Recently in Science & Technology Category

Eight weeks ago, I hosted Dr. Aubrey de Grey for his second talk at Google in Mountain View, California, a follow-up to his earlier Google talk in the SENS series, "WILT: taking cancer seriously enough to really cure it":

ABSTRACT

The intrinsic genetic instability of cancer cells makes age-related cancers harder to ... all » postpone or treat than any other aspect of aging. Any therapy that a cancer can resist by activating or inactivating specific genes is unlikely to succeed long-term, because pre-existing cancer cells with the necessary gene expression pattern will withstand the therapy and proliferate. WILT (Whole-body Interdiction of Lengthening of Telomeres) seeks to pre-empt this problem by deleting from as many of our cells as possible the genes needed for telomere elongation. Cancers lacking these genes can never reach a life-threatening stage by altering gene expression, only by acquiring new genes, which is far more unlikely. Continuously-renewing tissues can be maintained by periodic reseeding with telomere elongation-incompetent stem cells that have had their telomeres lengthened in vitro with exogenous telomerase. I will describe why WILT may become a uniquely comprehensive anti-cancer modality, and the practicalities of performing it and avoiding side-effects.

Some weeks back, my (now) friend Dr. Daniel Kraft, a physician scientist at Stanford, came to Google at my invitation to give a talk, "Everything You Wanted To Know About Stem Cells... But Were Afraid To Ask":

ABSTRACT

Stem cell technology and the debate surrounding it has generated a great deal of excitement ... all » and controversy in recent years. The field is surrounded by misconceptions, hype and yet very significant potential. In this talk we'll cover: defining what are stem cells really and where do they come from... the differences between embryonic stem cells and 'adult stem cells' (i.e. derived from our own bone marrow, fat, umbilical cord blood, placentas and even our kids teeth) and emerging technologies to utilize these cells in powerful and novel ways. We'll cover current clinical uses of stem cells, ongoing clinical trials in regenerative medicine (i.e. using marrow derived cells to treat heart attacks, vascular disease, stroke and even diabetes), upcoming trials utilizing embryonic stem cells, and some of the likely near term and future applications as well as challenges remaining in order for this field to reach its full potential.

Aubrey de Grey gave a Tech Talk at Google's Mountain View campus this week, and I was privileged to attend. I've seen him give a longer, earlier version of this presentation before - at Stanford in June 2005 - and was impressed more than ever. Enjoy:

ABSTRACT

It may seem premature to be discussing approaches to the effective elimination of human ... all » aging as a cause of death at a time when essentially no progress has yet been made in even postponing it. However, two aspects of human aging combine to undermine this assessment. The first is that aging is happening to us throughout our lives but only results in appreciable functional decline after four or more decades of life: this shows that we can postpone the functional decline caused by aging arbitrarily well without knowing how to prevent aging completely, but instead by increasingly thorough molecular and cellular repair. The second is that the typical rate of refinement of dramatic technological breakthroughs is rather reliable (so long as public enthusiasm for them is abundant) and is fast enough to change such technologies (be they in medicine, transport, or computing) almost beyond recognition within a natural human lifespan. In this talk I will explain, first, why (presuming adequate funding for the initial preclinical work) therapies that can add 30 healthy years to the remaining lifespan of healthy 55-year-olds may arrive within the next few decades, and, second, why those who benefit from those therapies will very probably continue to benefit from progressively improved therapies indefinitely and thus avoid debilitation or death from age-related causes at any age.

What a day! Just as I'm getting ready to attend Aubrey de Grey's talk at Google, I find out that a martial arts training buddy of mine, Dr. Pete Lohstroh, recently left his research position at UC Davis to take a senior scientist position at Telomolecular Nanotechnologies, specializing in the application of nanocircles to telomere extension therapy (one of several approaches they're taking). Congratulations Pete!

Nanomedicine opens the way for nerve cell regeneration

"The ability to regenerate nerve cells in the body could reduce the effects of trauma and disease in a dramatic way. In two presentations at the NSTI Nanotech 2007 Conference, researchers describe the use of nanotechnology to enhance the regeneration of nerve cells. In the first method, developed at the University of Miami, researchers show how magnetic nanoparticles (MNPs) may be used to create mechanical tension that stimulates the growth and elongation of axons of the central nervous system neurons. The second method from the University of California, Berkeley uses aligned nanofibers containing one or more growth factors to provide a bioactive matrix where nerve cells can regrow..."

