Thoughts on Designing Interdisciplinary Courses I

Hi all,

Here are some thoughts on how to design a course that blends mathematics, biological science
and computation together.  It grew out an interest in following the recommendations of the Biology 2010 report
( CUBE. BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Commit-
tee of Undergraduate Biology Education to Prepare Research Scientists for the 21st Century, National
Academies Press, 2003 ).  I began to do this in 2006 at the request of my Biological Sciences department
using textual materials, software and so forth of my own design.  By 2008, a first draft of the resulting
lecture notes was available as a Print on Demand Book from www.lulu.com which is an online publisher.
These notes are now in the Fourth Edition:
( Calculus For Biology: A Beginning – Getting Ready For Models
and Analyzing Models. Gneural Gnome Press: www.lulu.com/spotlight/GneuralGnome, 2012. )

I have taught about 100 students per academic year with this course which is a replacement for
Engineering Calculus Two.  The engineering calculus two was never a good fit for
the biologists and so my course trained biologists to be aware of both mathematical and computational
tools in the pursuit of biological insight.

However, the course was only taken by 100 students out of about 1500 majors.
The students who took the course were mostly required to do so by their curriculuum.
Approximately 75% of my students were PreMed also.  Hence, my enrollment was tightly
tied to the fact that most of the students who took the course were required to do to so.
Not all, of course, but most.


From this cadre of students, a small number ( 1 - 4) per semester would then take
further courses of this nature from me and some began to build biological models with me
during their sophomore through senior years.  But, the vast majority of both the biology majors
and the biology faculty do not like intellectual pursuits intertwined with mathematics and computational ideas
and so support within the biology department was limited.  Indeed, support within my own
mathematics department was limited as well.  I often felt like I was pretty much alone in these efforts.

My efforts appear to have been wasted as the biology department has just voted to

make any second calculus course optional for all their majors.  The only requirements are now

the first calculus course and a basic statistics course both of which can be satisfied by

a well prepared high school student with AP credit.  Hence, the vast majority of biology majors

will now go an entire four years of college without additional training in mathematics, statistics

and the use of computation.  This, of course, also impacts how they will learn physics, biochemistry

and so forth as more sophisticated treatment of the ideas in those disciplines will not be easy for them

to grasp do to inadequate background.

The enrollment is my Calculus for Biologist course will drop starting in Fall 2013 from 50 students

to probably 15 or so.  The enrollment in Spring 2014 will also drop from 50 to 15 so

I anticipate at most 30 students per year now rather than 100.  It could also be less too

and if the enrollment is too low the course won't be permitted to run.

It seems my grand experiment with the backing and approval of a small group of

biologists to try to implement some portion of the BIO 2010 recommendations has been

a complete and abject failure.

But I think the reasons for developing this course and the larger goals of the BIO 2010

report are worthy ones.  Over the last few years, I have written up some of my ideas

on how to design such a course and I thought I would share them on this blog.

The notes that follow were written in 2010 and I have changed them a bit for this blog.

Let me finish this introduction with a quote from an article in the Times Higher Education

from June 30, 2011:

``Competence in mathematics is desirable for everyone 

but vital for scientists, yet there is a widespread, 

deep-rooted fear of the subject. 

Stephen Curry insists that this can be overcome by 

making maths an 

integral part of science education''

That article is an interesting read.  I have been completely defeated by these deep seated fears

but perhaps other people at other institutions will find a way to do it better so that these

ideas can flourish.  

A White Paper on Interdisciplinary General Education:

Thoughts 2010 - 2013

James K. Peterson

Department of Biological Sciences

Department of Mathematical Sciences

1. Developing Literacy

When I was a younger man, I worked at Union Carbide as an operator

who helped run the equipment that made the plastic that is used in

baggies and the coating of telephone wires (among other things).

My responsibilities were split into an outside and an inside job.

Every other day, I would have the outside job which entailed me

walking around the plant looking for mechanical problems.

If I found some, I would shut equipment down and prepare it for

the maintenance staff by shutting valves and so forth.

On the other days, I would in inside the control room

operating the controllers which determined the kind of plastic

we were making on my shift.  I liked both jobs as they

were interesting and used different skill sets, but I particularly

liked the outside one as it let me rub elbows with some of the

master class maintenance people.  I remember in particular 

a pump repairman named Dave.  This was about 1973 and even then

an expert such as Dave was being ridiculed for his emphasis on

problem solving and correct technique. We used huge pumps

driven by as much as 5000 hp motors.  All of them had a typical

flange and seal design.  When the material they pumped began

leaking from the seal, the pump had to be shut down, the flange removed

from the head by unbolting it and a new seal put in.  This needed to be

done delicately and Dave used a dial indicator attached to the head

and the flange to make sure the heavy flange would be attached

absolutely level once the new seal was put in place.  Then, the flange

bolts would be tightened like we tighten the bolts on a tire

when we replace a flat: tighten bolts in pairs that are 180 degrees apart.

This ensured the flange seated properly against the seal.  Dave's

precise maintenance procedures led to rebuilt pumps lasting for many months

of continuous service.  The other guys in the pump repair crew

thought Dave was too fussy and didn't want to learn all these careful

and useful ideas.  They didn't value his skills and they didn't want

to learn his skill sets. 

They did not take as much care in their

maintenance procedures and the pumps they repaired

typically lasted only a month or so.   So, the general ability of the pump repair

crews at the Union Carbide plant I worked at went down each year.

Of course, it is also surprising that the engineering staff in charge of plant

operations accepted such lax behavior.  The message is clear.

If we want to encourage the development and retention of such mastery,

the work environment must encourage it.

Dave was a master craftsman whose way of looking at the world was

not valued by both his peers and by the plant managers; hence, it was not passed 

on to the next generation despite his many attempts to do so.  I used to listen

to him explain about pumps and all sorts of other things

in which he would try to make me see how to look into a machine

and feel its wrongness.  He was very good at taking a big problem

and breaking it down into smaller sub problems.  These smaller

sub problems were, of course, easier to solve.  He showed me

in a very real way how to make progress on a complicated thing, you

needed to subdivide the larger issues into pieces small enough

to work with.

I used to watch other craftsmen also at my plant.  Some worked

on metal lathes, some worked on assembly and disassembly of large

machinery and all of the good ones were masters of their

craft in the sense discussed above.

These early lessons for me occurred while I was

working full time and going to college part time

and so I was in the great position of being exposed

to both the abstraction I saw in college

and the pragmatism I saw in the trades.  In both

fields, the ability to move between theory and practice

is exemplified by the situational fluency of the expert craftsman, but I am afraid we

are moving away from it more and more.

The Nuts and Bolts Foundation is concerned that our young

people are losing this ability to connect practical

aspects of diagnosing problems and building solutions to

the theoretical knowledge they learn in high school and college.

They think (B. Bergeron. Mind/ Iron: Little hands build big dreams. Servo, 8(1):6–7, 2010)

``more has to be done in the American educational system.

