Biology (27)

18 Jan 2014


One thing that irks most laboratories is the cost of running a lab. Research laboratories are run in a non-profit mode with most of their money coming from Government grants or other sources of funds. Their motive is not profit and the primarily goal is to educate, discover and if possible invent. That requires money. Some money can be made by licensing an invention but for more basic researchers there is always a cash crunch. Laboratories tend to look for areas where they can repair and design new instrumentation.



Joshua Pearce at Michigan Tech makes some interesting products that will enable making of scientific equipment. They have been creating some interesting lab equipment using 3D printers that were really expensive to buy but now can be easily printed in the laboratory. There have been several collections that are openly available by the Michigan group - for example, see this pipettor that is available in Thingsverse. Interesting link is here and also watch the video below.



01 Dec 2013

There has been a superb paper in Frontiers in Zoology, that describes the landing patterns of birds. The paper writer is also an amazing feat of data collection. The team of Hynek Bruda noted landings of nearly 14 species of birds and observed nearly 15,000 birds. They noticed that the birds always landed in the direction of the earth's magnetic field. This is incredible because it serves to align all the birds in one direction and may help in collision avoidance. The sensors in birds are located in two places:

  • Magnetic iron oxide located in their beak and/or inner ear.
  • Magnetic sensitive reaction occurring somewhere in their eye that enables them to see the magnetic field.

This paper is worth a read but also implies that if other biological species like homing pigeons use the same magnetism. However, in pigeons they supplement magnetism with other sensors since in homing pigeons the smell is very important to homing.

20 Aug 2013

It has always been argued that breakdown in homeostasis is the real cause of disease. This point is amply illustrated by the recent PNAS article that correlated the miniscule amounts of copper in the mice diet with A-beta clearance and would have an implication for Alzheimer’s disease. In this case, the presence of copper affected the low-density lipoprotein receptor-related protein 1 activity which is responsible for clearing Ab- across the blood brain barrier. Additionally, the copper inside the brain, affected the inflammation tone in the brain and may further accentuate the effect of copper.

However, copper is an essential nutrient. It is a critical cofactor for many enzymes: oxidase such as catechol oxidase, galactose oxidase, bilirubin oxidase and the important superoxide dismutase. How the right balance of copper is achieved and maintained may be the critical factor in disease vs normal individuals.

As we look across biological systems, homeostasis seems to be the critical factor in the balancing act. Wonder how much attention should an engineer pay to homeostasis when creating a robotic systems? Right now the check and balance is primarily regulated by the operator but sensors regulating the activity of critical components might be important as our design systems get complex.

13 Aug 2013

Much of biological science and technologies are trying to cure disease. However, there are a large group of people who do not want to be cured. There are several instances and examples where they have objected vehemently about not doing things that would cure their ailment.

What ailment ?


Deafness has been cured to a large extent with cochlear transplant that translates the sound to the cochlear nerve signals. However, the community of deaf people is so strong that they actually have felt one with their disease, their secret sign language and the strong community and do NOT want to be cured of the disease.

Recently, a video of a child listening to his father has become very popular and shows the great effect technology has on all of us.

There have been cases where the deaf couple has resisted their children getting a cochlear transplant, they have looked for sperm that can guarantee them deaf children to match them. There is something more to this… deaf people have their sign language name, their community and a secret language and getting a cochlear transplant makes them like everyone else with the added problem of possible infections, not perfect pitch and sound sensation.

It almost makes people think that this does solve their hearing problem but loses them from the community.

As we biologists and technologists move forward to cure disease and deafness being an example, we have to remember that people like communities and keeping them as part of community is probably as important as curing disease.

21 Jul 2013

Plants communicate with each other. That much is known. However, what is not known is how plants communicate using symbiosis. Dr Johnson has reported new work in Ecology letters that shows that plants use symbiotic fungi to enable communication.

Communication also causes interesting secretion by plants when infected by aphids. These secretions that are volatile work very interestingly – they repel aphids but attract the wasps which eat aphids. This is amazing from the point of view of evolution and creation of chemicals that work in such multiple ways.


Either ways, communications are important for populations whether as email, facebook or plant chemicals!

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26 Jun 2013

It is amazing how much thought and science goes into producing food substances that we take for granted. The real wasabi owes its fiery nature to a volatile chemical called allyl isothiocyanate that binds to specific receptor in humans called TRPA1 – (Transient receptor potential) that is activated by heat in some instances. This allyl isothiocyanate is generated only transiently by the enzyme myrosinase acting on thioglucosides that are released when the cells of the plant rhizome is broken. This preparation of the plant may be critical since it is released only when the plant rhizome is ground up very finely. The allyl isothiocyanate lasts only transiently since the volatile component is lost very rapidly and is almost completely gone in 15 minutes. However, commercial wasabi may be prepared by other horse radish’s that are probably more long lasting.

