Biohazard46

Wolfram: Chapter Three, Conclusion, and Notes

timothylmayer@verizon.net — Fri, 4 Nov 05 15:34:00 UT

Okay, I made it through chapter three("The World Of Simple Programs") of the Book. Wolfram throws his entire arsenal at the reader to tell us how the most simple of programs can produce extraordinary complex patterns. In the Notes section to this chapter he shows how the programs can be run, mostly using his customized "Mathematica" system. He wraps everything up by trying to figure out why no one has ever noticed this stuff before.

What I did find interesting was his observation that the increasing complexity of a program does not always carry over into the results. Especially regarding his mobile cells, the more colors that go into the program do not produce more patterns or more nested designs. There seems to be a point here as to where the results drop off. It's almost as if you need to find the simplest program out there. "4" instead of "42?"

Also in the Notes section to this chapter he mentions how Alan Turing had no interest in actually building a "Turing Machine." It was all a product of his ideas and any practical application didn't concern him.

"...one of the problems with direct experiments is that they often generate huge amounts of data." No argument there. That is why a lot of places are now employing programs such as JMP and others to sort through all the mess. Design Of Experiment (DOE) has been a hot field for some time in which the statistical people meet the lab rats.

I'm starting to wonder if the Book has any application to Technocracy. There was a wild bunch I left behind years ago. "Wings over the world!" and society as being designed by readers of Amazing Stories. It was hot stuff in 1932. A lot of the early technocrats where disciples of Gannet and his wonderful charts. Also followers of Taylor and "scientific management." There may be a tie-in someplace.

Chapter Two: pages 51 to 99

timothylmayer@verizon.net — Thu, 3 Nov 05 16:27:00 UT

Mobile automata. Substitution systems. Turing machines. Where will the madness end?
As I go deeper into the Book, the expanse of Wolfram's knowledge becomes evident. Now he's taking the most simple of programing systems and showing how the patterns emerge from them. This doesn't always happen. He notes on page 57 that only about fourteen percent of cellular automata show complicated patterns. But oh those patterns. With three hundred steps they can start looking like the conclusion to 2001: A SPACE ODDESSY. He also finds 256 rules for cellular automata.
But he proceeds on to mobile automata, which allows for different rules. Instead of parallel cells, now only one at a time is active. This allows for 65,536 rules. Most don't look promising. Then it's time for "Turing Machines" a theorectical computer system developed by the tragic Alan Turing prior to WW2. Turing could see the promised land, but he was never able to reach it. I like Wolfram's use of the "switches" used in Turing Machines.
Substitution systems are organized so the cell number can change. In a branching system, such as a shrub, this can be quite interesting. Then he moves on to "Tag Systems," where the cell from one end of a line can go the opposite side of the next. I'm really having a difficult time understanding this one, and the cellular notation is starting to cause me to see spots. Once again, he can find "nesting" in some of these programs.
Again: the point he's trying to make is that it is possible to produce behavior of great complexity with very simple programs.
I have reached the section on "Register Machines." I'm trying to absorb it all.

Chapter Two and Notes: The Crucial Experiment

timothylmayer@verizon.net — Thu, 3 Nov 05 09:26:00 UT

Here Wolfram is closing in on the real reason for the Book. In this chapter, he lays out the ideas behind cellular automata, nesting, and nobody has paid much attention to any of it. The technical part really starts to kick in during the notes section where he shows how to run the experiments using his "mathematica" program. To give you some idea of the detail he employs, chapter two is about twenty-eight pages long, but the notes run another seventeen. And the notes are in much smaller type and set in two columns.

This is where he shows what happens when the most simple of programs are allowed to run on and on. I'm not going to even try and sketch out his notation for cellular automata. If you want to look at the rich illustrations for this book, go to www.wolframscience.com. The entire damn book is available on line.

But what you soon discover is that given a cell, you can build up an entire pattern from that one cell by, one line at a time, specifying a rule as to how each subsequent cell has to appear. Take a line of cells, all white with one black one in the middle. Then look at any cell and the one to the right hand side. If both of these cells were white on the initial or previous step, then the new cell must be the color of the one on the left. If they weren't, it becomes the opposite. Simple? Not really. Run it about eight thousand times and you discover the most interesting patterns where none existed before.

Now where did these patterns emerge? You can't analyze the pattern and create a simple formula that will, in one shot, duplicates the pattern. They appear random. The only way to get these patterns is to take the inititial concise cellular formula and fire it up. Such is the basis for the entire Book.

