Thursday, January 29, 2009

Real single particle quantum experiment

If the theoretical physicists ever studied how REAL observations are made (i.e. what are the practical principles behind the equipment doing the measurement) then they might find this video instructive.

Niels Bohr and Werner Heisenberg were smart guys, but both were dead before technology had advanced to the point where clean single particle measurements could be made, that's why the Copenhagen Interpretation is so lame. The problem is that theoretical physics became a religious tradition, i.e. it was more important to follow in the grand ideas of the venerated forefathers (Bohr & Heisenberg & others) then to actually clarify, repair & improve on the old ideas.

Many of the things that Darwin thought were not correct. Not because his overall ideas had gross problems, but rather because of incomplete knowledge in his time. For example, Darwin knew nothing of simple Mendelian genetics. Some people have even suggested that he might have been Lamarckian. Nonetheless, his overall theory stands as the greatest achievement in human thought of all time.

Biologists got the memo about keeping science scientific and thus the Modern Synthesis which repaired and clarified Darwin's ideas.

Tuesday, January 27, 2009

Corporate Culture

Years ago, as an engineer, I needed an I2C adapter to do work with a new integrated circuit. The I2C adapter was made by a small company where when you called the main number, you got the guy who founded the company. The adapter cost $300. I put in a requisition with our VP. All requisitions had to be approved by Jack. The VP had no authority to approve the $300 requisition. At this point we had more than 1000 employees and revenue close to $1B. My req sat for a month with me bugging the VP constantly. Finally with special action, the accounting department was forced to take it on. I waited another two weeks, then went to the accounting department to see why the order STILL HADN'T BEEN PLACED. The accounting guy told me that even though Jack had approved the rec, Jack now had an across the board rule that there needed to be at least three vendors for every rec'ed item. Since this was a unique item, I could only find one vendor. I bugged the accounting guy to get an exception for this rule. Waited another week or so, still no action. Went to see the accounting guy again. Now he says since there is only one vendor, the policy is that we must have a 15% discount off the list price. I called the founder of the I2C adapter company and personally pled with him to give us (me!) a discount. He refused. I was stuck. I gave up and didn't think about it anymore. A month later, the adapter showed up on my desk. I went to accounting to see what happened. The accounting guy told me he had called the I2C adapter guy every few days asking for the discount and constantly getting refused. Finally after MANY calls, the poor I2C guy gave up and said "fine! you can have the discount, just stop calling me!". The joke is... By the time the darn thing showed up on my desk, I didn't need it anymore.

Monday, January 26, 2009

Great Article on the Crash

I am fond of beating up on Theoretical Physicists. As it happens many of my best friends are PhD's in Physics (not Theoretical though). One of my particularly intelligent friends has worked on wall street for many years. He sent me a link to this article that explains the recent collapse of our financial system.

The End

New Atheist Pantheon

With this wonderful article in the New Republic Magazine:

Seeing and Believing
The never-ending attempt to reconcile science and religion, and why it is doomed to fail.
Wednesday, February 04, 2009

I hereby add Jerry Coyne to the New Atheist Pantheon!

Quote from the Book I am Reading, Life on a Young Planet

"Despite an almost bewildering diversity of form and function, all cells share a common core of molecular features, including ATP, DNA, RNA, genetic code, molecular machinery for transcribing genetic information from DNA into RNA, and more machinery to translate RNA messages into proteins that provide structure and regulate cell function."
- Life on a Young Planet, The First Three Billion Years of Evolution on Earth
- by Andrew H. Knoll

Friday, January 23, 2009

New Atheist Manifesto... !

PZ Myers: we don't believe, and we find no virtue in faith.

Nobody can give you freedom. Nobody can give you equality or justice or anything. If you're a man, you take it.
- Malcolm X, Malcolm X Speaks, 1965

Thursday, January 22, 2009

Wisdom from Austin Cline

Something that Austin Cline from wrote was so good that I am going to "enshrine" it on my blog:


The conflicts between religious faith and empirical science seems to be continual, but just as continual are the efforts to find some middle ground where both can co-exist. It's important for many Americans to find a way to bridge the gulf between traditional Christian faith and modern science, but can this be done? If it can be done, should it be done?

Science undermines the human conceit that the universe is or should be structured according to human whim. Science reveals that the universe is wholly indifferent to us, our desires, and even our suffering. Science also provides the means by which we ourselves can cause changes or alleviate suffering, but only by working with nature and with the way the universe is structured.

We cannot, for example, turn away a hurricane but we can use science to predict them and build structures better able to withstand the onslaught of the storm. Despite this, people pray for hurricanes to turn away and they visit astrologers who tell them how to avoid problems. Why? Because they believe that the movement of stars and atoms can be affected merely from the desire that it be so.

Science presents us with a stark choice about how to approach the world around us. One the one hand we can continue with the prayers that arise out of the wish that the order of the universe might rearrange itself according to the preferences or our hearts or, on the other hand, we can move forward with the scientific project of learning more about the universe and, therefore, learning how we can better make our homes with what we have.

Religion has never cured a disease, protected people from a storm, or saved anyone from the ravages of old age. Science, however, has made tremendous gains with all of these and more. There is a reason for that.


Sunday, January 18, 2009

Old School Artificial Intelligence and Determinism...

I used to work in the MIT Artificial Intelligence Laboratory. Many people there believed in the philosophy of determinism, especially as embodied by Causal Determinism. From their Computer Science vantage point, they thought of the universe as a giant Turing Machine. In this mind set, conclusions about Turing Machines can be applied to the universe at large. This leads to faith that reductionism can solve any problem because once you know the microscopic properties of a system, you can predict any complex behavior. Modern physics is rife with this philosophy. I formerly subscribed to this viewpoint until reading Ernst Mayr, Carl Woese and Stuart Kauffman. Carl Woese's article "A New Biology for a New Century" helped me see the light.

