Category Archives: Science

Radical Life Extension

The near-term inevitability of radical life extension and expansion by Ray Kurzweil:

It took 15 years to sequence HIV and from that perspective the genome project seemed impossible in 1990. But the amount of genetic data we were able to sequence doubled every year while the cost came down by half each year.
…
If we think linearly, then the idea of turning off all disease and aging processes appears far off into the future just as the genome project did in 1990. On the other hand, if we factor in the doubling of the power of these technologies each year, the prospect of radical life extension is only a couple of decades away.

KurzweilAI.net includes many articles on Kurzweil’s ideas, by him, and others. Major topic areas include: Nanotechnology, Will Machines Become Conscious? and Singularity. The ideas can seem crazy but as Kurzweil discusses the ability to predict with the tremendous increase in the power of technology. I still think many things like radical life extension is unlikely so soon but the ideas presented are interesting and worth thinking about.

Inner Life of a Cell: Full Version

This is an extremely cool 8 minute movie on the inner workings of a Cell. The earlier version we posted about back in September of last year has been one of our most popular posts – see our most popular posts. They have added the scientific explanation that I mentioned I would love to see in the last post.

update: Unfortunately Harvard seems to want to prevent people from seeing this educational webcast. Why they don’t want to promote science education is beyond me. I guess they have better uses for their $35 billion endowment than promoting science. I sure wish they would hurry up and realize this isn’t the 18th century. They say their mission is “The advancement of all good literature, arts, and sciences; the advancement and education of youth in all manner of good literature, arts, and sciences; and all other necessary provisions that may conduce to the education of the … youth of this country…” (Jun 2008). You don’t have to just educate a few privileged soles in ivy covered buildings. You can do that any provide great education material for others around the globe.

Animation created for Harvard’s Molecular and Cellular Biology program:

Harvard University selected XVIVO, LLC, a Connecticut based scientific animation company, to customize and develop an animation that would propel Harvard’s Molecular and Cellular Biology program to the next level of undergraduate education. XVIVO’s recently completed animation, titled “The Inner Life of the Cell”, has already won awards. The eight minute animation transports Harvard Biology students into a three-dimensional journey through the microscopic world of a cell.

DNA Repair Army

Analysis Reveals Extent of DNA Repair Army

Elledge’s group studied human cells in culture and mapped their response to ionizing radiation and ultraviolet light. Specifically, the group looked to see which proteins in the cell were chemically altered by the enzymes ATM and ATR, finding 900 sites on 700 proteins that changed in response to DNA damage. The discovery that so many proteins are involved in the process, Elledge said, was a big surprise.

Also see: Cell Cycle Regulation and Mechanisms of DNA Repair:

Despite the abuse our DNA endures, our individual genomes usually stay basically intact because DNA has a remarkable capacity for repair. Our cells have built-in, highly efficient machinery that finds and fixes “genetic typos.”
…
Researchers have learned much about the complex genetic machinery that cells deploy to fix broken, cut, mutated, and misplaced genetic materials. Out of that evolving understanding has emerged a deeper awareness that DNA is truly dynamic and that responses to genetic damage are nearly as fundamental to life—and health—as is the genetic code itself.

Communicating Science to the Public

Webcast above: Speaking Science 2.0 by Matthew Nisbet, School of Communication, American University, and Chris Mooney, Washington Correspondent, Seed Magazine, speak at the AIBS annual meeting, May 2007, in Washington DC. They discuss how to improve the transfer of science knowledge to the public (an important topic and one I am interested in). More on The American Institute of Biological Sciences conference: Evolutionary Biology and Human Health.

via: Framing Science

Open Access and PLoS

In An Open Mouse, Carl Zimmer discusses the conflict between closed journals and those that support open access.

And what do I now hear from PLOS? Do I hear the grinding of lawyerly knives? No. I hear the blissful silence of Open Access, a slowly-spreading trend in the journal world. PLOS makes it very clear on their web site that “everything we publish is freely available online throughout the world, for you to read, download, copy, distribute, and use (with attribution) any way you wish.” No muss, no fuss. If I want to blog about this paper right now, I can grab a relevant image right now from it.

