Tag Archives: Science

Synthetic Biologists Design a Gene that Forces Cancer Cells to Commit Suicide

Killing a cancer cell from the inside out

To create their tumor-killing program, the researchers designed a logic circuit — a system that makes a decision based on multiple inputs. In this case, the circuit is made of genes that detect molecules specific to a type of cervical cancer cell. If the right molecules are present, the genes initiate production of a protein that stimulates apoptosis, or programmed cell death. If not, nothing happens.

Because the genes used to create the circuits can be easily swapped in and out, this approach could also yield new treatments or diagnostics for many other diseases, according to Ron Weiss, an MIT associate professor of biological engineering and one of the leaders of the research team. “This is a general technology for disease-state detection,” he says.
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the researchers created a synthetic gene for a protein, called hBax, that promotes cell death. They designed the gene with two separate safeguards against the killing of healthy, non-HeLa cells: It can be turned off by high levels of microRNAs that are ordinarily low in HeLa, and can also be deactivated by low levels of microRNAs that are normally plentiful in HeLa. A single discrepancy from the target microRNA profile is enough to shut off production of the cell-death protein.

If all microRNA levels match up with the HeLa profile, the protein is produced and the cell dies. In any other cell, the protein never gets made, and the synthetic genes eventually break down.

More very cool research. It is exciting to see how much can be done when we invest in science and engineering research. Of course the path from initial research to implemented solutions is long and complex and often fails to deliver on the initial hopes. But some remarkable breakthroughs achieve spectacular results that we benefit from every day.

Is Dark Matter an Illusion?

Open access letter asks – Is dark matter an illusion created by the gravitational polarization of the quantum vaccum? by Dragan Slavkov Hajdukovic, CERN

Assuming that a particle and its antiparticle have the gravitational charge of the opposite sign, the physical vacuum may be considered as a fluid of virtual gravitational dipoles. Following this hypothesis, we present the first indications that dark matter may not exist and that the phenomena for which it was invoked might be explained by the gravitational polarization of the quantum vacuum by the known baryonic matter.

Let us start with a major unresolved problem. The measured galaxy rotation curves remain roughly constant at large radii. Faster than expected orbits, require a larger central force, which, in the framework of our theory of gravity, cannot be explained by the existing baryonic matter. The analogous problem persists also at the scale of clusters of galaxies.

The favoured solution is to assume that our current theory of gravity is correct, but every galaxy resides in a halo of dark matter made of unknown non-baryonic particles (for a brief review on dark matter see for instance: Einasto, 2010). A full list of the proposed dark matter particles would be longer than this letter; let us mention only weekly interacting massive particles and axions. In spite of the significant efforts dark particles have never been detected…

The scientific inquiry process continues to be used to try and explain the evidence we gather. Unsettled areas of science show how difficult the discovery process is. Once we have settled on theories it is so easy to explain why basic truths of evolution, geology, chemistry… result in what the evidence shows. But getting to the scientific consensus is a challenging process.

Dark Matter Is an Illusion, New Antigravity Theory Says

Physicist David Evans called the new study a “very interesting theoretical exercise,” but he said he isn’t ready to abandon dark matter just yet. “The evidence for dark matter is now very compelling,” said Evans, of the University of Birmingham, who leads the U.K. team for the ALICE detector at CERN’s Large Hadron Collider.

For example, in 2006 astronomers unveiled a photo of two colliding galaxies known as the Bullet cluster that purportedly showed the separation of matter from dark matter. A similar effect was observed in the Pandora cluster earlier this summer, said Evans, who was not involved in the study.

Hajdukovic said he is currently expanding his theory to account for these observations. His preliminary calculations, he said, suggest that “what is observed in the Bullet cluster and more recently at the Pandora cluster may be understood in the framework of the gravitational polarization of the quantum vacuum.”

