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lecture on the incredible rate of progress in biotechnology [32:52 minutes]

Highly recommended.

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international space station [iss], a truly international mission - the space robots

Canadarm2, Mobile Base System, two-armed robot Dextre, rail track. Image: CSAThis news item has been ‘promoted’ to its own page - space robots - international space station, part of a developing section on space, science and technology.

Canadarm2, the two-armed robot known as Dextre, the Mobile Base System and the rail track. Image: CSA


the web address for the article above is

human chimera

“One human chimera came to light when a 52-year-old woman demanded an explanation from doctors after tests showed that two of her three grown-up sons were biologically unrelated to her.

“Although the woman, "Jane", conceived them naturally with her husband, tests to see if she could donate a kidney suggested that somehow she had given birth to somebody else's children.”

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“In medicine, a person composed of two genetically distinct types of cells. Human chimeras were first discovered with the advent of blood typing when it was found that some people had more than one blood type. Most of them proved to be "blood chimeras" -- non-identical twins who shared a blood supply in the uterus. Those who were not twins are thought to have blood cells from a twin that died early in gestation. Twin embryos often share a blood supply in the placenta, allowing blood stem cells to pass from one and settle in the bone marrow of the other. About 8% of non-identical twin pairs are chimeras.” [Quoted from medterms.com]

A chimera. Credit: answersingenesis.org
Credit: answersingenesis.org

end note

In Greek mythology, the Chimera is fire-breathing female monster with a lion’s head, a goat’s body and a serpent’s tail. Its parents were Typhon and Echidna. In due course, the Chimera was killed by Bellerophon, a Corinthian hero.

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This news item has been ‘promoted’ to its own page - water cube - beijing2008: national aquatic center, part of a developing section on wondrous architecture.

The Water Cube at night, giving an idea of the building's scale. Credit: beijing2008.cn
The Water Cube at night, giving an idea of the building’s scale. Credit: beijing2008.cn

the web address for the article above is

programming biological reactions, like programming computers

We can program [tell] computers to do huge calculations, we can make word processors follow series of instructions, now researchers are starting to make biological processes act according to instructions. In this case, some DNA tells other DNA to ‘walk’ along a DNA track.

“[...] long-term vision of developing a "compiler for biomolecular function" that takes as input a modular conceptual device design and provides as output a list of biomolecules that interact to implement the desired function.” [Quoted from The Pierce Lab]

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“Ultimately, the development of an efficient catalytic DNA fuel delivery mechanism should enable the rational design of a completely artificial DNA walker that locomotes autonomously, allowing detailed programming of a motor protein mimic.” [Quoted from The Pierce Lab]


DNA 'walker' moving down another strip of DNA. Image: The Pierce Lab.

Right: “The diagrams depict (a) unbound walker, (b) walker attached to branch 1, (c) walker attached to branches 1 and 2, and (d) walker released from branch 1 to yield duplex waste.”

For those who are interested to a greater degree, here follows the detailed description of this walking process (note that the description is in science-speak).

“The system has four components (Table 1, which lists the DNA sequences used): a walker (W), a track (T), attachment fuel strands (A), and detachment fuel strands (D).

“The walker consists of two partially complementary oligonucleotides, with a 20-bp helix joining two single-stranded legs (each 23 bases).

“The track, constructed of six oligonucleotides, has four protruding single-stranded branches (each 20 bases) separated by 15-bp scaffold helices.

“Neighboring branches run in opposite directions, so spacing of 1.5 helical turns places all branches on the same side of the track approximately 5 nm apart [see diagram above].

“[As seen in the diagram], the walker strides along the track under the external control of A [attachment] and D [detachment] strands. An A strand specifically anchors the walker to a branch by forming helices with the corresponding leg (18-bp) and branch (17-bp).

“Single-stranded hinges adjacent to either end of these helices (underlined in Table 1) provide flexibility for adopting different conformations depending on the fuel species that are present. When both legs are bound to the track [ c) in the diagram], the trailing leg is released using a D strand that nucleates with the perfectly complementary A strand at a 10-base overhang and then undergoes a strand displacement reaction to produce duplex waste and free the walker leg for the next step [ d) in the diagram].”

end notes

  1. compiler
    A compiler takes a program written in a higher level language and turns it into a series of machine code instructions.

the web address for the article above is

on genetic addiction to ‘drugs’ - pathways

A common form of modern analysis is to take large numbers of papers, whittle them down to the most promising - a typical area being where there is replication of studies - and analyse them statistically to seek correlations of results. Below are extracts from such a study that started with more than 1000 papers.

Full original article.

Abstract from physorg.com.

“The team, led by Liping Wei, surveyed scientific literature published in the past 30 years and collected 2,343 items of evidence linking genes and chromosome regions to addiction based on single-gene strategies, microarray, proteomics, or genetic studies. They made this gene atlas freely available in the first online molecular database for addiction, named KARG, with extensive annotations and friendly web interface.”

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From report by economist.com

“She found 18 [genes] that were involved in addiction to at least one type of drug. Five, however, were common to all four types, and these five pathways therefore look as though they are at the core of the process of addiction. Three of the five were already under suspicion. Dr Wei's result provided strong statistical evidence to back up what had just been hunches. Two other pathways, however, had not previously been considered as being involved in addiction.