His post mentions the recent bad publicity Wiley received. It seems to me the Journals still don’t understand that their copyright of research results paid for by public funds are not going to continue. And that open access science is clearly the way of the future that their continued failure to deal with is increasing the odds monthly that they will find themselves on the outside of those practicing science in the 21st Century.

PLoS on the other hand recently hired Bora Zivkovic as PLoS ONE Online Community Manager. He will be great and continue to build PLoS into an organization supporting free and open science. I loved PLoS proactive action recounted by Bora, he posted that he was interested in the job:

Next morning, I woke up to a comment by the Managing Editor of PLoS ONE asking if my blog-post should be considered as a formal job application. My comment in response was a Yes.

Evolution In Action

the way they watched the process was to sequence the whole genome of each bacterial isolate. What they found were a total of 35 mutations, which developed sequentially as the treatment continued (and the levels of resistance rose). Here’s natural selection, operating in real time, under the strongest magnifying glass available. And it’s in the service of a potentially serious problem, since resistant bacteria are no joke. (Reading between the lines of the PNAS abstract, for example, it appears that the patient involved in this study may well not have survived).

The technology involved here is worth thinking about. Even now, this was a rather costly experiment as these things go, and it’s worth a paper in a good journal. But a few years ago, needless to say, it would have been a borderline-insane idea, and a few years before that it would have been flatly impossible. A few years from now it’ll be routine, and a few years after that it probably won’t be done at all, having been superseded by something more elegant that no one’s come up with yet. But for now, we’re entering the age where wildly sequence-intensive experiments, many of which no one even bothered to think about before, will start to run.

Very interesting. He is exactly right that the technology advances continuing at an amazing pace allow for experiments we (at least I) can’t even imagine today to become common in just a few years. And the insights from those experiments will allow us to think of new experiments… Wonderful.

Finding Open Scientific Papers

Sandra Porter has posted a series of posts on finding scientific papers for free: A day in the life of an English physician – What’s the best way to find free scientific publications? – My new favorite method – one more experiment

via: Finding scientific papers for free

Female Sharks Can Reproduce Alone

Female Sharks Can Reproduce Alone, Researchers Find

A team of American and Irish researchers have discovered that some female sharks can reproduce without having sex, the first time that scientists have found the unusual capacity in such an ancient vertebrate species. The[y] report that sharks can reproduce asexually through the process known as parthenogenesis
…
Though the three females had been caught before they reached sexual maturity and held in captivity for more than three years, researchers initially thought one had stored sperm from a male shark before fertilizing an egg. But the team — which included scientists at Nova Southeastern University in Florida, Queen’s University Belfast and the zoo — determined that the baby shark’s genetic makeup perfectly matched one of the females in the tank, with no sign of a male parent.

Mahmood Shivji — Nova Southeastern’s Guy Harvey Research Institute director and one of the paper’s authors — said that he and his colleagues determined that a byproduct formed when sharks produce eggs, known as a sister polar body, had fused with an unfertilized egg to produce the baby shark, whose DNA had only half as much genetic variability as the mother.

Chemistry of Common Items

The American Chemistry Society offers interesting articles on the chemistry of everyday products including: amber, henna, catnip and honey:

To make this delicious treat, foraging bees start out by guzzling nectar, a dilute solution of sugars in flowers. Then, they mix the nectar with enzymes in their stomachlike honey sacs. Back at the hive, the foragers pass the digested material to house bees who reduce the moisture content of the mixture by ingesting and regurgitating it. They then deposit concentrated drops into honeycomb cells. Over the next few days, bees fan the fluid with their wings to further concentrate it, and finally, they cap the cells with wax. At the same time, enzyme-mediated changes produce a range of sugars and acids in the honey.

Bee enzymes also show up in the finished product. Invertase is the most critical. It splits the sucrose in the nectar into fructose and glucose and also produces some erlose. Another enzyme, glucose oxidase, converts glucose to gluconolactone, which is then hydrolyzed to give gluconic acid, the principal acid in honey. Formic, acetic, butyric, and lactic acids are also found in honey, which explains why its pH typically measures 3.8-4.0 and bacteria have a hard time growing in it.

Engineering, Math and Physics Applets

Java applets illustrating concepts in math, physics and engineering including: Coupled Oscillations, Digital Filters, 3-D Magnetostatic Fields and Ordinary Differential Equations.