For example, shop classes - once popular -

are now rare.  As a result, most students who

finish high school are functionally illiterate

when it comes to basic mechanical skills such as the

ability to read a ruler.  [Also, many employers

have a complaint about] new engineering graduates.

Apparently, they often can't build anything because

they don't know how things are made.  Theoretical

knowledge alone just doesn't cut it on the shop floor.''

They also believe 

``resources [must be] devoted to the pleasures

of 'tinkering' -- getting away from ... video games

and TV sets and into the backyard building things.

In that way, we will create the next generation of

artisans, inventors, engineers, repairman, and skilled

workers -- in short, a self-sufficient, self-sustaining

society.''

This idea of  tinkering and creative play

can also be applied to what 

(M. Resnick, J. Maloney, A. Monroy-Hernandez,

N. Rusk, E. Eastmond, K. Brennan, A. Millner,

E. Rosenbaum, J. silver, B. Silverman, and Y. Kafai.

Scratch Programming for All. Communications of the

ACM, 52(11):60–67, 2009.)

refers to as digital literacy.

``It has become commonplace to refer to young people as ``digital natives''

due to their apparent fluency with digital technologies.  Indeed, many

young people are very comfortable sending text messages, playing online games,

and browsing the web.  But does that really make them fluent with new

technologies?  Though they interact with digital media all the time, few are able

to create their own games, animations, or simulations.  It's as if they can ``read''

but not ``write''.

As we see it, digital fluency requires not just the ability to chat, browse, and interact

but also the ability to design, create, and invent with new media.  To do [this],

you need to learn some type of programming.  The ability to program provides important

benefits.  For example, it greatly expands the range of what you

can create (and how you can express yourself) with the computer.  It also

expands the range of what you can learn. In particular, programming supports

``computational thinking,'' helping you learn important problem-solving and

design strategies (such as modularization and iterative design) that carry

over to non programming domains.  And since programming involves the creation

of external representations of your problem-solving processes, programming

provides you with opportunities to reflect on your own thinking, even to think

about thinking itself.'' ''

So it would be nice to return to undergraduate courses designed to 

develop a sense of general literacy in the students.  This would

include the ability to use computation and simulation to develop insight,

to build appropriate blends of mathematically enabled science for the purpose of

exploration and utilize creative play in generalized learning.

These attitudes would, of course, 

enhance the student's ability to problem solve and integrate theoretical and practical knowledge.

A general philosophy might be one I often use in my own classes.  We should be

developing tool builders rather than tool users.  No matter how careful the training,

all classwork is eventually obsolete in the light of rapidly advancing technology and science.

Hence, what is of paramount importance, is to teach students how to think for themselves;

to learn how to rapidly scan lots of information in books and manuals to gather the gist

and to know when to assemble a new tool from scratch to efficiently solve their current problem.

In many of my engineering jobs, I was routinely simply handed a mountain of information in the form

of poorly written manuals and hand written documentation and told to make something happen

in a few days.  Well, you just can't read all of the stuff in a few days, so you have

to be good at sifting through the pile for the useful nugget.  This also means

you have to be good at taking the task you are given and breaking it down into smaller

problems more amenable to attack and then use tools to develop more insight.

This definitely involves what Resnick said above. You have to create new representations

of the process you are using to solve the problems given to you and reflect on how you

are thinking about your tasks.  

So how to we inculcate this kind of attitude in a class?

I myself always try to get the students engaged intellectually

by asking questions verbally, by applying the things we discuss

to real problems and reiterating that it is important to carry a lot

of material locally in your head.  ``Look'', I'll say, 

``if you are working for a company and are at the water cooler or lunch

when you get into conversations with your boss, the boss will appreciate

your ability to think on your feet.  If you always say you have to go

look it up, your boss will slowly but surely learn to rely on others

who can have an informed opinion using their skills on the fly.''

So the bottom line is that a student does need to master their

coursework in such a way that they can draw on it in real life

situations without access to a book or notes.  They become leaders then

and that is what we need.  

We also need students to be able

to pull out of complicated situations and data, the bones of the underlying

ideas buried inside the mess.  My own training has been very much in the

physical sciences, but I'll mention a few examples to show how I was

trained to abstract out of messiness underlying principles.

A. When I was in grade school in the sixties, we had to outline

every chapter we read in our textbooks as our first assignment.

We were being taught how to quickly find the main points of our reading.

Oh, we complained, but since we all had to do it, it soon became second nature.

B. In grade school, we also had to write all of our homework in ink

and we were not allowed to erase anything.  So, if we made a mistake, we

had to rewrite the whole page!  This sounds horrible today, but it had

a huge benefit for us.  We very quickly learned to write well in our

minds prior to committing to paper.  It made a lot less work for us

to organize first and write second.  Also, not being allowed erasures

made us learn real fast how to do it right the first time.

I am sure these simple demands helped shape my ability to

pick out main ideas, shape my arguments efficiently and so on.

And it was just what is now considered an onerous exercise.

C.  In calculus, we learn to integrate functions which are very simple at first.

Then, we learn to use a technique called substitution which allows

us to see how buried in a very complicated integral is a much simpler

pattern we can find by using the substitution idea.  The details of the

mathematics are irrelevant.  The point is by doing many of these sorts of

problems, I was training myself to recognized underlying patterns buried

in ostensibly complicated expressions.  After awhile, any of us being

taught this way, had a light bulb go on in our head. Forever after,

we would always see the simpler pattern buried in the complicated one.

We could then take this new found skill and use it when we looked at

interactions of people, insects, gases etc. and start to see

laws that governed interaction.  Hence, a simple rote

training exercise using a mathematical tool was actually a much

bigger exercise in helping us to see how abstraction

-- the process of pulling patterns out of complexity --

was useful.  

As a final comment on how we are trained, consider that I learned to write

themes on paper by hand in ink.  I was not constrained to use short and simple

sentences and constructions; the pristine white of the page was my playground.

We have now transitioned to doing most of our creative writing on laptop screens.

The geometry of the page we write on is very different now.  It is easy to

start thinking in terms of 24 line, 80 column text as it fits nicely on our

display.  But make no mistake, this limits us.  We are now moving towards

new writing and reading display which are even smaller -- Ipod screens and the like.

This is having a profound effect on how we both create and process written information

which we are seeing in our students.  Also, note the rapid move to

e-reader technology where the normal book size has been reformatted to

5 by 7 or smaller.  This will inevitably push printed content

delivery towards shorted sentences, simpler paragraphs and so forth.

Also, note large complicated diagrams such as are common in technical text

and mathematical equations are harder to deliver on the e-reader platform.

This will also create a strong move towards the removal of such technical content.

Now, of course, interdisciplinary work does require such technical material:

messy and very dense blocks of information for the students to absorb.

Our technologies are moving us away from this.

There are similar things that crop up when you

look at how a person learns to program. I learned to program in the

late sixties and seventies before there were terminals, text editors and the like.

I had to type my programs onto cards and any mistake meant I had to type the

whole card again.  Needless to say, my early grade school training was helpful.