CERN physicist Michael Doser agreed that Hajdukovic’s ideas are “unorthodox” but did not immediately dismiss the new theory…
“In a few years,” Doser said, “we should definitely be in a position to confirm or refute [Hajdukovic’s] hypothesis.”

The Politics of Anti-Science

In the 1960’s the USA had an unrealistic view of how much studying and learning about science and engineering could do. Investing is science and engineering is an extremely wise economic (and cultural) endeavor but it isn’t going to solve all the problems that exist. Somehow today we find ourselves with a large number of politically powerful people we take strong anti-science positions. These tactics reduce funding and support for beneficial research and are short sited approaches to public administration. This is an unfortunate turn of events that is damaging the American economy and will have huge damages going forward.

Thankfully other countries have seen how wise investing in science and engineering is and have more than taken up the slack created by the anti-science community. Two favorite tactics of the anti-science leaders is to try and create confusion where there is none and to turn the focus away from serious matters and instead playing silly political games. The silly games will draw donors and voters so if they care about those things more than the country and the future of the country it is a sound tactic. The damage it causes the country however I would hope would limit the use of such tactics however that has not been the case recently.

‘Shrimp On A Treadmill’: The Politics Of ‘Silly’ Studies

Take the case of the “shrimp on a treadmill.” Burnett says the senator’s report linked that work to a half-million-dollar research grant. But that money actually went to a lot of different research that he and his colleagues did on this economically important seafood species.

The treadmills were just a small part of it, a way to measure how shrimp respond to changes in water quality. Burnett says the first treadmill was built by a colleague from scraps and was basically free, and the second was fancier and cost about $1,000. The senator’s report was misleading, says Burnett, “and it suggests that much money was spent on seeing how long a shrimp can run on a treadmill, which was totally out of context.”

John Hart, a Coburn spokesperson, said in an email that “our report never claimed all the money was spent on shrimp on a treadmill. The scientists doth protest too much. Receiving federal funds is a privilege, not a right. If they don’t want their funding scrutinized, don’t ask.”

What the politicians are doing is exactly what this spokesperson suggests – they are withdrawing from the anti-science culture created by some in Washington: they are moving their research to countries that support rather than attack science. That is a very bad thing for the USA. There are a number of very bad economic policies a government can take. Driving scientists and engineers into the arms of other countries is one of the worst.
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New Life Form Found at South African Truck Stop

Man discovers a new life-form at a South African truck stop

An order is one of the big categories of life, a big branch on evolution’s tree. Animal species are named every day, but finding another new order would be equivalent to discovering bats having not previously known they existed. Bats constitute their own order, as do primates, beetles, flies and rodents.
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The Mantophasmatodes look, inescepably, larval (they lack wings, for example, and have no ocelli) and so Picker like others mistook them for immature versions of some known creature, perhaps some weird kind of cricket. When more than three quarters of all species of animals are not yet named, it is hard to know which ones to get excited about finding. Picker went through his collections looking for specimens of Mantophasmatodes. Within weeks, he had found twenty-nine individual Mantophasmatodes. Thirteen living species of Mantophasmatodea have now been named and placed in 10 genera and three different families.

In other words, Zompro has done something more amazing than finding a rare new order of animals. He has discovered a common order of animals that everyone else had missed, a discovery in plain view.

Mantaphasmatodes are not a far away species confined to some remote hunk of rock. They are a whole suite of species, some of which live places as mundane as backyards. They are also a kind of a living extended metaphor for what lurks around us unnoticed all the time.

I was always told as a child that I shouldn’t question so much and just accept what adults have decided. I am sure I was very annoying questioning everything. Especially how amazingly boring they make school. I love learning stuff. In general I did not love school. But questioning that school really should do a better job of making it fun to learn was seen as being a bothersome kid. I should just accept this is how school is and learn. I still think I was right. School is horribly designed to nurture the innate curiosity of people. Rather than seeing the kids that point this out as troublemakers we should see those that perpetuate the current system as troublemakers.

