Tag Archives: biology

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.

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).

Wesley the Owl: Love Story of an Owl and His Girl

This story begins on Valentine’s Day in 1985 when biologist Stacey O’Brien meets a four-day-old baby barn owl in a fateful encounter that would turn into an astonishing 19-year saga. With nerve damage in one wing, the owlet’s ability to fly was forever compromised and he had no hope of surviving on his own in the wild. A young assistant in the owl laboratory at Caltech, O’Brien promised to care for the helpless owlet and give him a permanent home. O’Brien’s heartfelt memoir of life with this wild bird, Wesley the Owl: The Remarkable Love Story of an Owl and His Girl recounts their dramatic, and often humorous, life together.

For almost two decades, O’Brien studied Wesley and his strange habits intensively and providing a mice-only diet. With a heart-shaped face and outsized personality that belied his 18-inch stature, the gorgeous white-and-gold Wesley fascinated everyone he met, and touched many lives. Stacey and Wesley’s bond was especially deep; O’Brien discovered that owls are highly sentient beings with individual personalities, subtle emotions, and a playful nature that can also turn fiercely loyal and protective.

Cool fact: “While we hear in two dimensions, owls hear in three.” Owls can detect a mouse heartbeat under three feet of snow.
Related: Friday Fun: Cat and Owl Playing – Bird Brain (smart crows) – Using Barn Owls for Bilogical Pest Control in Israel
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Cambrian Explosion Song

via Smithsonian’s Surprising Science:

What does a music teacher do when he ends up teaching science? He teaches about evolution and the geologic timeline with music, of course, and that’s what Canadian elementary school teacher John Palmer did. He originally played “Cambrian Explosion” as a rock/hip hop creation in class but has since recorded an acoustic version. (The trio is called Brighter Lights, Thicker Glasses and consists of Palmer on the guitar/vocals, Michael Dunn on the dobro and Brian Samuels [from UBC civil engineering department] on the cello.)

The video was filmed in the Beaty Biodiversity Museum (Canada) atrium with the blue whale exhibit in the background.

Image of Map Showing Concentration of Life in Oceans

This image shows the abundance of life in the sea, measured by the SeaWiFS instrument aboard the Seastar satellite. Dark blue represents warmer areas where there is little life due to lack of nutrients, and greens and reds represent cooler nutrient-rich areas.

The nutrient-rich areas include coastal regions where cold water rises from the sea floor bringing nutrients along and areas at the mouths of rivers where the rivers have brought nutrients into the ocean from the land. NASA has posted a large gallery of great images for Earth Day.

Help Science Education in Tanzania

Students in Tazania using a microscope

Diana Hall, a physics teacher from Bell High School, Ottawa, Canada is spending 6 months in Tanzania helping build a more active science program. This reminds me of my time in Nigeria (while my father taught Chemical Engineering at the University of Ile Ife to help build a strong university program). It is great to see all the good that people are willing to do.

The objective of the Do Science, Tanzania project is to share teaching strategies and equipment with science teachers and students in Moshi, Tanzania. The goal is to facilitate a more active science program and to inspire students to continue studying beyond the secondary level.

The photo shows students at Reginald Mengi Secondary school, Tanzania, getting their first experience with microscopes in the classroom. There are over 210 Form I (freshman in high school, for you USA readiers) students in 4 classes. The 4 classes had an introduction to the microscope by preparing slides and viewing onion cells.

Working with science teachers is a big part of do Do Science is about. Their blog discusses a recent meeting where 50 science teachers from the Moshi area attended a workshop. The teachers at the workshop modeled thinking exercises, conducted sample labs, investigated computer simulations and interfacing equipment, looked at some DVD resources. and networked.

You can help by donating equipment or money. Or if you are a science teacher with workshop and leadership experience who would consider spending some time in Tanzania as a facilitator?

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How To Make Your Own Pesticide with Ingredients from Your Kitchen

Video by the Singapore National Park Board, on creating your own pesticide with just water, dish-washing liquid, chili, garlic and cooking oil.

Evidence of Extraterrestrial Life Discovered?