Interestingly, the same receptor that we use to sense wasabi is the same receptor that is used in snakes to sense heat. In pit-vipers the receptor is so sensitive that it can be used to measure the change in temperature of less that 0.009 C and may be like infrared vision in snakes allowing them to find their prey. This was discovered only recently in a publication in NATURE.

29 May 2013

Translational Medicine had a paper by Dr Dormitzer from Novartis and Dr Venter of creating a flu vaccine in just about 4 days and 4 hours, as opposed to months and weeks that it used to take previously. They used the sequence supplied by Biomedical Advanced Research and Development Authority and transfecting it into tissue culture cells and then producing Hemagglutinin and Neuraminidase proteins. They proved that the antigens work in Ferrets producing protective immunity.
This is a big step for Immunology and Vaccine Biology.

21 May 2013

Biology is complex. The cell or the organism has to respond to a wide variety of external stimuli and respond. The stimuli aggregation and response obviously happen at the brain and neuron level but also at the cellular level.

Dr Drew Andy of Standford University has created biological transistors based upon biological transcription that happens at the cellular level. He has created switches that would respond to the stimuli that is received. Combining the switches in different formats with different response elements makes the biological system behave as an AND gate, OR gate or NOR gate. These are the basis of computation.

The switches and the science behind them is not novel. The switches were first discovered in E.coli with the lac operon that was characterized in the 70-80’s. The operon as it was called was the response element that responded to the presence of lactose and controlled the enzymes of lactose metabolism that are synthesized. A cell typically performs this function normally but what Dr Andy has done is to combine these elements into an interesting mix that enables combining different elements such that the response of the cell can be used as a sum of operations.

Will this make a biological computer? Probably not. It is too slow and there are many biological molecules required but what this can enable is the ability to compute at the cellular level that can be programmed by the molecular biologist. It will takes weeks to program and probably require days to read out but ultimately could be a good model for biological computation.

The video explains the science very well and all the materials from this study have been made publicly available through Biobrick public agreement.





29 Apr 2013


Malcolm Gladwell in his book “Outliers” reported studies that it takes about 10,000 hours for any person to become an expert based on studies conducted in various laboratories. This is a big number. Consider an 8 hour day with a 40 hour week specializing in only one area. With 50 weeks that equates to about 2000 hours per year which infers to about 5 years to become an expert? Curiously, that is the length of average PhD! This amount of time is required to become an expert in any one area. Assuming that is absolutely true for many people that learn a profession, that would be the time for education. However, it is entirely likely that this would be different at different ages and probably much easier at an younger age.


Individual chunks of knowledge require becoming an expert as summarized in Ray Kurzweil’s book “How to create a mind”. One of the areas from where this was derived is comparing the strategy employed by human vs. computers while playing chess. Gary Kasparov has been assumed to learn about 100,000 board positions. Shakespeare composed his plays with 100,000 word senses, using about 29,000 words and medical specialist similarly learns about 100,000 concepts. It is possible that this amassing of knowledge takes the 10,000 hours that is required to program the brain.

28 Apr 2013

Dr Claudia Gravekamp from the Albert Einstein College of Medicine is exploring the treatment of cancer with bacteria after she observed that the bacteria, Listeria monocytogenes, seemed to be concentrating near the area of tumor.

Tumor targeting of drugs or radiation is a very big issue. Currently, there are several drugs that attack cancer cells but they are also potent for normal cells. If the treatment can be targeted specifically towards the tumor cells then the treatment would be more effective. Dr Gravekamp intends to use the bacteria for targeting the tumor.

Typically, bacteria are rapidly cleared by the immune system. However, in cancer patients, the immune system appears to be suppressed around the area of the tumor and hence bacteria that would normally be cleared now can survive and divide in the region around the tumor. By labeling the bacteria with radioactive rhenium it is possible to irradiate the tumor with these targeting bacteria. Interestingly, these bacteria are not affected by rhenium but the cancer cells are killed by the radiation. Thus, it makes it possible to selectively irradiate tumor cells and kill them.

As a additional consequence, if the tumor cells change by the radiation, it is possible that they will lose their immuno-suppressive effect and thus be susceptible to the immune system. However, there are several unknowns - what is the consequence of having lethal bacteria in the body? Liver and Kidneys show toxicity from the processing of metabolites of the dead bacteria but also having these bacteria in circulation may cause other unknown effects in an immune-compromised cancer patient.

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