Nanoparticles Delivery of 'Suicide DNA' Kills Prostate Tumors

"...using nanoparticles developed by members of the Alliance for Nanotechnology in Cancer, a team of investigators at the Lankenau Institute for Medical Research, in Philadelphia, has developed a DNA-based therapeutic agent that has the potential to treat both enlarged prostates and localized prostate tumors. When tested in mice, this new agent specifically targeted prostate tissue, producing no toxic effects in surrounding tissues..."

The world and the universe is an extremely beautiful place, and the more we understand about it the more beautiful does it appear. It is an immensely exciting experience to be born in the world, born in the universe, and look around you and realize that before you die you have the opportunity of understanding an immense amount about that world and about that universe and about life and about why we're here. We have the opportunity of understanding far, far more than any of our predecessors ever. That is such an exciting possibility, it would be such a shame to blow it and end your life not having understood what there is to understand.

Richard Dawkins, from an interview with Sheena McDonald

I'm about a month late in actually publishing a mention of my friend (and Reuters reporter) Tom Burroughes' interview with Cambridge University gerontologist Aubrey De Grey, "Lifespans soon to be decades longer", which, interestingly, seems to have been syndicated on the Indian version of Yahoo! News.

Forwarded to me by Perry Metzger, and independently brought to my attention by Tom Burroughes, published in Science as "Cancer Regression in Patients After Transfer of Genetically Engineered Lymphocytes":

Using adoptive transfer of lymphocytes given after host immunodepletion it is possible to mediate objective cancer regression in patients with metastatic melanoma. However, the generation of tumor-specific T cells in this mode of immunotherapy is often limiting. Using a retrovirus encoding a T cell receptor, we report here the ability to specifically confer tumor recognition by autologous lymphocytes from peripheral blood. Adoptive transfer of these transduced cells in fifteen patients resulted in durable engraftment at levels exceeding ten percent of peripheral blood lymphocytes for at least two months post infusion. We observed high sustained levels of circulating, engineered cells at one year post-infusion in two patients, that both demonstrated objective regression of metastatic melanoma lesions. This study suggests the therapeutic potential of genetically engineered cells for the biologic therapy of cancer.

I have the full paper, forwarded to me by a friend, which I'm reading slowly.

Mac OS X has always had problems with name resolution... both DNS, id->uid, etc. It's all centralized to one service and that service is buggy.

I joined XXXXXXX this year, but before that I spent 1.5 years running a medium-sized (but international) Mac OS X network. Half the problems we had all were traced down to name service.

The situation gets better with each release, but there are some fundamental problems still. Mostly they crop up with you have LDAP enabled.

Whenever I see the spinning rainbow ball, and no network traffic and little CPU use, I just steam and sit there imaginging a little gnome inside my computer holding the ends of two cables marked, "Don't disconnect: name service conduit! important!" laughing as he disconnects them, counts to 300, then reconnects them.

We must find, and kill, this gnome.

Thank you for listening.

Tom Limoncelli, with express permission

Part of the human condition is that we make an emotional investment in our hardware. We allow a caliber, cartridge, or specific firearm to define us rather than the other way around. It is understandable, as many of us are happy to say we are a "Bud-man," a "Harley-man," a "Swaro kind of guy," or a variety of other tenuous ways of describing nothing in particular. Though we talk of "inherent accuracy" (a dubious concept, indeed), few would attempt defining it, only parroting that it exists.

We take the same path in using unsophisticated terms to describe sophisticated events. "Knock-down" is one, a physically impossible concept that is never the less widely used. The same strained, tortured approach is used to define "kinetic energy" and "energy transfer." Autopsies are not fun reads; nor are obituaries. We will search long and hard to find a medical report that lists "kinetic energy" as the cause of death.

Surely, after all these years, there must be one recorded instance where a human being lost his life to a sudden gust of kinetic energy? Yet, medical journals are generally void of energy and velocity as causes of death. Perhaps it is because neither ever is. Those waiting for the Surgeon General to alert us to avoid kinetic energy exposure are in for a very long wait, indeed.