Wolfram:Chapter One And Notes

timothylmayer@verizon.net — Tue, 1 Nov 05 13:59:00 UT

The first chapter of the Book is also free of much technical detail. Entitled âThe Foundations For A New Kind Of Science,â Wolfram discusses what events led him in this direction. He talks about his personal story in writing the book and how it relates to other areas.

Chapter One is also plugged with notes. Wolfram just canât give me enough information. But I will admit, the story is pulling me into the Book, a little bit at a time. His big âsweeping conclusionâ is The Principle of Computational Equivalence. What this distills down to is that any complex system can arise from the same universal conditions. It doesnât matter if you start with bumblebees or ferrite ions, the important thing is what you end up with and how it got there. Got that?

He looks at past initiatives(âArtificial Life,â âChaos Theory,â âNanotechnologyâ) and finds them all lacking inâ¦something. It all goes back to a crude set of programs he tried to run as a young lad in 1973 on an old British computer. He tried it again in 1981 using a better machine and then things got real interesting.

A good term for what heâs pursuing might be the study of complex systems, but that one comes with too much baggage. Iâd like to see him use âNeo-Alchemyâ, because Iâm a chemist and I think it sounds neat. And he also points out in the notes to chapter one: ââ¦the notion of a single underlying substance that could be transmitted into anything- living or not- was also a centerpiece of alchemy.â So what we may have here is not the question to the answer âforty-twoâ, but the inscription that Hermes Trismegistos wrote on the other emerald tablet, the one we never saw.

Wolfram: The Prologue

timothylmayer@verizon.net — Tue, 1 Nov 05 09:13:00 UT

This is the will be the easiest part of the book to digest. There is little technical discussion in it and Wolfram describes what led him to write the Book. He also talks about why he thinks the Book is so important. Writing it was a fifteen year-long journey into the land of the midnight oil.
He estimates the Book to weigh in at 250,000 words. The "notes" don't even kick in until page 849.
Jumping to the back, we see a section called "General Notes." Here are the common terms("website", "writing style", "dates") on which he elaborates. From what I can tell, he likes to start sentences with conjunctions. And he does it often. But not always.
Wolfram doesn't shy away from making big claims. On page 850 he says:"The vast results in this book have never appeared in any form before." He's also interested in the educational aspect of the Book: he wants people to use what they've learned.
Okay, just what the heck is this book about? Cellular Automata. Huh? Let me see if I can explain it a little better: remember chaos theroy? Fractals? That damn butterfly flapping its wings in the jungle that causes all the hurricanes? These are steps in the right direction, but Wolfram wants The Big Question to cover everything.
Take some tiles. Some black, some white. Cover the mall floor in Washington D.C. with them. But first, devise a rule as to what tile can sit next the next one. Follow that rule carefully when you lay down the tiles. Now, when it's all done, walk to the top of the Washington monument and look down at what you've did. What do you see? Is it the eye of God looking back at you?
At least this is what I think the Book is about. By the time I get to the end I should have a complete and total understanding of what Wolfram is trying to say. Then I may have a better description.

Wolfram. Phase One.

timothylmayer@verizon.net — Mon, 31 Oct 05 13:19:00 UT

5.44 lbs.
200 cubic inches.
1197 pages, not counting the index.
This is the text of Stephen Wolfram's A NEW KIND OF SCIENCE.
In 2002, Wolfram, who had been working on this book every since receiving one of those McArthur Foundation "genius" awards in the early eighties, unleashed his tome on the world. There had been a lot a talk in scientific circles for years about what he was doing. Wolfram already was the CEO of his own company, Wolfram Research, which had marketed the Mathematica program to science and industry.
And the Book came forth. It was to be the big question to Deep Thought's "forty-two" answer. Many articles were written in preparation for the Book.
But then little was said about the Book. Some reviews were negative. Some said it wasn't really all that new. His basic idea, that cellular automata could explain the fundamental nature of Life, The Universe, and Everything, was flawed. And little more was said.
I think most of the reviewers couldn't hack reading the Book. I gave up after chapter one. Although Wofram writes in a very easy and conversational style, the math part is tough going and the patterns he uses to make his points can melt your eyeballs.
But I'm going to try it again. And this time I will get through the Book. And this is what I will write about here. Because there just isn't enough interesting things to write about elsewise. At least nothing that would add much to the million or so other Blogs out there.
So here it goes people. I just finished the preface and the notes which go with it. Tommorrow, I'll write about that. As the days go by, I'll write about the rest of the Book.
Batten down the hatches. Fasten your seatbelts. Phasers set to kill. Here I go.

