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Author Archive

Oct 2013 Links

Wednesday, October 2nd, 2013

Comic biography of Ayn Rand
Is the Advice of Economists Useful?
Repubs Worked to Engineer a Federal Budget Crisis
The MiddleMan comics and TV show
Reminder: lack of health insurance kills (Harvard Medical Schoo, 2009)
Using Windows XP in VirtualBox on Linux
Air-gap flash DIY
The roots of the 2008 financial crisis: Barry Ritholtz – November 6th, 2011 and Dean Baker Sunday, 03 July 2011
300KV Cockroft Walton multiplier
TIP120 transistor for power control
CR guide to health insurance

The Metabolic Theory of Cancer

Saturday, September 21st, 2013

Notes on “What Is The Origin of Cancer?” by Travis M Christofferson.

The most useful thing about this article is that it reminded me of the 2010 book, “The Emperor of all Maladies”, by Siddhartha Mukherjee.

The article has is divided into a few sections: a description and dismissal of the genetic theory of cancer, a discussion of the Cancer Genome Atlas project and a dismissal of it, and then the metabolic theory of cancer is described and touted.

The article starts by making some assertion about cancer to frame the discussion. “We are not winning the war against cancer; we are no closer to cures than when Nixon declared the war on cancer in 1971 – in fact, we may be further away.” Cancer has proved a difficult disease–there have been some improvements in survival times in some types of cancer, some cures, but the change in overall cancer treatment has been modest. Currently, a number of targeted cancer drugs are being used and making a difference. Let’s call them 2nd generation drugs to differentiate them from the chemotherapy drugs that kill dividing cells indiscriminately. There are also a bunch of new therapies, several different kinds currently in the works, let’s call them 3rd generation treatments.

In 1971, when the big push to cure cancer began, the difficulty wasn’t clear. At that time, not much was known about what caused cancer and how it progressed. Now we have a decent understanding of it, and there are *several* promising approaches that could substantially improve treatment and outcome.

We’ve understood cancer pretty well for some time, since the 90’s. Unfortunately, treatments have been hard to come by. Treatments are technology, and cancer is a hard nut to crack. Cancer is a body’s cells dividing without limit. These cells start ignoring the signals and controls that keep cells dividing only when and where they are needed. A treatment for cancer needs to get these cells to stop dividing or kill them. It is difficult to treat cancer for two reasons: 1) cancer cells are human cells, so treatments that kill cancer cells and bypass normal cells are hard to engineer, and 2) cancer evolves to resist treatments.

The second factor is the real killer. Think of a cancer of as a population of millions of cells, each a bit from the others due to mutations in DNA or other changes. A treatment that kills almost all of them leaves thousands that are resistant to the treatment. They continue growing and picking up more changes. A second, different treatment will have the same effect. While some of these changes make cancer resistant to treatment, others allow it to escape other limits. A growing tumor runs out of space and out of blood. So cells that can invade surrounding tissue or metastasize to a new place in the body are also successfully evolved tumor cells.

Cancer treatments usually run through these cycles: a treatment initially has great success, but then the cancer comes back. Some cancer cells have survived and they grow and divide and the tumor comes back, changed. If a treatment is repeated, it is less effective each time.

So a cancer cell is a cell that has changed to ignore the normal signals to stop dividing, and as a tumor grows cells that have additional changes keep occurring. Whether a change to a cell’s DNA or metabolism starts it dividing, the process will continue and the cancer cells will keep changing to ignore or bypass things the keep them from dividing. So if a diet change robs cancer cells of glucose or metabolic changes signal them to stop dividing, some cancer cells will not stop dividing and the cancer continues.

A number of genes are known to play a role in cancer, mutations in oncogenes or tumor suppressor genes are found in all (or pretty much all) cancers. The role of mutations in causing cancer is the Somatic Mutation Theory of Cancer. Changes to genes that are involved in controlling cell division allow cells to ignore the normal checks on cell growth and division.

When the Cancer Genome Atlas Project began, years of research had already identified the main cancer genes (hundreds of genes). This link summarizes the project (TCGA). The idea is to get a comprehensive look at what genes are changed in different kinds of cancer at different stages of the disease. Not really expected to be revolutionary, instead just round out the genetic picture of cancer.

A number of 2nd generation cancer drugs target these cancer genes. They knock down cancer for a while, and give patients added months of life. Eventually, the cancers pick up mutations in other genes and bypass the drug. So these drugs usually don’t cure cancer. New methods of characterizing cancer are beginning to reach the clinic that allow each patient to get the drug that targets the genes mutated in their cancer, so these drugs are becoming more effective.

I’ve met Bert Vogelstein, he’s an intense guy. He discovered how p53 mutations cause cancers, and the most common colon cancer gene, APC. He played a role in fleshing out the somatic mutation theory of cancer. The theory is holding up well–sequence a tumor’s DNA, and known cancer genes show up with mutations.