The Gut-Wrenching Nightmare of Caliber Worship
by Randy Wakeman

This quarter's physics lab is my favorite, covering topics in classical electrodynamics. Here's a characteristic curve for the charge/discharge of a capacitor:

Taken a few minutes ago, on Castro Street in downtown Mountain View, California:

The person in the shot - whom I don't know - ran up to the vehicle when I was composing this shot, and jumped into frame without a care. She is of The Billion Monkey Legion of people with digicams caught by other Monkeys with digicams. One Of Us. The vehicle in the shot is a T-Rex 3-wheel superbike.

Two nights ago, in physics lab, we replicated a version of the famous "e over m" experiment of J.J. Thompson, to experimentally determine the ratio of the charge of an electron to its mass, using a Helmholtz coil apparatus:

I took this grainy shot in relative dark with my Treo 650 cellphone, since the flash on my Sony would have been disruptive. This is a transfixing sight: a beam of electrons fluorescing in a rarified Helium tube, produced by a thermionic emission apparatus, made circular by a nearly uniform B-field.

I am fortunate to have a lab partner - an earnest young Japanese guy - who doesn't mind that we deliberately stick around to the bitter end doing these experiments, while many of our classmates try to finish early and leave. These experiments are things of grace and beauty, and should be savored and appreciated. Oh, and it helps that we generally get very good agreement with theory in our experiments by doing so: we were within 3.12% of the theoretical electron charge to mass ratio. On nights like this, I walk home from lab feeling more content than I can describe.

K. Eric Drexler informs me that his book "Engines of Creation: The Coming Era of Nanotechnology" has a new home on his website (migrated from its previous hosting at the Foresight Institute).

Check out the attribution on the entry page... I did the work 10 years ago, but I deeply appreciate the continuing credit.

There is no such thing as a nature/nurture debate. It’s something that caught on in the media because it rhymes. You can’t have one without the other. A gene can only work in an environment that triggers it to turn on. An environment can only express its influence through an animal by turning genes on and off. You can’t impose a culture on a rock. You can only impose culture on an animal designed by genes to learn from culture.

Joe Quirk

William Faulkner, in his acceptance speech for the Nobel Prize for Literature, called upon writers of the future to not write merely "for the glands." Of course, at that moment, Faulkner was being rewarded for being the best writer for the glands this country has ever known. Incest, serial killing, insanity, race war, castration, burial of the dead, biblical flood, hunting bear, rape with a corn cob - Faulkner did it all. The guy played our genome like a xylophone. Faulkner, in a suddenly noble moment, called upon writers... to transcend the endocrinological. He didn't set the best example.

Joe Quirk
Sperm Are from Men, Eggs Are from Women, p118

All of the liability problems of general aviation manufacturers were brought on by their own lawyers. They maintained that they couldn't afford to fight these cases, when in truth they couldn't afford not to. Ford fought their Pinto case to the Supreme Court and had a $125 million judgment against them thrown out of court. Nobody sues Ford capriciously anymore.

Scott Crossfield, aviation legend, who died yesterday at the age of 84 while piloting his Cessna 210
Courtesy of AVweb

Now that I've wrapped up what turned out to be a surprisingly subtle and difficult volunteer Japanese translation job (which I'm very happy to have done, I should note), I'm going to blog a bit more for fun. Combing my bookshelves, I pulled another several titles with interesting cover copy and art. Here's one: "Strike From Space: A Megadeath Mystery" by Phyllis Schlafly and Chester Ward, 1965, Pere Marquette Press:

Interesting author blurb from the back cover, above: "Phyllis Schlafly... was a ballistics gunner and technician at the largest ammunition plant in the world." This is particularly interesting, since the WikiPedia entry for her doesn't mention this, only her academic bona fides (I'll be correcting this omission later, wearing my WikiPedia Contributor hat.) Now, "the largest ammunition plant in the world" was, at the time of publication of this book - and still remains - Lake City Army Ammunition Plant (LCAAP) in Independence, Missouri... did she actually work there?

In preparing yesterday's "Little Red Book" post, I discovered that my US $99 Canon all-in-one scanner/printer/copier is an excellent proxy for a macro lens on an expensive camera (I have an Olympus E-1 but don't yet have that lens.) Here's another old school example from the many I have in my personal book collection, this one from 1956, "New Worlds of Modern Science":

I love this type of thing.