Science Education

timothylmayer@verizon.net — Wed, 21 Sep 05 12:14:00 UT

I went to my ninth-grader's open house last night with a heart full of expectation and joy. I wanted to see the enthusiasm in the faces of his teachers.
Okay, I'll tell the truth: My wife had to work last night and I pulled the meet-the-teachers job.
For those of you without children in school, this is an annual ritual in which parents are herded into a large factory-sized building and hauled around every ten minutes to meet another necktie or pearl necklace that informs you about "all the wonderful things your education dollar is buying." My wife has this advanced degree in education, so she is able to speak the same language as these people. Which is why I let her go and deal with them. Except last night.
By the way, I hated high school. I hated junior high school. I REALLY hated elementary school. So I'm not the best person to be sending into these places.
Anyway, I'll say the staff looked spiffy and seemed to know their stuff. What it must like there in the daytime with all the raging hormones is something I never care to experience. The "Tech Ed"(didn't this used to be called "shop"?) teacher even found my joke about cyborgs funny. I totally embarrassed myself in front of the Spanish teacher when I told him "good afternoon" en espanol at eight in the evening.
In vain I did search for a chemistry lab. I know one is there. They had to have been hiding it someplace. I was told the "chemistry classroom" was in fact mislabeled and was the domain of the biology teacher. But it's there; I felt the presence of it. And, by God, I'll locate that chemistry lab some day.
So I can't really say what the state of chemical education is like at the ninth grade level in the Commonwealth of PA. My son, whom I like to call XY Unit #2, isn't taking it this semester.
The geology class, oops, Earth Science, was nice and did have some rocks in it. The instructor and I even had a pleasant conversation about sundials.
I will say that I wasn't the only one having bad flashbacks there. You could see the look of horror on more than one parent when the PA system stared making the announcements. And I noted a lot of them giving the main office a wide berth.
None of us had to report for detention. That I know about.

"Dynamic Chemistry"

timothylmayer@verizon.net — Tue, 20 Sep 05 12:10:00 UT

I have neglected this chemblog too long. I'm going to try and post more often. The problem was, a friend reccomended the "Game of Ice and Fire" novels by George R. R. Martin. Now I'm hooked. I just finished #2 and will be starting on #3 tomorrow. #4 comes out this Christmas. I may pre-order that one as well. It took awhile, but I seem to have entered the Harry Potter universe.
Anyway, back to the Wonderful World of Chemistry. Better living. "The future is now!" All those wonderful things we would hear back in the glory days of the sixties, before someone started noticing the muck behind the factory.
Among my many hobbies, is the collecting of old chemistry textbooks. They are similar to old technical data sheets in that you can get access to information not given out any more. My early interest in the field of chemistry came from sorting through my father's old high school chemistry textbook from the early 1950's. To this day, I cannot fathom why someone would try and make a nuclear reactor look so easy to build. But those were different times, Jim.
So here we have DYNAMIC CHEMISTRY, a textbook from 1937 and you can hear the glassware clink just by leafing through it. It was written by two Cleveland High School teachers and published by Rand McNally. The chapter headings are descriptive and even the section headings are amusing. One is entitled "Smelling the lightning" (it's about ozone). Here on page 207 is a drawing of the too-young Michael Faraday cleaning up some mess in Sir Humphrey Davy's lab. And it does warm my little polymer chemist heart to see a picture of Leo Hendrik Baekeland on page 337. Page 556 has a picture of a "platinum refinery." The book also has a set of questions at the end of each chapter and easy to understand reaction mechanisms.
Books such DYNAMIC CHEMISTRY give the reader an insight into where the field stood right before WW2. What is suprising is how little has changed.