Cancers aren’t all the same. Each one is a cell that pciked up mutations and started dividing and then picked up more mutations. There are lots of cancer genes, so different tumors pick up different mutations, in different orders. The different types of cancer arise from different types of cells. For a particular cell type, it is easier to start dividing if certain genes mutate (a gene already turned on in a cell, for example) so certain cancer genes are common in different types of cancer. There is also a lot of flexibility as cells pick up mutations and lots of potential cancer genes, so each cancer is unique. This has been known for a long time in general terms, but new techniques are allowing each cancer to be characterized in detail. Volgelstein’s review in the journal Science describes this.

The metabolic alterations in cancer have been known about for a long time–biologists developed tools to study biochemistry before the method for genetic studies came along. Cancer cell’s great demand for glucose has been known for a long time. Cell growth and division and metabolism are tightly linked, so changes in cancer genes change cell metabolism and vice versa.

Can changing diet, starving a cancer of glucose stop it, cure it, or at least put it on hold permanently? I can only find a few published studies, mostly in mice. It seems like it may be effective in slowing the progression of some types of cancer, at least temporarily. However, ketogenic diets have been known about for a long time, and trying them for cancer seems obvious. So if it worked well for cancer, it seems likely it would be well known by now.

Thomas Seyfried has worked on cell metabolism in cancer for a long time. He has a book out on his work, and wrote a review for the Medscape site.

In the Medscape article, Seyfried calls “impaired cellular energy metabolism is the defining characteristic of nearly all cancers regardless of cellular or tissue origin”. This claim seems way too strong. There are many defining characteristics of cancer–things that differentiate it from normal cells. Each one is a potential line of attack on tumor cells, a target for drugs or other treatments. Hopefully, treatments that target metabolic changes can be developed, in addition to Metformin. They would be as welcome, and as profitable for drug companies as any other cancer drug. Most likely, treatments targeting cancer cell metabolism can be effective and retard cancer progression for months, but populations of cancer cells evolve, and they will most likely evolve to bypass each metabolic restraint.

Christofferson’s article touts the metabolic theory all out of proportion to the evidence for it.
He writes that a ketogenic diet cures cancer. He takes the disgraceful step of pulling out a few cases where cancer was ‘cured’ by this diet. Every one of the hundreds of scam cancer treatments comes packaged with patient testimonial ‘cures’. Christofferson quotes Seyfried as saying “If one was able to patent and package the ketogenic diet as a pill for cancer it would be a blockbuster”, but if you read Seyfried’s article in Medscape, written for doctors, he doesn’t make this claim. Either Christofferson or Seyfried isn’t being honest with us.

Library Ancient and Universal

Wednesday, September 18th, 2013

Does there exist a project to assemble an online library of ancient written works intended to be complete? It sounds ridiculous, I know. But, if you start back far enough–say 3000 BCE–there is hardly anything to compile. And then the project can work forward until the project spreads out too much.

There are practical problems–images vs symbols and alphabets, fragmentary or derivative manuscripts, arguments over translation, historical translations versus modern ones, organization by region or language, but they have all been worked over by traditional publishers. The result would look like a cross proto-Project Gutenberg / Wiki.

If anyone tries this (assuming I just haven’t heard of it), I fear one of the most frustrating issues would be copyright. Museums forbidding the taking or use of images of the rare manuscripts or tablets or whatnot that they control.

It seems that most of the ancient manuscripts are described are referenced in fragments in medieval studies books and rare manuscripts. I hear about this stuff by third hand descriptions rather than by to links to online reference copies.

Update: Thesaurus Linguae Graecae (TLG)

Sept 2013 Links

Sunday, September 8th, 2013

True Courage
Commandments for Using PICs
NYT tribute to Eugenie C. Scott
Chris McCandless, who’s death in Alaska was described in “Into the Wild” was likely killed by a neurotoxin, beta-N-oxalyl-L-alpha-beta diaminoproprionic acid, known as ODAP. HOW CHRIS MCCANDLESS DIED POSTED BY JON KRAKAUER, The New Yorker, Sept 2013
11 questions to see if libertarians are hypocrites
Catching the stars: Roger Angel is one of the world’s most brilliant and audacious engineers. Could he design the next energy revolution? by Lee Billings
7 Ancient Writing Systems That Haven’t Been Deciphered Yet
End run options to avoid the the US debt-ceiling
Steampunk coffee shop (SA)
MakerJuice selling reasonably priced UV curable resin
Fossils at Mazonia-Braidwood State Fish & Wildlife Area
GeodeFest, held in September
Copper Bracelets and Magnetic Wrist Straps do not work for Rheumatoid Arthritis. Richmond et. al., 2013. PLoS ONE
Costs of Obamcare (ACA) on fast food businesses: 0.5% of sales, 3 cents / sandwich. Benefits: higher productivity and reduce absenteeism and turnover, workers get their hepatitis and other communicable diseases treated, flu shots and other vaccinations

Aug 2013 Links

Saturday, August 24th, 2013

A case study of “disorganized development” and its possible relevance to genetic determinants of aging. Walker et. al. Mech Ageing Dev. 2009 May;130(5):350-6. PMID: 19428454
Delayed development syndrome (Brooke Greenberg from Reisterstown, Maryland; Gabrielle Williams of Montana; Nicky Freeman of Australia)
How An Engineering Toy For Girls Went From Kickstarter To Bestseller
Barrayar dreaming
Dolphins are not super intelligent
Bradley Manning and the Two Americas by Quinn Norton
Smallest geome: Nasuia deltocephalinicola. 112,000 base pairs. 137 protein-coding genes.
Two sleeps, sleep pattern before electricity
Mac speed comparisons

Documenting the voting restriction effort

Friday, August 16th, 2013

Boulder County DA Stan Garnett clears all 17 suspected illegal voters

Last month, Colorado Secretary of State Scott Gessler gave Boulder County District Attorney Stan Garnett a list of 17 names, all suspected of voting in the November election despite being non-citizens.