I still remember my sophomore year in high school I was taught by a biology teacher that new very little. They had been a 2nd grade teacher for like 15 years and due to seniority (they didn’t need as many 2nd grade teachers I guess) she bumped the biology teacher from the year before and we were stuck learning from her. In fact, any decently interesting question was more likely to be answered by a student (Peter – who then went to Princeton and then to play for the National Symphony) after the teacher said she didn’t know.

I found biology horrible. And it probably took a decade or more for me to finally notcie how amazingly cool biology. Fantastically cool. The amount of just super interesting biology is so vast that I have huge amounts of great stuff I get to look forward to learning. My teacher made it even worse, but frankly the way it is taught (I would imagine) is pretty bad even if the teacher is good. My high school was populated largely by the kids of Professors and compared to other schools in the USA I was told many times was fantastic (and the data seemed to support that – I believe we have more national merit scholars the year I graduated than all but 1 other public school in the country).

We need to do a much better job of harnessing the native desire to learn people have instead of killing it (which we do far to often). It really is a tragedy. It isn’t noticed because you can get by alright without loving learning. But it reduces the lives people have when they have their love of learning crushed. I didn’t have mine crushed but when I look around at many adults they seem to have done so to a large extent (sometimes it pokes through in a hobby or with their kids). And of course many adults kept a strong love of learning (all those geeks for example – and don’t forget the biologists).

Insightful Problem Solving in an Asian Elephant

Another example of very cool animal behavior. This Asian Elephant, seemed to consider the problem, devise a solution and then go get a stool to reach food that could not be reached without a tool.

Insightful Problem Solving in an Asian Elephant

The “aha” moment or the sudden arrival of the solution to a problem is a common human experience. Spontaneous problem solving without evident trial and error behavior in humans and other animals has been referred to as insight. Surprisingly, elephants, thought to be highly intelligent, have failed to exhibit insightful problem solving in previous cognitive studies. We tested whether three Asian elephants (Elephas maximus) would use sticks or other objects to obtain food items placed out-of-reach and overhead. Without prior trial and error behavior, a 7-year-old male Asian elephant showed spontaneous problem solving by moving a large plastic cube, on which he then stood, to acquire the food. In further testing he showed behavioral flexibility, using this technique to reach other items and retrieving the cube from various locations to use as a tool to acquire food. In the cube’s absence, he generalized this tool utilization technique to other objects and, when given smaller objects, stacked them in an attempt to reach the food. The elephant’s overall behavior was consistent with the definition of insightful problem solving. Previous failures to demonstrate this ability in elephants may have resulted not from a lack of cognitive ability but from the presentation of tasks requiring trunk-held sticks as potential tools, thereby interfering with the trunk’s use as a sensory organ to locate the targeted food.
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Further inspired by KÃ¶hler’s chimpanzee studies, in experiment 4 we conducted 8 additional sessions to investigate whether Kandula would stack items to reach food. For these sessions, the baited branches were hung at a height that could be reached by stacking three butcher block cutting boards or by the use of other objects. In addition, the elephant was given sticks and other enrichment items. Kandula first touched several items and then moved two items, a plastic disk and a block under the suspended branches, placing one front foot on each in an unsuccessful attempt to reach for the branch. He solved the problem in an unexpected novel manner, moving and standing on the object closest in size to the absent cube, a large ball. Standing on unstable platforms such as this had not been previously observed. He repeated this behavior 9 times during this session. During the session’s last minutes, Kandula picked up a block ~2 m from the food and placed it directly on top of a block that he placed under the food in a previous attempt. He stood on the stacked blocks and attempted to reach the food but was unsuccessful. He stacked two blocks again in the second and sixth sessions but each time his trunk was several inches from the food.

This is very cool research. I do wonder why they didn’t provide more videos (and in a more user-friendly format than .mov files). I made them available via YouTube.

It seems like a very interesting area to have more experiments with more elephants (and continuing to work with Kandula: he seems to be very curious elephant, good for him).