Frank Bieser writes:
> Perry E. Metzger wrote:
>> Without enough people working on the problem, we won't finish in
>> time. Right now, I'd say smart people are the biggest missing resource.
>
> And why might that be? Where did all the smart people go?

They didn't "go" anywhere. They've never been in the field.

How many smart people were working on orbital rocketry in 1920? A half
dozen, perhaps. Lots of people claimed the whole idea was bunk, too,
including the New York Times. Later on, lots of people joined up.

Today, not many people are working on Drexler's vision. That doesn't
mean it isn't worthwhile -- it just means that the field is young and
lots of people are still skeptical about it. I suspect that the number
of people actively working on it numbers less than 20, and possibly
less than 10.

There is enough work for thousands of people to push on this for many
years to come. At some point, we'll get IA or AI and the pace will be
able to pick up, but that point still seems pretty distant. Meanwhile,
direct molecular manipulation and molecular manufacturing pose a very
hard set of problems -- possibly the hardest engineering problem yet
faced by mankind -- and we need more minds to make progress. On the
flip side, MNT will also bring the biggest revolution in civilization
yet experienced, dwarfing everything that came before, so I see it as
a worthwhile problem to attack.

Still, we lack enough smart people working on it. As any good VC can
tell you, money is something of a commodity, but smart people are
rare. More smart people are needed.

Perry

I'm going through a year's worth of iPhoto archives and found this, taken in organic chemistry lab by my friend Jenny... me in Maximum Nerd mode:

I had an offer to get some free stick time in a friend's friend's luxury (pressurized cabin, an aisle between the seats, etc.) airplane for a trip he and the other guy were making to CES in Las Vegas, but I'm getting ready for school on Monday, so I declined. I'm taking in some of the show's highlights by way of reportage, and just saw this on one of the gadget/gimmick blogs:

"Radar Scope sees through walls"

Fascinating, and a bit terrifying at the same time. It's a handheld device for detecting people on the other side of a (presumably radiolucent) wall. The display device looks milspec/ruggedized, and the printed matter pitches to military application, but I'm quite sure they're being pitched to police departments too. I wonder, what are the relevant U.S. laws with respect to using this device in warrantless searches? I believe SCOTUS has already ruled that "standoff" search techniques are not covered under the 4th Amendment.

Four weeks ago, I had the pleasure of attending a Halloween party in Manhattan. I wasn't prepared with a costume, unless you count my normal get-up below as, um, "Visiting Silicon Valley Guy." On the left is Perry Metzger who is, ahem, a eusocialist insect:

Two days ago, I bought a copy of "Mathematica 5.2 For Students" from the campus bookstore for $150 after tax. This is the same software that sells for around $2000 after tax to non-students. It's a fantastic package, and I'm happy I bought it. However, yesterday, after having already installed a copy on my home's dual G5, I tried to install a copy on my PowerBook. Wolfram's licencing scheme doesn't allow that: I could either buy their $100/year "Premium Support" contract, which would allow me to run other copies on other nodes, or buy another copy. If I'd paid full boat for the original copy, that might have made sense, but at the student discount, it made more sense to actually buy another package entirely. FYI for science and engineering students.

A week ago, I caught a short segment of Fox News' business anchor Neil Cavuto interviewing Eric Anderson, president and CEO of Space Adventures, who was promoting his company's Deep Space DSE-Alpha program, a privately-funded Soyuz-based circumlunar expedition. I noticed, not for the first time, a surprising skepticism about private space travel from the normally highly pro-free enterprise Cavuto, who seems to be nurturing a serious blind spot on the matter, a dangerous case of NASA-romanticization.

Me, I'm sanguine about the DSE-Alpha, and hope to see Anderson's enterprise succeed. In the meantime, someone needs to buy Neil Cavuto a copy of Victor Koman's "Kings of the High Frontier." Abolish NASA, get the government out of the space business, and let people like Anderson do their thing without subsidy or interference.

An interesting blog article about the use of dendrimers in targetted drug delivery systems, sent me by Tom Burroughes in London.