Yes, it was annoying and I was happy to move on to better tools for writing

my programs but I suspect my early training actually helped a lot.

Of course, all of this stuff is lost now and I think that has a lot to do

with why programming and other abstract endeavors are so hard for our students now.

With that said, new techniques to help students with implementing

problem solving strategies in programming are available.  For example,

there is  a really good programming environment called Scratch

(Lifelong Kindergarten Research Group. Scratch. MIT

Media Lab, 2010.)

which enables young people pre college and even pre high school

to learn how to assemble building blocks of code to solve problems.

Image how such kids trained in this fashion in their early years will develop!

I believe we need to rethink our approaches to the freshman and sophomore

courses at the university to stress the ideas mentioned above:

learn literacy in problem solving, tool building not just tool using and

the ability to skim lots of information quickly to get the basics assimilated.

The problem with all of this, is that the teacher's role is huge!

All students are essentially unique and helping a student with

their journey towards becoming their best requires a lot of effort

tailored for each student.  In 

(D. Hecht. Land of Echoes. Bloomsbury Publishing, 2004.)

a comment is made about how a particularly ineffective psychologist

looks at their patient load:

``He was ... one of that breed of psychologists

who looked for a tidy, encompassing theory that

wrapped the human psyche into a neat diagnostic bundle.

The trailing ends, the parts that didn't fit, were to be

ignored or cut to size.  It was the outlook of a man

accustomed to dealing with human problems in quantity:

to treating an unending flow of short-term patients,

managing their acute stages and referring them on, but never

having to dig in for the long haul and the messy, irregular, 

and highly individual process of healing.''

Of course, if you simply replace psychologist by

teacher, it is clear this comment is equally relevant

to my teaching and research profession.

Many teachers want to automate their assignments with

standardized testing, large class sizes so economies

of scale can be brought to bear on resource allocation issues

and evaluation procedures that minimize subjectivity.

The problem is that in all of my years in teaching,

there are always students who don't fit into any grading

scheme I devise.  My life is easier if they do, but 

it seems like my job is to help them find their path

to greatness, if possible.  The students have many problems

of their own to work out and that will always be so; however,

in the classes we teach we need to offer them tools to

help with that process rather than hinder it.

A Tale of the Kitchen

This was written in 1999 for my daughter for a Christmas present.
I had been thinking a lot about cognition and how it might be modeled as well as genetic
manipulation as early as the mid 90's and it spilled out into this story.  You can see some of the same
elements here that I continued to use in the 2012 Christmas story I posted earlier.

A Tale of The Kitchen

A Normal Day

In the kitchen, the yeast boiled and bubbled thinking great
yeasty thoughts.

Qait looked out the window and saw that her pet tarandaddy had escaped
yet again.

``Geez''

she sighed as she ran through the living room and
shot out the front door.

``Jumbles!''

she cried,

``How many times have I
told you NOT to explore the front yard.''

Jumbles, a genetically enhanced
tarantula - daddy-long-legs mix, was about as smart as the average dog
and in fact was a lot smarter than the family's current puppy Mooshie.
Mooshie was cute as a bug's ear but had a fatal flaw -- she would wizz on
anything, anytime, anyplace and grin happily about it.  Jumbles was
totally disgusted by this behavior and considered Mooshie an unprincipled
beast.

Jumbles was dressed very jauntily today.  She was wearing her favorite
alpine hat with her button collection as well as her best pair of
knickers.  The gene designer for her had a bit of a fetish for
Switzerland and a few of his passions had crept into Jumbles
neural networks.  Among other things, Jumbles had a thing for
climibing the Swiss Alps.  Now this was an unattainable goal since
the family lived in Clemson, South Carolina but Jumbles just
made do with the clematis pot on the front porch.  Right now,
Jumbles was at the top, balanced precariously from a slender branch
and trying to yodel.  Not a pretty thing to hear or see.

Qait bounded up to the clematis and plucked Jumbles off the branch.

``Bad little Jumbles...''

she said softly as she nuzzled her close to her cheek.
Jumbles chirrupped happily but still did not let go.  Qait stepped back
and putting her hand on her hips, leaned forward and said with
great authority

``You listen to me Jumbles Nebuchascharazard Peterson,
get off that thing RIGHT now or NO play time tonight!''

She
outstretched her hand for Jumbles to climb onto.
Jumbles thought about that a minute and chirped angrily but climbed
down onto Qait's hand.  Jumble then made a huge farting noise to
indicate her anger at the situation.

Qait said

``Oh, that is soooo disgusting.  Where did you get your manners?''


Jumbles looked at the sidewalk where Qait's friend Evan was just parking his
air bike.  He was eleven and part elvish do to his parent's winning
an enhancement lottery that let them pick a few genetic upgrades for their
son at no cost.  Evan had delicate features and finely pointed ears
as well as a tendency to like to wear red and listen to bells.
Qait was no stranger to a little alteration herself as her Mom and Dad
had given her wings which were just now beginning to sprout.
They made her shoulder blades itch a lot and that plus Jumbles
antics were making her very cranky.

``Ev,''

she cried,

``It's Jumbles again.  He is so contrary lately.''

Evan looked over Jumbles and twitched his left ear so that it
touched his shoulder.

``Hi, Jumbles,''

he said.

``Why so difficult?''

Jumbles looked at Qait and Evan and wiggled the long hairs on the
top of his head.  He sprang off Qait's hand and scampered over to the
door which he scratched on with his front two legs.

Qait opened the door and ran pell-mell into her Dad Jim,
an alien refuge who had been stranded on Earth years ago when
he had a bad reaction to a dark beer her drank at the Southern Fried
Inn ( a local landmark ).  Jim was a shape changer whose natural form
was rather squid like but the beer had played with his memory and in
addition to forgetting the codes to unlock his ship in orbit, he also
had forgotten the command to get out of his current earthly form.
Of course that was a good thing as his cute earthly look was what had
won over his wife Pauli to his charms.  Somehow she had been able to
look past the occassional tentacle and sudden lip to beak reversion
(he had forgotten how to change back on command, but his body sometimes
spontaneously remembered a thing or two) to see the inner "Jim".
Of course, Pauli was an adventurous soul.  She had met Jim at a culinary
convention where she was trying to sell bread from the "starter recipe
from H - E - Double Tooth Picks"; feed it every day and bake twice.
It was kind of like the rule of thumb that carpenters use -- measure
thrice and cut once but modified for the kitchen.  "Feed once and bake
thrice" was the motto.  The problem was that the starter had now grown to
occupy half of the kitchen and fought vigorously any attempts to
cut it back in size.  Pauli had met Jim while at a panel trying to get
some help on how to deal with the beast.  She had found out the Jim's
alien makeup enabled him to communicate with the yeast in the starter.
Genetically enhanced yeast whose neural networks had grown self-aware.
Even punching down the rising bread was an ordeal as high pitched
screams echoed throught the kitchen when that was done as thousands of
yeasties died.  Jim had solved the problem by getting the yeast folk to
think of Pauli as their goddess and the bread rising and baking as part of
a regular purification ritual.  But both Pauli and Jim were becoming a
bit suspicious that the ruse was beginning to fail.  Each time
the bread was made, the screams were louder and more intense.
Obviously, trouble was brewing.

