Richard Gayle’s Old Blog

Well, my original personal blog will soon disappear. Userland is shuttering its Radio blogs at the end of this month.

I have been writing Richard Gayle’s Old Blog (the original A Man with a PhD) since 2002, a full seven years. On my first day, I wrote this:

One aspect of Radio that I love is that it serves as a personal archive of interesting info. Before, when I found a useful site, I’d either print it out or bookmark it. Now I blog it and can always find it, in the application I need to read it. Even if no one ever reads my weblog, I will need it.

Still true today. I’ll miss my old blog. It always felt like a kluge but there was nothing better for its time. In fact, it seems to be acting up today.

Don’t know when I’ll make my last post. But all things move on. You can still see what I wrote by clicking on the Web site (old) category). I expect I will move away from WordPress some day too.

An interesting article

Overexpression of TOSO in CLL is triggered by B-cell receptor signaling and associated with progressive disease:
[Via BLOOD First Edition Papers]
Resistance towards apoptotic stimuli mediated by overexpression of antiapoptotic factors or extracellular survival signals like B-cell receptor stimulation (BCR) are considered to be responsible for accumulation of malignant B cells in CLL. TOSO was identified as overexpressed candidate gene in CLL applying unit-transformation assays of publicly available microarray datasets. Based on CLL samples from 106 patients, TOSO was identified to exhibit elevated relative expression of 6.8 compared to healthy donor B cells using quantitative real-time PCR (p=0.004). High levels of TOSO expression in CLL correlated with high leukocyte count, advanced Binet stage, previous need for chemotherapy and unmutated IgVH status. CD38+ CLL subsets harboring proliferative activity showed enhanced TOSO expression. We evaluated functional mechanisms of aberrant TOSO expression in CLL cells and identified TOSO expression significantly being induced by BCR stimulation compared to control cells (relative expression (RE) 8.25 vs. 4.86, p=0.01). In contrast, CD40L signaling significantly reduced TOSO expression (RE 2.60; p=0.01). In summary, we show that the anti-apoptotic factor TOSO is associated with progressive disease and enhanced in the proliferative CD38+ CLL subset. Both association with unmutated IgVH and the specific induction of TOSO via the BCR suggest autoreactive BCR signaling as a key mediator of apoptosis resistance in CLL.

Afghans’ uranium levels spark alert

Granted, this is a small group, there does seem to be something interesting going on. It does not matter whether you believe in new fangled uranium weapons or not. For a boy to have 2000 nanograms of uranium per liter of urine suggests that someone’s measurements are wrong or that something weird is happening. I’ll wait for the papers, that are supposed to be coming out. Further work should clear up the matter.

Thu, 22 May 2003 16:26:08 GMT

Best SARS graphs yet. The best SARS graphs I have seen yet is this series of SARS graphs on Diaspoir.net by David O’Brien, an engineer in Hong Kong. He has a separate graph for every country that has reported a case of SARS! The graphs neatly show the number of deaths and recovered patients, and the big areas that represent people who are still sick with SARS. Highly recommended.

Thanks to RH for the tip. [SARS Watch Org]

Some very nice information.

Wed, 21 May 2003 13:57:43 GMT

Dog Genome Sequencers to Begin Ruff Draft of Boxer Breed: Chimp, Honeybee Almost Sequenced. GenomeWeb May 21 2003 0:12AM ET [Moreover - moreover...]

Everyone wants to find something to sequence. But it looks like getting the bovine sequence will be difficult. They still need to raise $50 million to match the funds from the government. Although Texas would like to give $10 million, in a time of budget problems, this could be problematic.

Wed, 30 Apr 2003 15:34:59 GMT

Circumcision does not dull sensitivity: study [Reuters Health eLine]

Thank Goodness. I would have loved to have seen the grant application for this work!

Wed, 30 Apr 2003 14:58:59 GMT

Where did SARS come from? The odds say zoonosis. I frequently get comments on SARS Watch Org and via email, suspicious that the SARS virus was created by somebody, because how could it appear from thin air? The probable answer is explained in this interesting article from the Boston Globe, Crossing the species barrier, which gives has some good background for the lay person on zoonosis, or the common spread of diseases from animal to human. The article gives examples of the many diseases that have crossed over from animals. A sample: When… [SARS Watch Org]

The Boston Globe article has some good info. One of the lessons from Jared Diamond’s classic book, Guns, Germs and Steel, was its convincing proposition that many of our most common illnesses came from the domestication of animals (i.e. smallpox). Zoonosis is an easy route for viruses to hop to a new niche. Until our immune systems adapt, they can cause huge problems. Pandemics always look like they appear from nowhere. That is the power of exponential growth.

SARS Watch

SARS is becoming more and more worrisome. A good place to get some updates about SARS is SARS Watch. Written by a non-doctor but good blogger. In particular some of the disturbing work suggesting that the coronavirus may not be the whole story. There is still some epidemiology to be done.