University of Michigan scientists have created the nanotechnology equivalent of a Trojan horse to smuggle a powerful chemotherapeutic drug inside tumor cells – increasing the drug's cancer-killing activity and reducing its toxic side effects.

Previous studies in cell cultures have suggested that attaching anticancer drugs to nanoparticles for targeted delivery to tumor cells could increase the therapeutic response. Now, U-M scientists have shown that this nanotechnology-based treatment is effective in living animals.

This type of news carries a special type of urgency for me, as I've recently been informed that my good friend Chris Tame, in London, has been diagnosed with epithelioid angiosarcoma of the bones (spine & hip so far.) His oncologists are working hard to find the primary source of the cancer. In the meantime, any new developments in the effectiveness of chemotherapy with short & medium term time horizons are of great personal interest to me and my friends.

...the digital (PDF) version I'm reading now, but Charlie Stross tells his readers not to do so. I will, however, be buying several copies from Amazon as gifts to friends. Damn it's good!

I needed to my online investment bank's customer service center, which was given on its website in the form of "800-555-CALL", one of those supposedly helpful mnemonic phone numbers with letters corresponding to digits. Well, my Treo 650 smartphone has a QWERTY keyboard with a digit keypad superimposed on the left side of the board, no 3-letter-to-single-digit DTMF tonepad overlay. I had to dig an old phone out of my "sell on eBay" box to puzzle out my bank's phone number, since they didn't provide a digits-only version of that number.

Year by year, a third of the [American] labor pool emerges with a college degree. Most of these degrees are in the humanities and social sciences.

Meanwhile, China produces over 450,000 college graduates a year in science and engineering – as many scientists and engineers as the United States has, total. Then, next year, China will do it again.

Gary North

The first principle is that you must not fool yourself -- and you are the easiest person to fool. So you have to be very careful about that. After you've not fooled yourself, it's easy not to fool other scientists. You just have to be honest in a conventional way after that.

I would like to add something that's not essential to the science, but something I kind of believe, which is that you should not fool the layman when you're talking as a scientist. I am not trying to tell you what to do about cheating on your wife, or fooling your girlfriend, or something like that, when you're not trying to be a scientist, but just trying to be an ordinary human being. We'll leave those problems up to you and your rabbi. I'm talking about a specific, extra type of integrity that is not lying, but bending over backwards to show how you're maybe wrong, that you ought to have when acting as a scientist. And this is our responsibility as scientists, certainly to other scientists, and I think to laymen.

For example, I was a little surprised when I was talking to a friend who was going to go on the radio. He does work on cosmology and astronomy, and he wondered how he would explain what the applications of his work were. "Well", I said, "there aren't any". He said, "Yes, but then we won't get support for more research of this kind". I think that's kind of dishonest. If you're representing yourself as a scientist, then you should explain to the layman what you're doing -- and if they don't support you under those circumstances, then that's their decision.

One example of the principle is this: If you've made up your mind to test a theory, or you want to explain some idea, you should always decide to publish it whichever way it comes out. If we only publish results of a certain kind, we can make the argument look good. We must publish BOTH kinds of results.

Richard Feynman
"Cargo Cult Science"

Thanks to Perry for bringing this to my attention: "Rapid Gene Synthesizer Will Enable Custom Microbe Construction."

I am really, really enjoying my biology class, a concentrated term of cell & molecular biology. Students in this program spend about four times as much time in lab, learning industrially useful techniques, as do students in comparable programs in the University of California system. In the last three weeks, I've had hands-on time doing protein electrophoresis, conjugation (bacterial DNA transfer), and DNA electrophoresis. Here's an image of our team's first DNA gel:

The DNA is from purified coliphage Lambda virus, 48,502 Kb (kilobases) in length. Lane 1 is pure, uncut DNA. Lane 2 is DNA restricted (cut) by Eco RI enzyme, Lane 3 restricted by Hind III, and Lane 4 by both (the restriction sites are different, resulting in more, smaller DNA fragments.)

Lanes 5 through 7 are subsamples taken from 2 through 4, subjected slowly and thoroughly to the action of the enzyme DNA ligase, resulting in outrageously long, randomly recombinant strands.

The gel is purified agarose treated with ethidium bromide. The image above is a high-contrast Polaroid of the gel UV-transilluminated to fluoresce in the visible spectrum (reddish orange, here shown in black and white).