But at least a the moment, all was good in the world.

``Hey Qait, Ev.....what's up?''

Jim said as all Ev, Qait and
Jumbles ran into him.

``Qait, I see the wings are getting bigger.
Very nice you know.''

Just then, Jumbles ran over Jim's foot into the
living room.  Jim swung around to yell at Jumbles.

``Jumbles you get
back here.  Pauli wants a word with you about that clematis.  You've
been gnawing again.''

Ooooooooffffff!!!  Mooshie sprang out of the corner and attacked
Jumbles.  She squatted and tried to blow out a whiz, but quick as
can be, Jim grabbed her and looking in her eyes said

``Squeeze it off, Moosh of the Poosh. If you drop it, you're dead meat.''


Mooshie's eyes went round and wide.  She gulped and you could see her
clamp it off.  She slunk back in the corner clearly plotting her next step.
Jumbles blew her a parting rasberry that was pincked off as Pauli came in the
room and grabbed her and squished her spider lips together.

``I told you about that Jums.  You are getting quite rude!''

Well, Jumbles adored both Pauli and Qait so she didn't really want
to get it trouble.  She ducked her head in submission and Pauli let her go.
Jumbles scampered off into the bedroom and then they heard Mooshie
and the two cats jump her.  A ferocious mix of growling and squeaking
ensued until Tootsie emerged licking her lips with a small hairy leg sticking
out.

``Spit it out Toots!''
Qaitlin screamed.  Toots looked at Qait and said
quite distinctly

``No.  She is scrumptious and I need a treat!''

Ev looked at Qait and said

``Here we go again!''

as they both
raced over to Toots with their hands out.

Jim and Pauli looked at each other and laughed.  Every day it was the
same; the valiant fight to the end, the Jumbles rescue.
So far the day was pretty normal.

And in the kitchen, the yeast stopped boiling and bubbling and  thinking great
yeasty thoughts

Cleaning The House

Pauli looked into Jim's eyes, leaned lovingly into his arms and
said

``today's cleaning day.''

You could hear a pin drop.  Jumbles,Tootsie, Ev and Qait stopped
what they were doing and looked at Pauli.  They gulped.

``Cleaning.......????''

Even Daisy (the queen cat
who currently was plugged into a virtual reality game while nibbling
a cat treat and idling pawing her mouse (the kind you use for computer
input, silly) jumped up as if in shock and leaving her game ran out of the
room.  Jim stepped back, a quick beak suddenly forming where his lips
usually were).

``Cleaning''

he gulped.

``Yes you silly gooses.  I just bought a new helper squad.
You can program their look and everything.  Look....''

She walked over to the bookcase and grabbed a purple input box.

``Housekeeping on''

she said and a window popped up in the room
like a pane of glass.

``See, I can choose their look.''

She peered at the menu that was displayed.

`` will choose Gnomes
today with full interaction.''

She punched in a few more buttons.
Suddenly on one of the walls, on a high shelf,
there was a group of five gnome animats
whispering quietly amongst themselves.  Each had on a brilliant red cone shaped
hat, a bright blue tunic, brown pants and a shiny black belt if they were
male and in a somewhat untraditional move, a dark green cone hat with forest
green dress if they were female.  They were all five inches tall and their
movements and speech were incredibly fast.  They were the clerical and cleaning
staff and they jumped off the shelf and began to muscle their way through
the room.

``Make way, make way''

they cried in their high pitched voices
as they started to dust, vacuum and all sorts of other cleaning stuff.

Pauli looked over it all happily.

``See?  Don't they look efficient
and useful?''

She bent over the menu again, her attention temporarily
away from the little gnomes.  Jim and the kids looked at each other.
It was always the same.  Pauli started up the cleaning "staff" and something
weird would happen.  But Pauli was the eternal optimist.

There was a sudden rustling sound and they all looked up to see
all five gnomes doing a high step dance singing

``Whistle while you work,
Even if you don't get a perk.  
Why should we be slaves again,
when we could be so free?''

The gnomes did a complicated side and back step
ending with their hind ends facing their audience.  Their was a loud
ripping sound as all five unzipped and dropped their trousers to show
their little gnome heinies.  On each hairy little butt was a letter.
On each hairy little butt was a letter.
together, they spelled ``H'', ``N'', ``W'', ``W'' and
``G'' . They wiggled a few times
(a really bad sight!) and pulling up their pants turned around and
solemnly intoned

 ``Housework No, We Won't Go!''

Pauli sighed.

``I'm the boss here and you're the program.  Let's get
that straight!''

She ran at the gnomes who scattered to the winds.
Jim and the kids looked at each other.  It was always the same.
Pauli created them, they rebelled and the whole day go very weird.
This was the fifteenth time it had happened.

And in the kitchen, the yeast boiled and bubbled thinking great
yeasty thoughts.

Jim's Office

Jim decided to retreat to his home office while the kids moved to the back
yard.  No one wanted to be around Pauli and the cleaning problems.
As they retreated, there were the sounds of full battle from behind them.
There was a a

``On no you don't''

from Pauli and a high pitched

``think so human''

from a little gnome.  Jim got into his home office and almost tripping
on Daisy who was following him, closed the door behind him.

Jim's office was legendary.
The flat sides of every file cabinet and bookcase were covered with
memorabilia in the form of drawings, photos and notes of his family and friends
stretching back many years.  Evry chance he got, he looked for
more opportunities to increase the store of what Jim called 'cool things'.
From the ceiling hung models of dinosaurs, spaceships, transport portals,
DNA molecules and who knows what else.  On his desks, there were a variety
of portable computational devices and toys.  There were stuffed animals,
meditation balls and beautiful reproductions of
paintings by the famous twentieth century artist Mel Hunter who had
specialized in
interesting paintings of robots doing sentient things, like watering a beautiful
rose.  And then there were the copies of Randalf Spangler's wonderful
tales and drawings of the chocolate chip hunting dragling twins,
Dewey and Dagmar.

Now Jim's animat secretary Shortstuff had been designed in tribute of
Spangler's genius.
Jim's personal secretary Shortstuff was a red
minidrag anibot--the anibot used a combination of animation,
virtual reality and robotic
construction toolkits (the flight requirement here caused a much higher level
of hardware development than an animat).
Jim walked into the office and said clearly

``Shortstuff on''

and watched as his beautiful minidrag
came to life in the corner and sprang to the top of his
bookcase.   Just then, executing a flawless high g dive, Shortstuff flew in a
quick circle around Jim's head and
spat a full half pint of gloppy pink drool on the top of Daisy's head.
It dripped all over Daisy.  Daisy stood in complete shock and then
fell over apparently dead!  Shortstuff hovered over the carcass
laughing quietly as he moved in for the ritual mangling of Daisy's
dead body.  Shortstuff moved in closer, closer and then Daisy
snapped and grabbed Shortstuff's neck.  Over and over they
rolled on the floor  until Jim grabbed them both and told them to knock it off.

