The Fractal Gene

When you look at trees, cauliflower and blood vessels you can see an intricate pattern with a unique property called fractalness. In simple terms, a fractal is a pattern that when you zoom into it, the pattern reappears across all scales. Thus, for examples, each tree species has its own branching angle to its branches, smaller branches, leaves and veins within the leaves. Similarly, cauliflower has "bumps", wherein each bump has smaller ones with the same proportions deeper and deeper. Our blood vessels are also patterned in a similar fashion.

These biological properties of living organisms develop as a result of the genetic code. In each of our cells, we have a whole copy of our genetic code, and during development, and also in adulthood, patterns emerge according to "blueprints" in our DNA. Thus, each cell knows if to become a liver cell, an endothelial cell in a blood vessel or a neuron in the brain. The development of blood vessels, as well as sprouting of branches and leaves, is (mostly) dictated by the genetic code.

One can also look at it from an information point-of-view. Fractals are very "compact" information-wise, i.e. with a simple code, or formula, one can code beautiful intricate designs. The complex structure of a tree, from its trunk up to its leaves' veins, can be "coded" in a single gene that regulates the branching ratio in all these levels. Blood vessels might also conform to this strategy, to encode complex intricate webs in our body by a single (or a small number of) genes.

Wouldn't it be wonderful to discover this "fractal gene"? Is it a single gene for each species, dictating the branching ratio? Is it a single complex of genes across species, whose ratio in each specie dictate the emerging pattern?

Perhaps discovering this wondrous "fractal gene" can help designing complex artificial patterns. Maybe coding this ratio in the design of nano-structures, such as carbon nanotubes, will enable self-assembly of complex fractal patterns of tubes. Perhaps, even, these structures will be stronger and have unique properties.

One caveat to this hypothesis, though. Fractals appear even in inanimate objects, such as clouds, mountains and riverbeds. These amazing patterns emerge through interaction of complex phenomena, without any "guidance" of biological control. There is the possibility that tree-shapes, as well as our blood vessels architecture, are the emergent property of the opposing interaction of growth, resources and gradients of chemicals in their surroundings. Probably, as in all these gene-environment discussions, the answer is somewhere in the middle. Yet this implies that there is such a "fractal gene", and it might play a role in the buildup of some of the most beautiful structures in nature. 

Universal programming language

In recent years there has been an increase in the number of programming languages which, as proclaimed by their respective disciples, are "the best one". In this list one can include Python, Java, Ruby, Scala, c# and probably many more I didn't even hear of. Once one is familiar and adept in one language, the transition to another is usually not that hard, where one has to only learn the new syntax and some idiosyncrasies of that language.

I would like to propose a "linguistics" approach to this topic and try to compose, similar to Esperanto, a "universal programming language". Via research on the development of programming languages, one can, in complete analogy to spoken and written languages, learn the evolution of society, technology and hopefully to predict and analyze future directions of developments.

I recently encountered an amazing site, http://rosettacode.org/wiki/Rosetta_Code, in which a (rather) complete list of programming languages is detailed. The most amazing thing in this blessed endeavor, is that you can ask a question regarding programming, e.g. how to find if a file exists, and get the answer for more than 50 programming languages. A short comparison indeed shows that they are extremely similar in most respects, but have small modifications, alterations and quirks.

I think two interesting projects can evolve from such a Rosetta-code (probably both are currently underway or finished, but I unfortunately am unaware of them). The first is a language-to-language translator. Many coders are required to transform code from one language to another due to a new language appearing or a demand from a customer. Wouldn't it be nice if it could be made with a single click?

The second, more ambitious project is to create a "universal programming language". Combine all known programming languages under one common roof and allow one of two things: either attempt to make the "optimal" language under specific constraints, e.g. performance, ease of use, shortness of written commands, etc; or allow a completely customizable instantiation of novel languages - if a coder wants to enjoy all worlds such as performance of c and each of Ruby, why shouldn't she. She just open the "universal programming language" settings, choose level of performance and ease of programming and a novel easy-to-operate language is created.

I for one, would have enjoyed the results of both projects, so if you, reader, know of such things, I'd appreciate a reply/comment. Thanks.

Portable Motor

This post is more an idea of a product rather than a research project, but I think it's ok. There are many new and exciting projects that try to produce exo-skeletons, i.e. devices that are mounted on the body and supply power for lifting and moving large things. Their main usage is for handicapped people and military stuff. The product I'm suggesting is along these lines but at a much smaller scale and for everyday use.