Were Remains of a Baby Woolly Mammoth Discovered this Week?

Our blog received a spike in traffic to one of our previous posts (Well Preserved Baby Mammoth Discovered in Permafrost), taking a look at what the cause was I found out is was due to a new baby woolly mammoth possible discovery.

Woolly mammoth calf fossil? No, just a wayward walrus

Authorities in the Yamalo-Nenets region said yesterday morning they were scrambling a helicopter to the location. “If what is said about how it is preserved turns out to be true, this will be another sensation of global significance,” said the leader of the expedition, Natalia Fyodorova.

Disappointment was in store, however. “It turned out to be a walrus skull; apparently a fossilised one,” said Ms Fyordorova, who is the director of the local museum.

All the sites I look at that published the discovery news give no indication that they have learned new info, so I don’t really know what the status of the “discovery” is.

MIT Scientists Find New Drug That Could Cure Nearly Any Viral Infection

New drug could cure nearly any viral infection

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory‘s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.
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There are a handful of drugs that combat specific viruses, such as the protease inhibitors used to control HIV infection, but these are relatively few in number and susceptible to viral resistance.

Rider drew inspiration for his therapeutic agents, dubbed DRACOs (Double-stranded RNA Activated Caspase Oligomerizers), from living cells’ own defense systems. When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple path pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Very cool stuff and potentially hugely beneficial. Just a reminder: this works against viruses – not bacteria (just as antibiotics do not work against viruses).

Swarmanoid: Cooperative Robot Networks

Very cool cooperation between robots. It seems more and more research is going on in cooperative robotics. It would seem this would let us have specialized robots for various tasks instead of having to have robots that can do everything (which is very complex and difficult). Plus cooperating robots are just cool. See the Swarmanoid project web site and the overarching Swarmbot site. I look forward to what these scientists and engineers can create for us.

Quantum Information Theory Postulated As Source of Emergent Theory of Gravity

I love the advances we have made using our understanding of science and engineering, like the internet, air conditioning and antibiotics. I also love the discussion of research where we really have only educated guesses about what the scientific inquiry process is telling us about the way things are. This research from the University of York is very interesting.

Escaping gravity’s clutches: the black hole breakout

Professor Braunstein says: “Our results didn’t need the details of a black hole’s curved space geometry. That lends support to recent proposals that space, time and even gravity itself may be emergent properties within a deeper theory. Our work subtly changes those proposals, by identifying quantum information theory as the likely candidate for the source of an emergent theory of gravity.”
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Dr Patra adds: “We cannot claim to have proven that escape from a black hole is truly possible, but that is the most straight-forward interpretation of our results. Indeed, our results suggest that quantum information theory will play a key role in a future theory combining quantum mechanics and gravity.”

It is too bad the University of York supports closed science and allows work to be withheld from the public to support outdated publishers business models. Luckily scientists often support open science and publish material openly – I have provided a link for those interested in science instead of the link the University of York gives to a publishers closed system.

Black Hole Evaporation Rates without Spacetime

Verlinde recently suggested that gravity, inertia, and even spacetime may be emergent properties of an underlying thermodynamic theory. This vision was motivated in part by Jacobson’s 1995 surprise result that the Einstein equations of gravity follow from the thermodynamic properties of event horizons. Taking a first tentative step in such a program, we derive the evaporation rate (or radiation spectrum) from black hole event horizons in a spacetime-free manner. Our result relies on a Hilbert space description of black hole evaporation, symmetries therein which follow from the inherent high dimensionality of black holes, global conservation of the no-hair quantities, and the existence of Penrose processes. Our analysis is not wedded to standard general relativity and so should apply to extended gravity theories where we find that the black hole area must be replaced by some other property in any generalized area theorem.

What Happens If the Overuse of Antibiotics Leads to Them No Longer Working?

