don't PASS. In mass production, individual FAILED components may be discarded as not worth reworking,
Complex components usually have a LOWER Yield Rate ( being typically easier for them to fail their testing ).
Short run/specialized items often have a LOWER Yield Rate - as not as much effort would be put into developing/perfecting a better Manufacturing Process. 
Products made up from multiple components can also be tested and pre-repaired/reworked.
This is another factor in the Higher Expense (Cost) for things manufactured in Rapture ( and secondarily for their repairs - Cost of spare parts ... )
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Bio-Electronic "Trainer" Rig (Tool) :
Part of the Process of Manufacturing various Bio Electronic components ( the complex ones that are 'grown' ).
Can be controlled/automated by Big Clunky Computers(tm) - the older (WW2) existing technology. Mainly it is done by repeatedly applying electronic signal patterns (to the cells) in the Training process. Then reading and checking adjustment results and using simple logic to continue with further corrections. Finally, the system is used to do reliability/quality/confirmation testing on the produced Bio-Electronic components. The process is USUALLY applied to 'batches' and definitely allows for individualized corrections.
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FET (Field Effect Transistor) as Part of the Bio-Electronic Tech :
Date of tech dev real world =
Is basically the magnetic field from one conductor controlling current flow in an adjacent semi-conductor across a gap. ( Similar to the way a vacuum tube works ). Some of the Bio-Electronic mechanisms work this way ( when it is easier to build a 'gap' than to get cells to do something unusual with direct electrical connections. )
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Building Electronic Components in Sections :
Unlike our single IC chips that are made as just one part ( It is why they are so cheap for us these days ), and which have to be discarded when they are found to be faulty.
Raptures more complex Bio-Electronics would often be made from smaller individually built sections, constructed and tested separately -- each section is STILL equivalent to many individual 'discrete' (individual simple) components ( which is what Electronics/Computer were built as upto the 1960s ) and thus Raptures could be is far more compact.
Complex products can be modular, allowing replacement and rebuilding the mechanism. The preferred production process is to find defects BEFORE assembly, but sectional replacement can be effective (when possible) rather than discarding the whole complex mechanism (very costly when it is a "Computer".
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Sea Slug Brain Tissue - Interesting Properties :
Rapid change of logic structure 'learning' which allow adapting/training for diverse logic patterns.   Think of them as biological PLAs (programmable logic arrays) or Microcontrollers ( Real World minimal CPUs ), and to some extent using NN (Neural Net) style of programming.
The training consists of being repeatedly subjected to data inputs and stimulating the natural feedbacks for success/failure to reinforce correct outputs.   Depending on the complexity of the input patterns effective logic can form rapidly.  More complex logic takes longer to form.  Often logic sub-groupings are built independently to hold down the total complexity for one 'brain' circuit.  Complex solutions ( like the Flybot controllers ) then employ many sub-brains circuits to achieve their complex behaviors.
Heh - since each 'Brain' is grown independently some may have a few logical glitches which can be used as an excuse for real glitches/shortcomings in the MMORPGs Games program logic ( at least until the bug is identified and then fixed ).
Logic has its limitations and the circuitry can only respond correctly to patterns it has been trained in, so that various machine wont be brainiacs, and will have known many ways of fooling them.  ( BTW, same thing goes for this MMORPG, but it has an updating mechanism that allows bugs/deficiencies to be eventually fixed/elaborated ).
Thinking about it, In-Game Machine Logic is yet one more thing that Player Creators can work on to improve ( to try to simulate correctly what the machines would act like in Rapture ).  I can imagine a game design spec saying that this X.123 machine has to in-game simulate being this smart (and no smarter) to represent realistic limitations.  Some machines will simply be pretty dumb -- as they will suppose to be ( particularly later when Rapture's technology has taken a nose-dive ).
There may be some crossover that an improved  'circuit' be developed via Player Creation programming ( named after its creator no doubt ) that can correct/improve In-Game machine behaviors, and become a "product" to be developed ( via research and development mechanisms ) to make that upgrade product available to the Citizens of New Rapture.
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Bio-Electronics ( 101 uses for a Dead Sea Slug ... ) :
Those round ports are for the disk trays for the multitudes of logic disks use for much of The Thinker's processing mechanism.  
The logic disks are bio-engineered from sections of (non-ADAM) Sea Slug brain, regrown and then doped with various semiconductors and baked into electrical circuitry.  The still living neural sections, before being 'fixed', are re-trained with the desired logic patterns (neutral nets stuff). Once they function adequately are crystallized and converted to X-isters.  The tiny features of the brain tissue is preserved and often is equivalent to many thousands of multi input logic 'gates'.  The logic being electronic also 'switches' thousands of times faster than natural brain tissue does.