“The existence of these five central pathways helps explain a lot about addiction. First, it gives weight to the belief that some people are more susceptible to all sorts of addiction than others are. That contrasts with the thought that addictions are substance-by-substance phenomena, though the two ideas are not mutually exclusive since changes in the 13 substance-specific pathways clearly also result in addiction.

“Second, the particular pathways involved help to explain why addiction is so hard to reverse. Several of them take part in strengthening the connections between nerve cells, which is the underlying basis of learning. Unlearning something by breaking these connections is hard.

“Third, Dr Wei was able to link the five central pathways together into a network, and show that this network has four positive-feedback loops in it. Work on other species in other contexts suggests that the mixture of loops she found was one that often results in rapid and irreversible biological processes - which is exactly what is seen in addiction.”

related material
Drugs, smoking and addiction

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$30 million of your payments for windows goes towards $400 million asteroid telescope

Cerro Tololo Interamerican Observatory, Chile. Credit: NOAO/AURA/NSF
Cerro Tololo Interamerican Observatory, Chile. Credit: NOAO/AURA/NSF

“Bill Gates and ex-Microsoft executive Charles Simonyi have donated a combined $30 million to the Large Synoptic Survey Telescope, which will feature the largest digital camera ever constructed. Scientists say it will provide a "color movie" of the universe.”

“The telescope is to be built on 9,000-foot Cerro Pachon in northern Chile. It will take an image every 15 seconds nightly, and its camera - the world’s largest and most powerful digital device - will read out the image in 2 seconds.

“There are lots of things that happen every night in the sky, and no one has been able to track them and detect them," Sweeney said.

“With the telescope operating, he said, scientists will be able to quickly find Earth-threatening asteroids and supernovae, and will be able to map out 100 billion galaxies.”

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Large Synoptic Survey Telescope on Cerro Pachon, northern Chile [Artist’s impression].Image: Michael Mullen Design, LSST Corporation
Large Synoptic Survey Telescope on Cerro Pachon, northern Chile [Artist’s impression].
Image: Michael Mullen Design, LSST Corporation

“Google, the world's largest Internet search engine, has joined a group of nineteen universities, national labs and private foundations that is building the Large Synoptic Survey Telescope (LSST).” [Quoted from wired.com]

the web address for the article above is

cuckoo butterflies and a battle of smells

Maculinea alcon butterfly. Credit: David Nash.Come to Denmark. There, a kind of large blue butterfly ensure that their caterpillars smell like ant larvae, so the ants will taken the caterpillars home and feed them. When the ants catch on, change the smell of their larvae and start ignoring the caterpillars, the butterflies go and parasite on a different, closy related, ant species.

[David Nash:]
“The caterpillars first start developing on a food plant, but after they reach a certain stage they leave the food plant and wait on the ground to be discovered by these ants, and they mimic the surface chemicals that the ants have on their own brood. So again, they’re producing a signal which says, I’m an ant brood. And we’ve been able to show that the closer that mimicry is, the faster they are picked up by ants and taken back into the ant nest and put amongst the brood. And once they’re there amongst the ant’s own brood, they become highly virulent parasites; they eat some of the brood, and they will also get fed by the worker ants, and they’ll get fed in preference than the ant’s own brood.”

Maculinea alcon caterpillar with a Myrmica ant. Image: David Nash “ [...] we think in some areas the butterfly can actually suppress that ant colony so much that it becomes very rare and is no longer worth exploiting for the butterfly, and then it tends to use the other ant species as a refuge while that other species recovers. One way you can put it is, if we have one species where the ant is exploited at a relatively constant rate, and we have another species which, when it’s common, is exploited even more than you would expect, but when it’s rare it’s hardly exploited at all.”

Where neighbouring ant colonies are closely related genetically, David Nash and his colleagues found the ants to be changing their surface chemistry, and so the way they and their larvae smell, in response to the parasitism by the butterflies, and in some cases, they seem to be avoiding parasitism that way.

The above is excerpts from the transcript of a Science and AAAS [American Association for the Advancement of Science] podcast interview [MP3 format]. The interview is the first item after the intial fluff and self-advertising.

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risk analysis - climate change

  • The serious content of this seven-part video lecture series is an introduction to risk management (there are 82 videos listed, most of which are just under 10 minutes). The series, given by Greg Craven [also known as wonderingmind42], is applied to AGW, but that is not the prime value of the talks.

    Part 1 part 2 part 3 part 4 part 5 part 6 part 7

  • Going even deeper - this is a reasonable entry point for those comfortable with the concepts concerning risk management.

    Videos: part 1 part 2 part 3 (with explosions!)

  • And here is a short version for those who don’t want a headache, and who also have faith! This video has been watched several million times and is available in many copies. It has only been on the web less than a year single-part version.

There is much more from this person - here is a 9+ -minute video ‘index’.

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methology groundwork

the web addresses for the article above are
risk analysis - climate change: http://www.abelard.org/news/science0801.php#risk_climate_030108
methology groundwork: http://www.abelard.org/news/science0801.php#scientific_method_070108

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