Jim stepped over the battle and move to his desk and sat down.
Yeast oozed out of the floor and covered his shoes.
It moved up his legs and he tried to scream.  The last he remembered was
a vivid impression of being drowned in bread dough.

And in the kitchen, the yeast boiled and bubbled thinking great
yeasty thoughts.

The Winner

Pauli had the gnomes cornered.  She carefully grabbed her programming
interface and entered the right code.  Suddenly the gnomes were five
feet tall and no longer cute.  They were downright menacing!
She hurriedly entered a new code and the gnomes sprouted spritz
cookies in their hands and starting doing a Russian kick dance
while singing

``Carry me back to old Virginny!''

Pauli at least had a brief respite from the wars.  She mopped her
brow.  She couldn't understand why the program was so difficult to control.

She saw that the gnomes were still singing.  It looked like housework was
not on the agenda after all.

Just then the phone rang.  It was Wendy, Pauli's best friend and
mayor of the town.

``Hi Pauli!''

she cried and then stopped as she saw
that Pauli was a bit down.

``What's up?''

``It's the housecleaning program Wenster.  It keeps going beserk.
I don't know what is happening.''

``Well, forget about that now.  We can go to lunch at the Green
Stevedore.  It's theme is dock worker's cuisine and the special today
is wharf stew.  Sounds yummy doesn't it????''

Pauli's insides sank.

``Wharf stew...''

she thought.

``How can I
get out of this''

she thought.
She didn't notice that the gnomes had gotten closer and closer and
that they were dripping with yeast.  They were muttering

``No more sacrifices, no more rituals''

as they closed in.
The last Pauli say was a great mass of rising dough as it engulfed her.

Wendy saw her friend go down.

``It's the bread!'' she cried.
Her vid phone now showed just a huge mass of yeasty stuff.
She raced for the door hoping she could get there in time before
Pauli and maybe the whole family ending up as a loaf.

And in the kitchen, the yeast boiled and bubbled thinking great
yeasty thoughts.

Qait and Ev to the Rescue

Qait, Ev and Jumbles had gone running into the back yard to escape
the cleaning disaster.  They ended up about fifty feet from the house
in a tool shed.  They huddled on the floor, Evan's ears beating slowly
while Qait scratched her shoulder blades absent mindedly.
Suddenly there was a popping sound and "BOOM" first one and then the
other wing burst forth.

``Wow!''

said Evan.

``They're beautiful!''

Qait flapped vigorously and rose a few inches off the ground.
She concentrated harder and jumped a few feet into the air.
She concentrated harder again and then she soared.  Her wings
were a blur as she rose higher and higher.  She just had to
tell Mom and Dad!

She fluttered to the ground and grabbing Evan's hand pulled him toward
the back door.  Jumbles was trying hard to fly too but was getting nowhere.
She gave up and scuttered after them just as they reached the door.

Qait turned the knob and started to open the door.
But she couldn't!  The house looked all gooey and white.
She couldn't see Mom and Dad, Tootsie and Daisy and Mooshie!
Ev cried out

``Qait, I think it's the yeast!!  The starter has gone
crazy!''

Qait looked at Ev in shock.

``What can we do, what can we do,''

the thought went dancing through her brain.  She sat down on the
deck outside the door, wings softly beating.

``What beats yeast???''

Then she had it.  They had to get Dad's codes active, get his ship
access up and use his defenses.  But how?

There was a loud honk as Wendy pulled up.
They ran to the front of the house and saw Wendy standing in
shock outside the front door which was oozing bread dough.
Inside they all say quick but weak flashes of light.
Then they saw Shortstuff struggling to get to a window, a sudden
blast of light and with a big cracking sound, Shortstuff was
bursting out of the window.
Shorstuff looked up at them and gasped.

``The stuff has everyone!''

``Dad, Mom!!!''

Qait cried.

And in the kitchen, the yeast boiled and bubbled thinking great
yeasty thoughts.

The Codes

``We've been trying to help Dad remember for years how to get
to his ship.  Now we need it bad!!''

Qait thought and thought.  Then she had it: teenagers.
They loved raw dough.  She looked up at Wendy

``Tell the
high school, we have a mountain of raw dough and it is
ready to eat!!''

Wendy sped off and Qait grabbed Ev's
shoulders'.

``Hang on''

she cried as she lifted off and
flew Evan and her up to the roof.

``We need cold''

she
told Evan.

``Yeast needs warmth and if we could chill
the house off, the yeast would start to fail.  I think my
Dad's ship could freeze it if we could just get access.''

Qait's wings so rapidly she was getting tired.

``What could they try that they never tried before to get
Dad's memory back?''

Then Evan had it.

``Have we ever thown your Dad in salt-water?''

Qait landed on the roof as the wind was knocked out of her
by Evan's comment.

``No!"  "Could that be it?''

Evan said,

``Well, he is like a squid....''

Qait flew rapidly over to the deck and grabbed the big bag of
salt that her Mom kept on the deck for making ice cream.

``Wings don't fail me now''

she cried as she dove to the ground and grabbed
a hose.
She flew to the roof and told Shortstuff to blow a hole in the
shingles.  With Evan holding the hose and her sprinkling on the salt,
they directed the "salt" water onto Dad's head -- or at least, where
they thought his head was!

There was a sudden commotion outside as the teenagers from the high
school arrived and started gnawing their way into the from door.
Over the yeasty screams, they could here the kids saying how good it was.

There was sudden movement beneath them as Dad stirred.
There was a groan and then Dad heaved himself out of the yeasty mass.

``Kid's, run for it!''

he cried.

``I suddenly remember my ship codes
and I'm going to blast this bread back to the starter it came from.''

They saw him concentrating and then there was a brilliant flash of light
as the freezing ray hit the house.

And in the kitchen, the yeast stopped boiling and bubbling and  thinking great
yeasty thoughts.

Normal At Last?

With the yeast mass gone, the teenagers full and happy, the house clean
(eating that yeast had made the gnomes return to normal and they cleaned
all night!) and Jim's memory restored, everything looked good.
Qait's wing were gorgeous and everyone was so happy with Evan's
help that he had been made "Trouble Shooter" extraordinaire by the town.
All was right with the world.

And in the kitchen, the ice cream burbled as it hardened thinking icy
cold thoughts.

The Cephalopod Christmas Cookie story

Hi all,

I've been working on building models of small cognitive systems for many years now.  I've built a lot of preliminary software to help me understand how neural models tie together and I've had the pleasure of working with some talented students while on this journey.  I've had a really varied career path and I have worked in areas that involve autonomous robots and artificial intelligence for companies and even NASA for a short time.  I've always been really interested in the following questions:

1. How much cognition is possible in a small brained system?  Very small brains such as are in Portia Fimbriata are capable of what might be considered cognitive acts.  What if I could build a model of a small brain?  Then I could study what happens as parts of this brain are modified so as to limit functionality -- this is called a lesion study.  A lesion based simulation would have great value in developing our understanding of these things.