One fine day in September

timothylmayer@verizon.net — Wed, 7 Sep 05 12:16:00 UT

So here we are seven days into this lovely month and I haven't added a thing onto this blog. To tell you the truth, I've been too busy to write anything with just getting back from vacation, a bout of the flu, my wife's knee going out, and too many projects at home to mention. I did get the outside of my side porch painted; thank heaven for acrylic latex emulsions.
I can't seem to find many other chemisry blogs out there. No end to endless ramblings by PhD candidates in biology or post-docs that whine about not being able to find a suitable tenure-track position at a major university. Note to kids in college: just because your professors have the ability to torpedo your academic career does not make them into god-like beings. They put their pants on one leg at a time too. And don't think they'll EVER let you have a place at their table unless you find a way to create life (in their department, of course).
No I'm not going to say a thing about a recent storm that hit the Gulf. I am not qualified to do so. There will be plenty of blame for what happened going around for years.
And I did see another episode of COLUMBO that involved a murder of a chemist. Also from the third season of the show. And the chemist in question also had a spiffy lab in his expensive California home. Is there some kind of pattern here? Oh, and you will find this hilarious: the killer took a can of herion out of the dead chemist's lab, trying to make it look like the motive for the crime. When Lt. Columbo asks why the chemist had a can of herion in his house, he is informed that "the man did a lot of research for the government."
Suuuure. A reputable chemist waltzes home with a controlled substance that you can't even dispence for medical reasons. He dosen't even put it in a safe. Uh-huh.

In Search of Lost Techniques

timothylmayer@verizon.net — Fri, 26 Aug 05 11:53:00 UT

The other day I was reading Derick Lowe's Blog, "In The Pipeline", and he made a comment that struck a chord in me. Actually, he made the comment in the comment section based on one of my comments, but it is still a comment worth elaborating upon. Got that? Good. To continue, he mentioned that it had been over twenty years since he'd had to do a titration. And then I though about it: how many of those old wet chemistry methods we learned in college are still in use? I hardly ever do titrations. In my field it isn't needed much. But I used to do them all the time over twenty years ago.
The sad truth of the matter is that a lot of those old time-consuming methods have been automated. There seems to be a robot for just about every wet chemistry technique imaginable. Total Base Number? Done. PH? Ditto. And I really can't say that I mind too much. Because I hated those things. Sitting around waiting forever for the color to change in a flask and - Oh No!- I just missed the endpoint. Now start over again. Some people did turn it into an art form. There's really nothing like watching an elderly chemist in his seventies showing you how to do it RIGHT.
Beyond lost techniques, I wonder about the eventual destination of all those triple-beam balances we used to employ. Will they end up in antique shops? This seems to have been the fate of the microbalances that every analytical lab use to have. The old microbalances were things of beauty, made out of brass, kept in wood and glass cases. I've seen them on display in living rooms right next to the metal compass.
I've seen a few of the old optical balances floating at the places I've worked. They always have that sickly blue-green plastic case and never work right. Even when I used them in college they were a pain. I always made sure to check the things before I weighed anything. Often as not, I'd have to "thump" the side to get the scale to work properly. They'll all likely end up in the trash.
And there's the chart paper IR's. About fifteen years ago, cheap FTIR's made reading an infrared chart a whole lot easier. Hook them to a PC and suddenly everyone was an IR specialist. It's now possible to run an IR on a sample and instantly compare it to a mega-database. No more of the old "Uhm, I think that peak might be the amine group." And you can store the results in a hard drive, so no longer do you see chemists hauling around bound books of IR charts.
Years ago, I had the dubious privilege of touring an industrial junk yard. The place was filled with ancient card sorters and all kinds of vacuum tube relics. Perhaps that will be the final resting place of old lab equipment.

"Lovely But Lethal"

timothylmayer@verizon.net — Mon, 22 Aug 05 13:40:00 UT

One of the few joys I have in life is watching another episode of COLUMBO when it comes in from Netflix. The third season of the series has been released on DVD and I'm getting them in one at a time. I always enjoyed the bumbling detective, so excellenty portrayed by actor Peter Falk, when he was part of the "Sunday Mystery Movie" in the early seventies. There was just something awesome about watching him pull the rug out from all the snobby rich people who thought their status protected them from the little man's deductions.
So why do I bring up Detective Columbo now that I'm back from vacation? Because the episode I watched last night, "Lovely But Lethal," had to do with chemists. That's right, Columbo gets called in to find out who offed a research assistant (played by Martin Sheen). It being an "open" mystery, we already know that the killer was Vera Miles, who heads a cosmetic company. Her rival is played by Vincent Price.
Things I learned about the state of cosmetic industry chemists, circa 1973:
1) It's okay to introduce a skin care product to the public if it hasn't undergone extensive validation and testing. The FDA wasn't even mentioned once. Wasn't it around then?
2) There was a definate chain of command back in those days in the lab. Columbo describes Martin Sheen as: "An assistant chemist, not really a scientist."
3) Cosmetic lab guys must have really been making big $$$ because Martin Sheen lives in a mansion. But then why was he trying to sell the secret anti-wrinkle formula to Vincent Price?
4) A bifocal microscope makes an excellent murder weapon.