Those names were among 155 people identified statewide as possible illegal voters.

But an investigation by Garnett’s office found that all 17 people were citizens and were able to easily verify their status, the district attorney said Wednesday.

Related: Common Cause page on Voter Supression and Secretary Scott Gessler

Links for July 2013

Tuesday, July 2nd, 2013

FBI ignored plot to assassinate Occupy protesters
12 Very Real Voter-Suppression Tactics
Electro-Permanent cargo gripper
Electropermanent Magnetic Connectors and Actuators: Devices and Their Application in Programmable Matter by Ara Nerses Knaian
ALNiCo magnets
Sand resonance pattern video
MEAM waterjet, senior design project, 10k psi
Nothing About Abortion in the Bible
Iodine’s effect on IQ test scores–15 pts in iodine-deficient areas
Replacing Samsung SGH-T679M Digitizer
Silicon Valley (and the history of toxic waste)
Makers of Things
Human vestigial tail
A hundred proofs the Earth is not a Globe
History of Inequality
The Tea Party’s paranoid aesthetic by Kim Messick

June 2013 Links

Sunday, June 2nd, 2013

Allpaths-LG genome assembler
ELM327 interpreter chip provides an RS-232 (serial) interface to ODBII car network
About universal basic income
Catsup tank video
Article on a CBO report on tax breaks
CBO report: The Distribution of Major Tax Expenditures
in the Individual Income Tax System

We Already Tried Libertarianism – It Was Called Feudalism by Mike Konczal
Spiders do not Bite
Perspective on Institutional Secrecy and Leaks
High Price: A Neuroscientist’s Journey of Self-Discovery That Challenges Everything You Know About Drugs and Society by Carl Hart
Books to read: The Invention of Religion by Alexander Drake
Books to read: Euclid’s Window: The Story of Geometry from Parallel Lines to Hyperspace by Leonard Mlodinow
ChildbirthConnection.org evidence-based information on pregnancy

May 2013 Links

Sunday, May 5th, 2013

Solar panels could destroy U.S. utilities, according to U.S. utilities By David Roberts, source pdf
Article about the 2012 Chicago teachers strike and the school bus driver strike in NYC this year
Competing theories of the genetics of the Jews. It will be interesting to see how this turns out.
Watch making project blog
Glasswing Butterflies
Glasswing
CSS element browser support
BatchPCB is now OSHPark
Sharps and Flats by John Nevil Maskelyne (1894)
Octopus intelligence
Potoo
Illegal surveillance on US activists continues
Wingnut rumors: Will the IRS hire 16,500 new agents to enforce the health care law?

App ideas

Thursday, April 18th, 2013

Micro movement sensing

Use the orientation sensor in a cell phone to monitor small regular movements. For example, the movement due to the heart beat. It might be possible to measure breathing movement. It may also be possible to measure anomalous movements–tremors, the sway due to microadjustments involved in standing.

Also, if the heartbeat moves a phone to a noticeable degree, does this make cell phone photos blurrier? If so, add heartbeat detection to the camera app–have pictures be snapped between heartbeats.

Basically, orientation data would be collected, and a frequency analysis done to detect the freq and amplitude of the movements. I don’t know how fast the orientation can be polled. If it is too slow, it may be possible to use intermittent polling at precise times to identify the frequency of movements.

Shadow boxing

A related use would be as a shadow boxing app. This would clearly be better as a wrist strap standalone device, but might work as an app. Hold the phone in a hand (or strap it firmly to the wrist), and follow the movements of the hand/arm, recording punches and the speed of them. The user would indicate the hand being scored in setup, and then as hands are switched, the punching of the two could be compared. Groups of friends could play together to see who can punch the fastest or do the most punches in 30s.

Spectrophotometer

This app would run simultaneously on two phones. One phone would display bands of pure red, blue, and green. A sample would be placed across one half of the bands. The second phone would take a picture of the first phone. Image analysis would compare the brightness of the control and sample covered regions and calculate absorbance in the three channels. Cell phone displays are either OLED or IMOD. There are a range of displays used in phones, so this would never be super accurate without calibration. The OLED displays seem to have fairly narrow spectrum pure colors while the iphones have broader colors.

This could be used either as an exploration tool–test substances and record spectra, or reference data could be used to make guesses at substances.

Or you could use a diffraction gratings and make a real spec.