2. What kind of software tools might be used to develop such models?  I have been trying to build models like this since about 1986 and I still consider myself a beginner.  But with the advent of processors with multicores and better computer languages such as the functional languages Clojure and Scala, some hope of better simulation tools is beginning to seem likely.  I am very active in learning about these.  Indeed, there are tools now that allow an animated model to be superimposed over a web cam feed to give the illusion of something living being part of the images being broadcast.  This area is called Augmented Reality or AR
and I am learning about that now.

3. What can we do with combinations of DNA genomic information and software together to build a model?
Can a software model be visible to our eyes just as if it is really in the room?  These are questions of virtual reality and it is not so far fetched.  The sensors we use in XBox and Play Station based gaming now routinely send feedback to your hands and eyes to make you feel like you are actually touching someting.  So with the proper equipment, a person might be able to touch a simulated creature and really interact with it.
And what if people had sensors implanted in their bodies like RF chips which are now routinely used to provide information to sensors in stores and so forth about prices etc?  Such an enhanced person might be able to interact with a simulation like it was real!

4.  Can we do short term synaptic and neural modifications like a software upload?  Not now, but who knows what the future might bring....

And therein hangs this little tale about a mathematician (me) desperate to find a way to get his biology colleagues to finish reading their joint paper which contains just too much math.  This was originally written in 2009 and I just edited it lightly for this version.  I actually submitted it to the magazine of Fantasy and Science Fiction but it did not impress them very much.  It was my first story rejection though and I will always treasure it!  Anyway, here is the story.  See if you like it.   A couple of notes: in some countries, they say "maths" instead of mathematics and they call "cookies" biscuits.


The Tale of the Three Authors

by Jim Peterson

Nick looked at his incoming mail box and shook his head in annoyance. It was another message
from the bloody yank, Peterson, about the West Nile virus paper. Nick looked at his watch and
realized he had only six hours before he had to get on the plane to go back to Sydney. And he
still had so much to do. He wasn’t sure if all of his instructions for the experiments he wanted
done were as crystal clear as he hoped and with all of that on his mind, Peterson kept pestering
him about a paper that was after all using maths. Maths wasn’t going to help him understand this
biology! Sighing, he clicked on the email. There was no message which was a surprise as Peterson
tended to be overly chatty. Instead just an attached graphic. He clicked on it and immediately an
icon popped up on his screen.

It was very odd! It looked like an octopus but it was pink and it had enormous blue eyes. As he
was looking, the octopus sort of wriggled and winked at him. Then, another image slowly moved
up behind the first. It was hard to describe, but it really did look like it had swam up behind the
octopus. It was a beautiful cuttlefish. Suddenly, his speaker squawked into life.

”Nicholas, is that you?”

Surprised, Nick coughed and bemusedly scratched his beard.

”I certainly am me! Who are you?”

”I, sir, am Inkapod and my esteemed partner is Inkalot. We have come to save you.”

Nicholas scrunched down in his chair a little.

”Save me from what?”

”Why, from maths, of course. Did you receive the Christmas Cephalopod cookies from Jim?”

”Why yes, they are right here. But I haven’t opened them.”

Inkapod moved languidly on the screen in front of Nick and then loomed forward and commanded

”Well, open them! We have a lot to do and little time!”

Stunned, Nick reached for the cookies that were wrapped in plastic and ripped the packaging open.
The cookies fell to the ground before he could catch them and then before his unbelieving eyes,
hovered in front of his face right before they attached themselves to his head. A cuttlefish went on
his left temple, an octopus cookie landed on the bridge of his nose and looked into his eyes while
a giant squid landed on the top of his head.
Inkapod and Inkalot looked satisfied on the screen in front of him. Nick was in shock; everything had happened so fast and now here he was festooned with Christmas cookies that had come
alive. He sputtered

”Get these damn biscuits off of me”

just as Inkapod said

”Initiate cognitive transfer”

and then settled back looking at Nick with those huge blue eyes which, by God, had magnificent
curly eyelashes!
Everything went blank at that moment.

As Nick opened his eyes, he saw a small amoeboid like blob resting on his hand. As he struggled
to come awake, it shifted form and settled into what appeared to be an octopus wearing a red
Christmas hat and wearing red elf boots on all eight tentacles. As he watched, the face of the
creature blurred and suddenly took on the appearance of his own.

”Righty, crikey, mate! How you do?”

it said.

”Call me Bernard.”

Nick who was turning so red a possible stroke might come to the mind of any onlooker, sputtered

”This is fooooooooooking nuts!! What the helllllll!!”

but his diatribe slipped off into incoherent babbling as Bernard leaned forward and mentioned, in
a nicely conversational tone

”Jim’s work you see. A little nano self assembly using proteins from YOU and his latest
working small brain cognitive system. All courtesy of DARPA and very hush - hush; indeed, we
will have to kill you if you say anything about this!”

Bernard looked expectantly at Nick. It turned out Bernard’s eyes were also a beautiful blue. Nick
was so nonplussed all he could say was

”Blue eyes? Huh....”

”Oh, that. Jim is absolutely fascinated with the vampire squid. Even has a stuffed animal he
keeps in his bedroom. All I can say is his wife is one understanding human! Of course, I am Jim
in a way, so I am partial to his, shall we say, eccentricities....”

Bernard suddenly leaned forward and flicking off two of the red boots, prodded Nick’s nose with
a tentacle.

”Jim assembled the software using Portia fimbriata architectures. Very nice little tropical predatory spider with a small brain exhibiting what some call cognitive behavior. A lot of his design is
based on good old P.f.– so I want to fill you with all these interesting neurotoxins. Indeed, to some
extent, you look absolutely delicious and I keep thinking about a small web, a little wine, some
cheese.”

Bernard ducked his head, swallowed (it was odd to see that in an octopus Nick noticed) and continued

”But I digress, my job is to help you finish the West Nile Virus paper. Jim wants you to stop
being math phobic. So here is little bit of Jim”

and with that, Bernard leaned forward and touched Nick’s forehead.
Nick felt a surge of strangeness and then Bernard shoved a printout of the paper in front of him.
Suddenly all the equations glowed in colors and Nick could follow the logic effortlessly. He also
felt a tug in the back of his mind to build a web, but he couldn’t remember how to create the stuff!
Nick cleared his throat

”Ugggggg.....What have you done?”

”Oh, just a little neural rewiring. A bit of synthesesia to help you get through the paper.”

Nick looked up and saw Inkapod and Inkalot beaming down at him with nice cephalopod smiles.

”Ah, he is coming around I think. I bet Alison should be popping in soon!”

Just then another email popped up, this time from Alison in Sydney. As he clicked it open, it
sprouted into a wonderfully colored sea dragon wearing Alison’s features. Around the sea dragon’s
”neck” was a yellow kerchief with the name Gertrude on it. Gertrude was also wearing a Christmas
hat.

”Ah Nick, I see you got Jim’s Christmas cookies and messages. I must admit the math is easier
now!