In response to any discussion of the universe as a Turing Machine:

All observations of quantum behavior have so far shown that particle motion at quantum scale is truly stochastic. The physical universe is itself fundamentally non-deterministic. The determinism in finite state or Turing models (infinite or not) is simply an abstraction that exists in the human mind. It is a useful heuristic for making decisions in an environment where the standard deviation of physical parameters is so small that it can be ignored without ill effect.

Technically, even a digital computer is not fully deterministic. At any given clock cycle there is a finite probability that the next state will not be the intended one. Embedded systems designers have been aware of this for a long time, which is why they always include watchdog timers in their designs. Even in a Pentium, the probability of failure is high enough that in continuous operation, it will probably fail once every few years.

Friday, January 16, 2009

Biology in a few sentences...

Where does life come from? All cells alive on the planet earth today came from a "parent" cell. Just like grandfather had a father that we call great-grandfather, great-grandfather had a father we call great-great-grandfather. What does our great-great-great-great...lots of greats!-grandfather look like?

We can often tell people are in the same family because they have features in common. They look alike. What common feature do all cells have? All cells have ribosomes! Every living thing on this earth is our relative. Every living thing on this planet earth is part of our family. We know we are all related because we share a common feature, ribosomes.

There is a tree of life that follows what all our ancestors looked like. At the base of this tree is a cell type that we all descended from. We call this "LUCA", for Last Universal Common Ancestor. In Asia, ancestors are respected and honored. In this same way, we should revere LUCA. LUCA is our ultimate ancestor and as such demands our ultimate reverence.

A personal digression...

Sadly, tonight I just found out that Jack Gifford died. He was a larger than life character and maybe someday they will write a book about him, so here are a few of my memories...

The Athletic Competitor:
The area where we played grass volleyball at lunch was right behind Jack's office. Jack had a fenced off outdoor area next to his office that I think he sat in sometimes. For many months we played and finally one day he came out and said he wanted to play too! We played at a reasonably advanced level and having the CEO come out and challenge us to a match was quite a surprise. Jack partnered with Jeff Kirsten and I had my usual partner, Krishnan. Boy, was Jack aggressive! He came storming up to the net on every point! He was in his 50's at the time and we were early 20's/30's. No matter! Jack kept up the furious pace for the entire match. At one point when I went for a spike, he flew under the net and smacked right into me pretty hard. Then he grunted at me. Kind of intimidating!

Marketting Guy?:
When I first joined MAXIM, I didn't know much about Jack. I assumed he was some kind of MBA guy and not necessarily technical. One time, out of the blue, Jack sent out a memo asking for ANY business idea from ANYBODY. The idea didn't even have to involve chips. Fuzzy logic was all the rage in the industry and one of the business managers, Eric, asked me to partner with him to propose fuzzy logic control chips. I didn't know much about controls but had read up quite a bit on fuzzy logic and figured I could wing it. We met with Jack and gave our spiel. At the end, Jack says "You know I did my master's thesis on electronic control systems and I'd like to ask you guys some detailed questions." Both of us were flabbergasted... We turned pretty red. We looked like total dopes because it turned out that Jack knew way more about control systems then either of us did and I was was supposed to be the technical guy!

Lab Surprise:
One time I was working in the lab and the door popped open. Jack came in and just started looking over my shoulder. The CEO! Breathing down my neck! Ahhh.... He didn't say anything to me and finally another guy asked Jack what was up (I was too scared to say anything). Jack replies and I remember this vividly, "Just checking on the chickens".

Newton Chips:
The Apple Newton palmtop had just come out and there was quite a bit of buzz about it. We proposed building handwriting recognition chips for Newton like products. My boss, Len, obtained a Newton and let me and some of the other guys play with it. We, of course, taught the Newton to recognize the handwritten word, FUC* (replace the * with letter K). In the big meeting, Jack signed his name and as his signature was notoriously illegible and his first name has four characters, the Newton prompty responded FUC* !!! So Jack says "What the fuc*!", throws the thing down and so much for handwritting chips...

Thursday, January 15, 2009

Molecular Biology in a few sentences...

Everything alive is made of cells. Cells are very small. If you grind up cells in a blender, you get three types of things: proteins, nucleic acids and lipids.

Muscle has lots of protein in it. Muscle is usually red in color. A steak from the supermarket is mostly muscle. People like to eat protein because it tastes good. Proteins are chains of amino acids.

Nucleic acids are the white fuzzy stuff in the picture on the left. Nucleic acids are chains of nucleotides. Nucleic acids store information like a book. Nucleotides are the letters in the nucleic acid book. The plan to build anything alive is in the nucleic acids of its cells.

There are many different kinds of lipids but most of them look like candle wax. Lipids won't dissolve in water. Some lipids when placed in water, make little hollow bags called vesicles.

Every cell in all living things has ribosomes which use the information in the nucleic acids to make different proteins. The ribosome is made of nucleic acids and proteins.

I have a 5 month old son. He is named after the famous 19th century professor of physics who unified the equations of electromagnetism,
James Clerk Maxwell. I often think about how to raise him to be as intelligent and capable as possible. It would be nice to teach him the basics of the scientific world view at a young age (maybe 5? :) . I am trying to think of ways to talk about scientific concepts in a straightforward way. Some of this blog will be about that topic.