VACATION

timothylmayer@verizon.net — Sat, 13 Aug 05 20:57:00 UT

I will be on vacation for the next week. Hard as it may be, sometimes you just have to leave the lab. But I'm sure it'll be there when I get back.

Mad Science Movies

timothylmayer@verizon.net — Wed, 10 Aug 05 15:30:00 UT

Now that I'm in the mood to make a list, I'll do it by listing my favourite movies and TV shows that featured mad scientists. While other kids were dreaming of being the next Cincinnati Red's pitcher, I wanted to be Dr. Frankenstein. To my knowledge none of the kids I grew up with made the team and I never created life from dead bodies. Anyway, here goes:

"Frankenstein" and "Bride of Frankestein." It's alive!
"Gattaca." In the future, biology is destiny.
"The Decay of Strange Particles" episode from The Outer Limits TV show.
"The Mad Doctor of Market Street."
"2001"
"The Time Travellers"
"The 4D Man."
"The Unearthly." Love the part where John Carridine can't figure out why his experiments are going wrong. I've had days like that too.
"The Lathe of Heaven(1980)."
"The Thing With Two Heads."

And that's all I can come up with right now.
Igor, bring me the flask!

Famous Chemists I have known (Part 1)

timothylmayer@verizon.net — Mon, 8 Aug 05 09:40:00 UT

Over the years I have tried to remember some of the chemists who have influenced me since entering the chemical industry twenty-five years ago. Most of them never won a prize of any sort; some didn't belong to distingushed organizations. One of them never even graduated high school (he was drafted into WW2). But I'm going to try and talk about each of them as I find time.
Today I'm remembering Mr. Alan Varker. I worked with Mr. Varker at a polymer company when I first came to the Philly area about twelve years ago. Mr. Varker had been there for about ten years himself and was an analytical chemist. He ran the High Pressure Liquid Chromatography machine we had there, among other things. The HPLC wasn't used much, but when we did need it, such as to show visitors, he had that sucker fired up in minutes. Mr. Varker could show you chromatographs all day long and tell you what each band meant. He could do the same for FTIR data.
He'd worked at a number of battery companies over the years and had many stories to tell. One involved reccomending a ruby blade used to cut polymer battery sheets to keep the them from shorting-out. Another story of his was about a chemist who created an unstable organometallic. This man nearly blew himself and the lab up trying to take a melting point on the compound. Fortunately, no one was seriously injured.
He was an older man, nearing seventy years of age at the time. I was always astonished by his wealth of chemical knowledge. And Mr. Varker was never the sort of man you wanted to try and "impress" with your grasp of chemistry. He could easily challenge any half-baked ideas you might have. He was also the sort of man who could whip through a newspaper cross word puzzle in minutes.
One of his big accomplishments was a patent for purifying bisphenol A epoxy so that it could be used for cardiac applications. He held many patents, but didn't brag about them.
I last saw Mr. Varker the day they let him go. The higher-ups decided we had one too many chemists in our group and he was the one who lost the draw. I do hope he was able to land something else.

Background Music

timothylmayer@verizon.net — Tue, 2 Aug 05 12:38:00 UT

The other day I was thinking of what type of music goes best in the lab. I used to work with an older PhD who loved to play opera while he ran experiments. Myself, I've become a power metal fan over the years, after quitting punk army in the early days. Which is why I roll my eyes when I see mohican kids trying to freak their elders.....
Anyway, while I listen to MANOWAR in the background, I have came up with some tunes for your local mad scientist. here they are:

1)"Science Gone Too Far"- The Dictators.
2)"They Blinded Me With Science"- Thomas Dolby.
3)"Funtime" - Iggy Pop ("Last night I was down in the lab...").
4)Any of the background music from "The Outer Limits."
5)"Clone Warfare"- Chrome.
6)"Frankenstein"- The Edgar Winter Group.
7)"Cults Of The Shadow"- Therion (hilarious line about "the great charge of alchemy").
8)"Monster Mash"- Bobby "Boris" Pickett.
9)"Genetix"- The Stranglers.
10)"The Elements Song"- Tom Lehr.

There has to be a lot more, but these are all that I can think of at the moment.