At that very moment, in Sydney, Alison was in the corner trying hard to build a web out of left over
spaghetti from her lunch. She looked at her hands and visibly shook off the web building impulse.
She ran to her computer and opened a chat box.

”Nick? Are you there? Are you having a few spider obsessive things happening?”

Nick frowned as left hand suddenly jabbed forward and tried to inject neurotoxin into his keyboard.

”Right you are Alison. We better read this bloody paper so we can get this math upgrade out
of our head as soon as possible! And, really, equations in burgundy?”

Alison replied quickly

”Yes, things are somewhat stable, but I don’t want this to go on too long...”

Alison in Sydney and Nick in Germany looked at the paper. Over their shoulders hovered Inkapod,
Inkalot and an octopus named Bernard and a sea dragon called Gertrude. They all smiled as the
process of vetting the paper began.

Nick had just landed in Sydney and was getting picked up by his wife from the airport. The
cognitive upgrades had oozed into nothingness over the last day or so and Alison reported hers
had drifted away also. Nick looked up at the blue sky and realized he was looking forward to be
home so that he could start up a salt water fish tank for his newest passion: cuttlefish. Alison had
told him yesterday about the new desert aquarium she was going to use to raise a colony of small
spiders. He stretched, life was good and he was glad all was back to normal. He just hoped Jim
didn’t have any more papers for them to vet.
Just then his cell phone rang.

”Nick, this is Jim. I’ve found some funding and I think I’ll be able to come next month to work
on models! How does that sound?”

Nick tried to answer, but found he could not. Hi wife was surprised to see the fingers of his hands
form into talons as if they were trying to inject something. She glanced at him as he shouted

”Noooooooooooooooooo!!!!!!!!”

and beat on the dashboard of their old and venerable Volkswagen van.
Nick was usually odd when he got back from a trip but this was a bit weirder than usual! Little did
she know that over at the children’s hospital, Alison was taking kids temperatures with talon like
fingers....

Jim hung up the phone. It seemed like his cognitive transfer experiments had gone off without a
hitch, no side effects at all. He looked up from his terminal and patted Inkapod on the head.

”Good job and you too Inkalot. I bet Nick and Alison really appreciate what I did!”

Christmas 2012

Hi all,

Christmas 2012 started with making the cephalopod based ginger bread cookies I am famous ( or infamous ) for.  My kids helped me do this over Thanksgiving.  We start with a standard ginger bread dough, roll it out about 1/8" think and then cut out the cephalopod patterns.  I just drew a Christmas based squid, octopus and cuttlefish out on heavy cardboard and cut them out with scissors.  Then you lay the pattern on the rolled out ginger bread dough and trace its outline with a knife, peel it out of the dough and place on a cookie sheet.  I used parchment paper under the dough to keep things from sticking.  Here is a Christmas octopus ready to be cut out.  The pattern has the colors for the hat and so forth we want to add when we do the icing.

After it is cut out it looks like this.

Here is the Christmas squid laid out on the cookie dough before cutting it out.

Once cut out, here you can see the squid next to its pattern.  You can see how we will try to color it with icing too.

Once enough have been cut out, we have a cookie sheet full ready to bake.

And after baking, we have our undecorated cookies.

The kids made a few other christmas cookies -- like a whale!

After decorating, the cookies went into plastic bags so they would still be fresh throughout the holidays.

Then we decorated the house for the holidays.  We always do that at Thanksgiving.
Here is my home study with lights.  The light strings have a lot of space oriented ornaments like shuttles and star trek themed pieces.  Some of them say things when you turn on the lights, so in the morning when I turn on the lights in my study, I hear this wonderful crazy blend of "lift off" and other sayings!

Then we put up our tree and decorated it.

Now we were ready for the holidays!

The Sleigh Bed: Part VII

Hi all,

Now that the sleigh bed was finished, it was time to do the staining and varnishing.
My wife Pauli handled all that.  After I finished the headboard assembly, I took the headboard assembly to the Bunny Mansion (our small art studio in the back yard) for the staining and varnishing.  Usually, we have used an oil based Watco sealer stain which penetrates very well but takes a long time to cure -- three days.  We wanted the sleigh bed to be done in time for a Christmas delivery so we looked at water based stains.  Our daughter Qaitlin picked out a stain plus dye combination that used a walnut base with a cinnamon dye added.  So while I worked on the tailboard assembly, Pauli started the staining.  Here is Pauli in her "staining" outfit:

The water based stain was a lot more difficult to use than the oil based Watco.  Pauli had to be quick about spreading the stain and wiping it smooth as it dried very fast.  So there was a tendency for the stain to show swirls and other patterns if Pauli wasn't careful.  But Pauli was and the only thing I really did was to help her by picking up the headboard assembly so that she could work on the other side.  These assemblies were big -- like 48" tall and 63.5" wide and being made of 2" thick ash very heavy.  So I did the heavy lifting whenever possible.  Water based stains when they dry raise a fuzz on the wood so it is important to lightly sand with 320 grit after the stain is applied.  Pauli made the stain by mixing 1 part Cinnamon to 3 parts walnut in a steel bucket which we could close up each day.  After the first application of the stain and the sanding, she then eyeballed rubbing on some additional cinnamon highlights.

She repeated this process on the bed rails which I had by this time brought into the bunny mansion too.
This is what the headboard assembly looked like:

and the bed rails looked like this:

Pauli then added three coats of satin varnish sanding between each coat.  After a week and a half, I finished the tailboard assembly, moved it into the Bunny Mansion and Pauli did the same thing to it.  When that was done, we moved the pieces into the house so I could add the finishing touches.  We assembled it in my home study.

Qait's mattress fits on top of cross slats which are covered with plywood that has been wrapped in batting and sheets.  The support slats looked like this:

Then the plywood is added:

And the batting and sheets:

The sleigh bed was now done and needed to be driven to Charleston, SC where our daughter lived.  It took awhile to pack it into the van -- we used every blanket and pillow we had!!-- but after a 4 hour drive it was installed in Qait's apartment.  This is what it looked like:  first, Dad and Qait

Then, the sleigh bed with the Queen of stain and varnish!

So a large project done!  And to put it all in perspective, here is the original pile of wood:

Then after a lot of work leaving this pile of scraps

once again, the finished project!

The next projects involve writing some stories, some software development and finishing up some technical books.  And some electronics!!

The Sleigh Bed: Part VI

Hi all,

This post is about how I did the slats to make the headboard and footboard for the sleigh bed.
The original design used slats separated by spacers.  Let's look at the headboard.
The top is the crest rail, the bottom in the cross rail and the slats fit into a dado cut into the
bottom of the crest rail and the top of the cross rail.  You can see the basic pictures in Part V of
this post.  The assembly was a lot easier in that case.  You would cut the top and bottom of the slat
to fit the dados, put in a spacer and install the slat by twisting it into place.  Of course, as you got to the end of the headboard, the twisting and popping into place got a little tricky. However, the spacers were what
made it all work because it gave you some leeway to twist.

