Saturday, December 7, 2013
Wednesday, December 4, 2013
As pleasing as this tree is, it seems to have more and more problems. Recently, the tree has been transformed into a bush of life. It is a bush because the branches do not start growing slowly as time passes, but burst into existence quickly at certain times.
The tree of life idea has become even more complicated. If you try to construct a tree of life using a particular set of measurements derived from morphology or genes, you get a solid tree. Unfortunately, if you use different measurements, you get a different tree. The two trees are in strong conflict.
To understand why the trees are in conflict, a reasonable approach would be to pick a particular organism, in this case yeast, and create a solid tree from that organism. Once you had that tree, you could take the method and extend it to other organisms and have a solid tree of life.
Unfortunately, even this simplified approach does not give a single tree. It gives trees that are method dependent and that conflict with each other.
If you look at dog genealogy, you get the dog bush of life where, once again, there is no consistent pattern.
Fossil by fossil, the story gets more complicated.
The complications increase. 400,000 year old human DNA from southwestern Spain contains genes that connect it more recent human DNA from southwest Siberia. It contains little DNA from these human's neighbors, the Neanderthal.
First version on 18 June 2013.
All of these posts can be put together to make predictions about the future of Los Alamos and about the future of many other communities. These predictions can be treated as posterior odds and standard errors on these odds.
The hypothesis with the highest odds is that Los Alamos, the community and the Lab, will continue to decline unless there are substantial changes in world view of the agents involved and that the likelihood of these changes is small. This is too bad.
On the other hand, the prediction techniques appear to be robust and can be used in many other places. Ask for details. The prediction techniques are much longer than a blog post and include details from many of the books reviewed here.
Here is a brand new article on the same lines. It starts with Phil Mickelsen and then expands from there. The idea of this article is that millionaires, whose companies are not in retail or real estate, will move to other states and take their taxes and those of their employees with them. The subsidiary idea is that once millionaires start leaving (5,000 millionaires pay 50% of the total taxes collected in California) then more taxes are leveled against the remaining in state wealthy, who then leave. The owners of real estate and retail lose part of their wealth as people leave the state and then must be taxed more reinforcing the downward spiral. Christensen talks about these events in detail.
A big insight, after I understood some micro and macroeconomics, is the huge role that agents and their world views play in what actually happens. For instance, many in Detroit or the upper front range in Minnesota kept pouring money and time into failing industries--autos and iron ore mining--for decades after it was clear that pouring money into these industries while maintaining non-competitive practices was futile. You have to understand agent behaviors to get a credible prediction.
This post was first published on 25 January 2013.
Tuesday, December 3, 2013
Sunday, December 1, 2013
Saturday, November 30, 2013
Now there are attempts to connect these two things. Arnon Grunberg is recording brain activity while he writes. This experiment is the latest attempt to understand neuralaesthetics--what the brain is doing when we appreciate art, music, or literature.
Friday, November 29, 2013
Now another experimental piece is falling in place. Happiness seems to improve the functioning of the immune system.
Thursday, November 28, 2013
I am finding the book very useful, interesting, and a little annoying. It is annoying in the beginning because too much of Venter's ego shows through but then Venter is telling the story parts that he was involved in and the ego disappears from the writing. Venter, like Muhammad Ali, has accomplished amazing things and is presenting what his team has done. The book is interesting because it gives Venter's detailed view of some world changing events in biology. It is useful, at least to me, because it is heavily referenced. Many of the references are standard ones, but about 10% are new references to old studies that I did not know about. I will use these references in my own talks.
Venter's main point, which he repeated in an interview on Charlie Rose, is that life used to be confined to nature, but we can now transmit instructions for life, new or old, anywhere that radio waves can reach and could then build the life that those instructions encode, for instance a new infection fighting bacterium, on site as needed. The book is clearly worth a read. The reading is a bit slow going because the thoughts are densely packed. The payoff is for reading is large.
The biggest payoff for me were the approximately ten pages, towards the end of the book, that talked about the current state of the art in simulating cell processes and their genetics in a computer.
I would love a scientific discussion on the meanings of the terms used in duties. I would like the discussion to include sources of funding, biases in both governmental and non governmental funding decisions (for example the finding that most Nobel prize winning work was unfundable at the time of its discovery), and how each scientist has to adapt in order to feed their family. A related topic would be how the same set of experiments changes from morally good to morally bad to morally good over time, even in a single country, as fashions change.
More thoughts when I have some time for them.
Some of this junk DNA is junk no more. The region of DNA is needed in the production of RNAs, not proteins, that are required for accurate brain development.
Now evidence of dark matter particles has also come up empty after promising earlier results.
Here is a review.
And it gets worse for dark matter. There was satellite evidence for positrons created during the annihilation of dark matter particles. Now theorists claim that the evidence was created by cosmic rays, not dark matter destruction. This is good for understanding cosmic rays, not so good for the detection of dark matter.
First published on 31 October 2013.
"I finished "Dancer" several days ago and am still spinning. This is a beautiful book, layered with all the nuance and sweat and discipline that accompanied Nureyev's genius. In the purity of the storytelling, in its flawless narrative construction, this is prose that is itself a dance." Jeffrey Lent
"Rudolf Nureyev was an extremely complex person, yet Colum McCann has admirably captured the essence of this great man. " Maria Tallchief.
McCann's "Let the great world spin" captured the essence of New York in the time surrounding Petite's tightrope walk between the two towers of the World Trade Center. In this earlier book,McCann captures the complexity of Mureyev by viewing him through the eyes and voices of those who knew him best--family, friends, lovers, dance partners and himself. McCann also captures the reality of life in the Soviet Union. He does this through beautiful and concise writing including those small details of a scene that capture the essence of the scene and that we all notice but never say out loud.
"That evening I sat with Iosif and heard the elevator's pulleys screeching in the hallway. When it stopped on our floor I could hardly shuck the thought that they were coming to knock at the door. I packed a bag with what I imagined I would need. It included a Gorky novel with money pasted beneath the cloth cover. I put the bag under my bed, had nightmares of being chained to a table."
Read this, savor it, dance with it. Then read "But Beautiful" which is prose jazz in the way "Dancer" is prose ballet.
Wednesday, November 27, 2013
Now there is another such event. Physicists, after many years of work, determined that high energy gamma rays are emitted as certain stars go nova and then collapse. The pattern of going nova and collapse has key signatures of how long the explosion lasts, when the majority of visible light is emitted, and when the largest amount of gamma rays are emitted.
This new gamma ray event does not seem to have read the theories. It violates most of them. It emitted gamma rays that are too energetic and not in the predicted time sequence. It lasted too long. It emitted visible light when it was not supposed to.
New theories are needed, especially since this new black hole does not make sense.