This stuff is outrageously fun.

Monica, you can take my blog off the "Missing in Action" list on your blogroll: I'm out of school for three weeks, concentrating on work but taking a few minutes a day to blog.

Speaking of school, the last few weeks of organic chemistry were split between the standard track material (in this case reactions of alkynes) and a series of lectures on NMR (nuclear magnetic resonance) in depth. When I return to school, our department's new NMR machines will be in place, so this preparation is essential to actually using these machines productively. I'm really looking forward to adding NMR to my toolkit.

This just in from my distant friend James Bennett: his announcement today of the website supporting his new book "The Anglosphere Challenge." This seems like a very enticing book, and I plan to read it during winter school break.

A college student challenged a senior citizen, saying it was impossible for their generation to understand his. "You grew up in a different world," the student said. "Today we have television, jet planes, space travel, nuclear energy, computers..." Taking advantage of a pause in the student's litany, the geezer said, "You're right. We didn't have those things when we were young. So we invented them."

Unattributed, sent to me by email from Terry Egan

Most of us are familiar with the events marking the Ansari X Prize winning flights of SpaceDev's SpaceShip One recently. Far fewer, however, know of the story of the American Rocket Company (AMROC), the pioneering company whose intellectual property lives on in that prize-winning ship: the revolutionary hybrid rocket engine that sent it to the edge of space, twice. Read on...

In science, 'fact' can only mean 'confirmed to such a degree that it would be perverse to withhold provisional assent.' I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

Stephen Jay Gould

Here's a term I'd not expected to hear: "cosmetic neurology" (via John Venlet).

Computer, compute to the last digit the value of pi.

Spock
TOS, Wolf in the Fold

We finally started into dissections in biology lab tonight. My own specimen was this rather stout, well-endowed female Ascaris lumbricoides, an intestinal parasite of humans:

I'd suspected that although our college's brand-new science center was state of the art in facilities, our gear would be knackered, so I brought my own gear (probes, pins, scalpels, various forceps, etc.) just in case. I was correct in my assessment: all the school-supplied gear was thrashed. One other guy in the lab, an Air Force PJ (USAF Pararescue) who's med-school bound, brought his own gear too; it was interesting to compare kits.

Since this specimen was pseudocoelomate in its body plan, there was no mesentary tissue to complicate the incision process. I was able to do really well with a #15T surgical blade: small enough, with a fine tip for starting an incision, but a sufficiently curved blade belly to continue incisions without nicking the viscera.

One gets the impression after laying this open and spreading its innards with a blunt probe that it is all uterus, wrapped in oviduct... two strands of Top Ramen cloaked in angel hair pasta. This thing is even more dedicated to reproduction than it is to feeding. Brrrrrr.

I seemed to have been the only person this morning other than my instructor to have paid attention to the warning on the bottle of crotyl chloride, "Danger: lacrymating agent!"

It was also amazing to see the number of people dispensing silver nitrate without gloves... low toxicity risk, but high chance of Rorschach tattoos on one's hands (hint: silver nitrate is photosensitive.)

A scientist can discover a new star, but he cannot make one. He would have to ask an engineer to do that.

Gordon L. Glegg
American Engineer, 1969.

A discovery is like falling in love and reaching the top of a mountain after a hard climb all in one, an ecstasy induced not by drugs but by the revelation of a face of nature that no one has seen before.

Max F. Perutz

The other way makers learn is from examples. For a painter, a museum is a reference library of techniques. For hundreds of years it has been part of the traditional education of painters to copy the works of the great masters, because copying forces you to look closely at the way a painting is made.

Writers do this too. Benjamin Franklin learned to write by summarizing the points in the essays of Addison and Steele and then trying to reproduce them. Raymond Chandler did the same thing with detective stories.

Hackers, likewise, can learn to program by looking at good programs-- not just at what they do, but the source code too. One of the less publicized benefits of the open-source movement is that it has made it easier to learn to program. When I learned to program, we had to rely mostly on examples in books. The one big chunk of code available then was Unix, but even this was not open source. Most of the people who read the source read it in illicit photocopies of John Lions' book, which though written in 1977 was not allowed to be published until 1996.

Paul Graham, in "Hackers and Painters"