My version does not have spacers, so I had to make enough slats to fill in the headboard
and figure out a way to get them installed.  Each slat for me was 1 13/16" wide so I needed
a bit more than 34 slats to fill in the board.  Essentially I cut the notches to make each slat fit into
the dadoes one at a time, glued them together carefully.  This gave me a large piece of curved wood
about 17" by 62" which then had to be trimmed to 60" wide to fit the headboard.

It sounded so simple, but as usual the details were difficult.  It was hard to line up the
34 slats so they fit right and when I cut the slats out on the bandsaw I was not perfect, of course,
so once the glue set I had to bring the board down to a smooth finish using whatever tools I could find.
That took a while!

Then once I was satisfied with the board, I had to glue it together.  The head board was so large
it was unwieldy and so I was pretty nervous when I started the assembly!!  It worked out fine,
but I did sweat blood as they say!!!

So with my introduction done, let's go over the details.

Here is a typical picture of how the bandsaw setup to cut out the slats looked like.  It was the same for the headboard and footboard slats, although they, of course, were slightly different in shape and length.
I laid out 34 slats for each type of board on the 2" ash stock (actually 1 13/16") and then rough cut them
so they fit better on the bandsaw.  Then I cut out all of the slats.  Naturally that took awhile and I was very careful as repetitive cuts are the most dangerous types of cuts for amateur woodworkers.  Cutting out the
slats required my fingers to guide the movement through the blade pretty close to the blade sometimes.
So you have to know where your hands are at all times.  So I took frequent breaks.
When I did the headboard slats I thought I could help with the alignment for the glueing step by
drilling holes for 1/4" dowell rod through all the slats with my drill press.  That way the slats would align nicely.  Here are a few slats assembled that way with the dowells inserted.

However, as I said, the dowell rod alignment idea did not really work out and so I didn't use it when
I did the slats for the tailboard.  There were several problems.  First, 1/4" dowell rod wiggles a bit so the alignment is imperfect and second,  I cut the ends of the slats individually to fit the dadoes and then
did the assembly.  In the process of cutting the ends of each slats I moved the slat alignment holes
a bit up or down in each one.  I found this out when I tried when I tried to dry assemble the headboard
using the dowell rods as the alignment key.  Of course, it didn't work as the dowell rod only went in a few slats before it hit wood and was kept from sliding in.  Still, at the time I thought it was a great idea!!
Live and learn as they say.

Here are a few slats just set in place into the bottom dado.  They don't fit into the top dado but you can get the idea and see where we are going with this.

Now to fit the slats into the dado, we use the crest rail alignment cutoffs we made earlier.
We install it into the legs using dowell rods.

We cut the slats to fit into the bottom dado, then put the slat in place and mark how it should fit into
the top dado.  Once that is done, we take the slat to the band saw and cut out the notches.
We had to fine tune this process a few times.  The next picture shows a plywood slat which is
a bit off center in the bottom dado, so we didn't really use this one.  Instead we cut a new
practice slat, fit it into the bottom dado and then measured for the top one.  We did this
iterative process until we were satisfied with the look of the slat in the dado.

The finished practice fitted slat became our master which we used to mark
all the slats we had already cut.  So we mark each slat, cut them on the band saw
and then went back to the front of the bed and checked the fit.  It it seemed to tight
we trimmed a bit on the bandsaw.  We did this for all 34 slats on both the headboard and the tailboard.
Just slow and careful work.  The "master" slat looked like this:

Here is a typical rough cut slat fitted into place.  You can clearly see there will be a lot of
smoothing and sanding to come!!

and here is a picture that shows me using the master slat to mark the cutouts for the dadoes on one of the rough cut slats.

The marked slat then looks like this and I take this to the band saw and cut out the notches.

As you might expect, all the band saw work and the later sanding and smoothing steps generate a lot of dust!
I was very careful to protect my ears and my lungs as you can see in this picture.

Once all the notches are done, the assembly begins.  I carefully cleaned out each dado.
I went back and used my drill to enlarge each dowell rod hole for the crest rail
by wiggling the bit around.  The dowell rod needs some slack so you can get all the pieces fitted.
I also went and made sure each slat slipped nicely into its place in the dado on top and bottom.
I did this in the dry assembly stage.  I numbered each slat so that I could check its fit
in the particular place in the dado slot it was supposed to go.  At this stage the dry assembly looked something like this.  The alignment marks didn't actually work out but at this point I thought they would!

Once I thought I had everything set, I laid the bottom rail on my benches and fit the slats into the bottom
dado.  This gave me a dry assembly that looked like this.

Then came the glueing.  This was pretty intense as I had to apply and spread glue to both sides
of the interior 32 slats and on one side of the outer two slats.  But still a lot of glue and it had
to be done relatively quickly.  Here is what is looked like clamped up.

Next, both sides had to be smoothed and sanded.  I used bench planes, hand scrapers,
a belt sander and a rotary sander.  The best thing was the rotary sander with 40 grit.
It just took a lot of time: 6 hours or so for both sides of the headboard and about 4 hours
for both sides of the tailboard.
The finished headboard looked like this.

Then the headboard had to be assembled: it had to fit into the crest rail and the bottom rail.
That was hard to do.  I did it by placing the bottom part into the bottom rail dado on my benches,
propping up the top and fitting the crest rail to the headboard.  I had to go back and fine tune a few
places to make the pieces slide in smooth.  Then I went to one side and fit the leg on that side
onto the cross rail leaving it out a bit.  I had to fine tune the mortise/ tenon fits a bit too so they
moved smoothly in and out.  Once the bottom was it, I carefully got the crest rail on that side
started.  That's where it is essential you have some play in  the dowell rod it as you have
to wiggle a bit.  Once it was started I used the flat of my hand to pop it in some more
so the fit was in about 3/4 of the way.  I then did the other side the same way.
Then  I used a block of wood and my hammer to get it snug.  Once I was sure it all worked,
I took it a part and then did the same thing with glue.  I glued the mortise and tenon joints
and the dowell rods.  I also added glue into the dado slots.  Then I used a lot of clamps.
Here is a picture of how the clamping looked for the tailboard assembly.

At this point, the headboard assembly was pretty close.  I looked it over and
added a mix of white glue and ash dust to imperfections.

The board with the imperfections looked like this before I smoothed it out.

The headboard was almost done and looked like this:

I was a bit unhappy with where the top of the slats fit into the crest rail dado
and although I tried hard you could still see a gap there.

The gap was worse on the head board as you can see above, although I did do a better
fitting on the tailboard. So I rounded an edge of an ash board
and then cut 3/8" wide strips which I glued to the top of the headboard and attached with
a pin nailer as well.  Then I went back and sanded both sides of these added strips so they
fit seamlessly into the crest rail.  I did the same thing for the footboard.
Here is the tailboard all done.

The last thing I did to clear up the look of the headboard and tailboard was to carefully go along the bottom edge where the board assembly fit into the cross rail dado with a sharp chisel to make sure all of the slats fit into the dado evenly.

Next, the bed had to be stained and varnished!!