Has evidence of extraterrestrial life been discovered? In Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites , Richard B. Hoover, Ph.D. NASA/Marshall Space Flight Center, puts forth his evidence on the discovery of evidence of cyanobacteria in meteorites.

Dr. Hoover has discovered evidence of microfossils similar to Cyanobacteria, in freshly fractured slices of the interior surfaces of the Alais, Ivuna, and Orgueil CI1 carbonaceous meteorites. Based on Field Emission Scanning Electron Microscopy (FESEM) and other measures, Dr. Hoover has concluded they are indigenous to these meteors and are similar to trichomic cyanobacteria and other trichomic prokaryotes such as filamentous sulfur bacteria. He concludes these fossilized bacteria are not Earthly contaminants but are the fossilized remains of living organisms which lived in the parent bodies of these meteors, e.g. comets, moons, and other astral bodies. The implications are that life is everywhere, and that life on Earth may have come from other planets.

The importance of this claim is hard to ignore. The journal includes a statement from Dr. Rudy Schild, Center for Astrophysics, Harvard-Smithsonian, Editor-in-Chief, Journal of Cosmology:

Dr. Richard Hoover is a highly respected scientist and astrobiologist with a prestigious record of accomplishment at NASA. Given the controversial nature of his discovery, we have invited 100 experts and have issued a general invitation to over 5000 scientists from the scientific community to review the paper and to offer their critical analysis. Our intention is to publish the commentaries, both pro and con, alongside Dr. Hoover’s paper. In this way, the paper will have received a thorough vetting, and all points of view can be presented. No other paper in the history of science has undergone such a thorough analysis, and no other scientific journal in the history of science has made such a profoundly important paper available to the scientific community, for comment, before it is published. We believe the best way to advance science, is to promote debate and discussion.

Read the full paper.

The filaments have been observed to be embedded in freshly fractured internal surfaces of the stones. They exhibit features (e.g., the size and size ranges of the internal cells and their location and arrangement within sheaths) that are diagnostic of known genera and species of trichomic cyanobacteria and other trichomic prokaryotes such as the filamentous sulfur bacteria. ESEM and FESEM studies of living and fossil cyanobacteria show similar features in uniseriate and multiseriate, branched or unbranched, isodiametric or tapered, polarized or unpolarized filaments with trichomes encased within thin or thick external sheaths. Filaments found in the CI1 meteorites have also been detected that exhibit structures consistent with the specialized cells and structures used by cyanobacteria for reproduction (baeocytes, akinetes and hormogonia), nitrogen fixation (basal, intercalary or apical heterocysts) and attachment or motility (fimbriae).
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These studies have led to the conclusion that the filaments found in the CI1 carbonaceous meteorites are indigenous fossils rather than modern terrestrial biological contaminants that entered the meteorites after arrival on Earth. The Î´13C and D/H content of amino acids and other organics found in these stones are shown to be consistent with the interpretation that comets represent the parent bodies of the CI1 carbonaceous meteorites. The implications of the detection of fossils of cyanobacteria in the CI1 meteorites to the possibility of life on comets, Europa and Enceladus are discussed.

Has life been found in a meteorite? by Phil Plait
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Most Genes? A crustacean the size of a grain of rice

photo of Daphnia, a crustacean

“Daphnia are ubiquitous in freshwater ponds and lakes and are often used to assess the health of ponds. Since the creature is so well studied by ecologists, knowing its genetics should reveal a lot about how genes respond to different environments.

The first scientists to describe Daphnia thought they were a kind of flea because they assumed the red color came from sucking blood as fleas do. It turns out they’re not bloodsuckers – they’re blood makers. Daphnia have genes that make hemoglobin, so when the animal is stressed out, those genes switch on and the animal looks red.

In fact Daphnia have an astonishingly large number of genes. “We count more than 31,000 genes,” says [John] Colbourne. By comparison, the human genome has more like 23,000 genes. If Guinness tracks such things, Daphnia would hold the record for the most genes of any animal studied to date.

“Many of those genes – we estimate around 35 percent of them – are brand new to science,”

Daphnia can grow its own spear and helmet when threatened by an attacker