Antibiotics have been a miraculous tool to keep up healthy. Like vaccines this full value of this tool is wasted if it is used improperly. Vaccines value is wasted when they are not used enough. Antibiotics lose potency when they are overused. The overuse of anti-biotics on humans is bad (especially the huge amount of just lazy, not scientific use). But the massive overuse in livestock is much worse, it seems to me.

The health system in the USA is broken in a huge way in which it is broken is the failure to address creating systemic behavior that promotes human health and instead just treating illness. It is much better to avoid a situation where we breed super bugs and then try to treat those super bugs that have evolved to be immune to the antibiotics we have to use.

When antibiotics no longer work

While the source of the current salmonella outbreak remains murky, we can reasonably speculate about the genesis of the bug’s drug-resistance: the reportedly endemic overuse of antibiotics by the agricultural industry.

Drugs are given to livestock for multiple reasons. An obvious one is for the treatment of diseases. When livestock are sick, veterinarians administer a significant dosage in hopes of eliminating the animal’s affliction. Another reason is preventative. Animals in close quarters are more susceptible to infection, so farmers will often administer medicine to healthy animals in order to nip anything nasty in the bud. Most controversially, though, members of the agricultural industry use antibiotics for the express purpose of promoting livestock growth.

It’s a well-known, if not entirely intuitive, fact that healthy animals who are fed small, or “sub-therapeutic,” doses of antibiotics will wind up larger than their unmedicated counterparts. In many such cases, these drugs are given to livestock through their feed or water, and without the prescription or oversight of a veterinarian, according to Dr. Gail Hansen, a senior officer at the Pew Campaign on Human Health and Industrial Farming.

An estimated 80 percent of all antibiotics in the U.S. are given to food-producing livestock, according to the FDA. And approximately 83 percent of that medicine is “administered flock- or herd-wide at low levels for non-therapeutic purposes, such as growth promotion and routine disease prevention,” according to a lawsuit filed against the FDA in May. These figures could have very real consequences for public health, because the Catch-22 of this antibiotic abandon is the widespread development of drug-resistant bacteria, colloquially referred to as “super-bugs.”
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In 2006, the European Union banned all use of antibiotics on livestock for growth promotion. And the U.S. Senate will consider similar legislation this year. Sen. Dianne Feinstein, D-Calif., reintroduced the “Preservation of Antibiotics for Medical Treatment Act” last month, which would significantly rein in agricultural drug use, and strictly prohibit the application of sub-therapeutic doses of drugs that have benefits for humans.

Still, the agricultural industry disputes data about its use of antibiotics and the rise of super-bugs, and it has aggressively fought efforts to legislate the matter. As a result, it’s hard to tell how far the legislation might proceed.

The end of the era of antibiotics

How did this happen? The driving forces are Darwin and human carelessness. Bacteria are constantly evolving, adapting to the changing conditions they face. Antibiotics usually kill bacteria. But sometimes a bacteria will develop a biological defense – particularly if too small a dose is used.
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Antibiotics require a prescription in America, but our nation is still very much a part of the problem. Patients routinely demand these drugs, and doctors acquiesce, for respiratory infections and other ailments that will not respond to antibiotics because they are caused by a virus. We use soap with antimicrobial agents when regular soap does equally well. And we allow farmers to feed antibiotics to livestock in horrifying amounts, not to treat illnesses but to make farming more efficient.

The Potential Role of Concentrated Animal Feeding Operations in Infectious Disease Epidemics and Antibiotic Resistance

This working group, which was part of the Conference on Environmental Health Impacts of Concentrated Animal Feeding Operations: Anticipating Hazards—Searching for Solutions, considered the state of the science around these issues and concurred with the World Health Organization call for a phasing-out of the use of antimicrobial growth promotants for livestock and fish production. We also agree that all therapeutic antimicrobial agents should be available only by prescription for human and veterinary use.

Antibiotic Resistance in Livestock: More at Risk Than Steak
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