Biocomputing – Ants as a model

Eric Bonabeau will be discussing how to connect small dumb parts to get smart swarms. Nature has already done this so use that as a model. Use social insects because they DO connect dumb parts to create smart actions.

Create artificial insects. Flexible. Robust. Decentalized. Self-organized. Bottom up approach. How do we shape emergence? [Can we?] How do we define individual behavior to produce desired emergent behavior? Again, look at Nature [the environment. Not the magazine].

Actually, look at Double-Bridge experiment.[Sorry. I do not know if this is free. I just used google to search fordouble bridge experiment ant, and this was a top link. try one of the other links.] But this figure uses exactly what Eric describes [t should since it is from his Nature paper]. Evaporation adds robustness to the trails but preventing a convergence to a local minimum if there is a better path somewhere else.

Now discussing traveling salesman problem. Hard to compute. This is from his Nature paper also. Using virtual ants, you can get a solution. In fact it also finds more than one solution. Also can alter if some of the nodes (cities) disappears or changes. So it allows almost real-time analysis. This permits dynamic factory scheduling.

Goggle found another article discussing some of Eric’s work at Science News. He is discussing bucket-brigade approaches. Ants again helped identify how to do this optimally. It is being used by many companies.

[Font problems. It is all in Greek right now.]Discussing Aggressor-Protector game.

Problems with simple rules. Army ants and circular mills [here is a picture from last years meeting. This is from May Woo's site who is supposed to be at this meeting.] Vicious cycle. No one ant is in control. Same idea with nest building in wasps. hard to find the rules for building complex structures. Took him some time to define rules.

Here is a powerpoint presentation to Eric’s talk from last year.

Thu, 17 Apr 2003 23:38:14 GMT

New technologies make it so much easier to visualize and examine new discoveries. Here is a graphical representation of the putative structure of the SARS virus genome provided by Evan Carmichael, using software from his company,Redasoft:

The genomic sequence was only determined a few days ago. Now you can get an idea of which genes are where. Attempts at vaccines will be next.

Sun, 13 Apr 2003 19:30:23 GMT

Recent Living Code writing:

• SARS Sequence
• Possible Cannabilistic Ancestors
• Difficulty Cloning Humans
• Consumption and Birth Rate

My Writings At Living Code

Recent material examines:

• Cancer and Bacteria
• Human Cloning
• Melanoma
• Ebola and Apes
• Sheep without Hair
• Sudden Oak Death

Guardian Launches Science Page

The Guardian, taking the NYT as a model (for journalism if not openess of archives), wants to have science articles slug it out on an even footing with other stories. If it succeeds, I may have to put the Guardian on my A list. This editorial does describe some of the real needs for good scientific journalism, since so much of the major impacts on our lives come from science, whether it is a cancer sure or pesticide that can be used as a nerve agent.

Sun, 06 Apr 2003 06:45:30 GMT

The New York Times Changes Access to Old Content. The New York Times has just changed their archival policy so that all links we’ve used in the bIPlog that are more than 30 days old will redirect to a page requesting that you purchase the article for $2.95. Links have worked before now, even though articles were months or years old. Vin Crosbie, President of Digital Deliverance, talked last week at the JSchool about news online, and the mechanisms and logic that publishers use… [bIPlog]

This could be the end of the Times as a source of links in the Internet. I will no longer link to any of their pages since no one would be able to see anything after 30 days. Why tell anyone else about something interesting if they will have to pay 3 bucks to read it? For anyone to have to pay $2.95 to read a single article that is over 30 days old is ludicrous. You can get a great deal by paying $25.95 for access to 25 articles. Wow!! That is so nice of them. Plus you get 6 months to use this. Actually, all you buy is access to the article, not the article itself. You can look at the article (without pictures or graphs) for 90 days. Then you have to pay again. And, apparently, this holds true even if you are a subscriber. At least there is nothing on the payment page that says differently

What is funny about this is that scientific journals are going exactly the opposite direction. It costs money to read the current issue but many are making all their work open to everyone after a period of time. PNAS, for instance, allows open access to anything 6 months older or more. So, at least here there is a benefit to having a subscription. You can get access to 6 months of material at a reasonable price. But, if you can wait a while, you will eventually get older material. Plus, if you do not want to buy a subscription to get those 6 months of access, you can access all the articles at their site for for seven days for $15. Now, scientific papers may age more rapidly than newspaper articles. But I am skeptical. The NYT just lost its premier role in links and moved itself way down the list of places to read. (I wonder if the writers get any of that $3 as a residual?)

SARS and The Tipping Point

This graph from the New England Journal of Medicine provides some insight into the number of cases reported each day. I wonder where we are on the tipping point for this outbreak. If the curve tails off, we have it under control. If it reaches exponential increase, we are into a pandemic.