The physiological logic patterns were such that the same manufacturing process is used to build the optical interpretation (visual sensor) circuits for fly-bots and security scanners.  The simple structure of the sea-slug's eyes  are converted to visual input devices ( equivalent to mini TV camera ) directly compatible with the interpretation.  circuits.   Mechanical optics/filtering/frequency converters feed the images to these 'eyes'.
Human brain tissue was tried, but like most higher lifeform's were too complex -- Their structure of Input-Processing-Output would not fit in any acceptable circuit size.   More problematic, it was too difficult to train properly.  
Training consists of stimulating patterns of inputs one case at a time and inducing neural 'learning' adjustments ( a natural biological process modifying brain structure ) until the correct output is produced matching the input.  Many thousand of training cases are used, building up a generalization capability (pattern matching) or an exact logic function(calculator).  A number of repetitions are generally required to slowly mutate the Sea-Slug brain into the desired processing ability.
One of the most significant advancements, was folding the circuit back upon itself so that it could feed 'output' data back into the 'inputs' and create much more complicated algorithmic functions within a single disk.
Once a 'logic disc' is created, it can then be merged into The Thinker (or other Comp-U-ter), stacked by the hundreds in large parallel cylindrical assemblies (processing cores). A much smaller stack of such disks makes up the brain of the Flybot Security units.  Later 'disks' dispensed with much of their bulk and were made paper thin, allowing many more to fit in each 'core'.
The great power of The Thinker comes from all these multi thousand circuits processing simultaneously.
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Other Technologies With Similar ADAM Recharge/Use Requirements ( or Needed For Its Manufacture ) :
* So that the ADAM material still has its value in New Rapture, even though Citizens have supposedly 'kicked the habit'...
* Logic 'bio-logic' Disks for repairing the Thinker/other Computers (trained Sea Slug brains flattened out and 'backed' into a semi-conductor that does complex logic operations much like a small CPU)
* Components for other  'intelligent' machines ( Fly-bots/Turrets/Scanners/Bathysphere Auto Pilots/Access Keys/locks )  
* Medical Equipment, biology based genetic scanners (or components for)
* Other medical/industrial uses modifying plants/tissues to create useful bio-chemicals/organics
* Miniature TV 'eyes' (many of those TVs have been watching YOU)
* Decoders for TV/Radio/Datalinks (the digital age)
* New batches of high-efficiency Bioluminescence chemicals used for the new lights.
* A Scientist named Alan Parson developed a 'project' of some momentous importance, but then the Rapture %27civil war%27 happened and he and his 'project' were utterly destroyed, and that great world-shaking achievement was lost to oblivion ( sometimes you Open the Box and the Cat is Dead ... ).
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Bionicle (Not Monocle at the Rapture Chronicle) :
An ADAM BioTech enhanced vision device ( eye tissue is something that could be manipulated, as it already has relevant functions without massive genetic redesign ).
Infrared, Low Light, Movement Detection, Magnification, Eagle Eye, Stabilization ?, etc ... ( Sorry, NO X-Ray vision )
A Nifty Glowing eye effect ... ( Was probably all 'the rage' back before the 'civil war' ruined Rapture's partytime ... )
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Polar Bear Hair as Optical Links ( How does he come up with this shit ... ) :
Clear 'light-pipe' hair core conducts sunlight into the bears skin past dense inner fur (for vitamin D production in dim arctic light)  Length 2-6 inch,
We see those 'bear' trophies in the museums and apartments, and some Brain Boosted Crank got an idea ( probably  started via the opposite use - interior fur lighting effect, some rich person requested - glowing fur with points of light to show off ... ).
Combined with Bio-Luminescence Tech from the Sea Slug research, as well as light sensitive nerve cells.
What does this mean ?   Grids of data 'light' fibers connecting 'brain' modules in The Thinker.  Modules made from Simple Sea Slug brains, trained for a variety of processing tasks.
No Smoking in here !!  Smell of burnt hair and someone gets immediately fired ... And weeks of work now needed to fix those parts ...
This she-it is getting too weird ?  Weirder than some of the things shown in the concept art ??  It is just little detail bits trying to make BioShock 'Sci-Fi', as it is SUPPOSED to be.
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IDEA : Jellyfish Organism with simple Eyes as source for Bio-Electronic devices ( DNA research into producing bio-tech optical light sensor/components ).
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