The concept is that nowadays electric engines are becoming light and commonplace, as you can see in Segways, electric scooters and bicycles. They all have a small electric engine that mount on top and supply the juice for operating the vehicle. I want to propose a different usage for the same electric motor, namely, helping people move uncomfortable and heavy wheeled things over rough terrain, such as bad walkways and pavements. For example, old people or weak ones have trouble moving the loaded shopping carts from the supermarket or grocery store. Imagine that they have a portable small and light-weight (or even draggable) motor that they can easily attach to the shopping cart and thus help them move it. Mind you, this is not for speed, as the usage for the electric scooters, but simply supplying lacking power in "pushing" the cart.

Another example is a baby trolley for young mothers. Some pavements and gardens require maneuvering for a large trolley, especially for twins. Also, mothers after birth have less strength to carry the trolley (and the associated bags that come with it). Imagine that a simple engine is attached to the trolley and, like Segway, respond to the mother's directions and supply the juice for moving the trolley without any effort or strength.

As for marketing and pricing issues: if such engines can be mounted on kids' bikes, I'm pretty sure they are cheap and easy to operate. Adding some guidance mechanism for them should also not be an issue and since their usage is for short walks, as opposed to an electric car, their size can be small and they can be recharged easily.

Sono-luminescence with Nanotubes

Sono-luminescence is an intriguing phenomenon where sound waves (sono) impinging on a liquid create flashes of light (luminescence). The physics behind this is quite complicated, yet recent research had shed some light on it. It appears that bubbles created by the sound waves inside the liquid, due to negative pressure, suddenly implode very fast, an event called cavitation, creating such high pressures and temperatures that they cause inside atoms and molecules to radiate. In other words, sound waves propagate through the liquid, alternating between high pressure and low pressure of the liquid medium. Due to the high intensity of the sounds waves, the (relative) negative pressure causes bubbles, i.e. pockets of gases, inside the liquid. These implode, i.e. the liquid crashes the bubbles, so fast and hard that the temperatures inside these bubbles are so high that anything inside the gas bubbles emits heat and sometimes, in unique conditions, radiation in the visible spectrum, i.e. light. Sono-luminescence has even been suggested as a possible avenue to cold-fusion, the alchemist stone of the modern age.

Nanotubes, on the other hand, are very small (nano = 10 to the power of -9, of a meter) tubes made out of carbon atoms. They hold great promise in many research areas since their properties are quite unique. They are extremely strong, yet bendable; they can be either conductive or isolators, depending on their condition; and they can be (relatively) easily manufactured in different sizes, length, shapes and constellations. The tubes circumference is made of covalently tied carbon atoms in a unique arrangement. They are usually produced in a liquid solvent.

Here comes the crux: the inside of the nanotube is very small, yet can accommodate the molecules and atoms that are part of the liquid the nanotubes are in. I suggest a sono-luminescence experiment in which the liquid contains nanotubes. The reason such an experiment could have interesting effects is that the cavitation, i.e. the implosion of the bubbles, can happen inside the nanotubes. The effects of such harsh conditions, namely, high pressures and high temperatures, on the nanotubes can be of great interest in the now extremely growing community. Furthermore, since there is a unique interplay between sound waves and electromagnetic waves in a nanotube environment, there could be interesting interactions between acoustic resonances (phonons) and electromagnetic ones (photons). The small size of the nanotubes makes the strength of these interactions very strong as they can be a waveguide and/or cavity-like amplifiers for both types of waves.

Uterosound

The ear develops during pregnancy at an early stage. There is also clear evidence that some learning and adaptation occurs in-utero in many sensory organs, such as smell, sound and even sight. The latter is unique, since there is no light in the uterus; nevertheless, the neurons in the retina are activated in a specific way, called retinal waves, so as to (in my opinion) optimally adjust and "calibrate" the upstream neuronal processing. Hearing is known to be developed in-utero, since there is evidence that one and two days old babies show preference for their mother's voice than to other people voices. From this information, several attempts to introduce "sophisticated sounds" to the womb have been made, in a marketing pitch that "if you play Mozart to your unborn child, she will come out smarter".

However, there is an obvious obstacle in developing such a device: sounds travel and distort on their journey from the outside world, until they reach the fetus's hearing organs. Sounds travel differently in liquids than in air, i.e. the speed of sound is much higher. Furthermore, women's bodies are not a uniform liquid (although made mostly of water), since they have many non-liquid organs, such as bones, muscles, kidneys etc. Hence, there is no clear relationship between the produced sound from the speakers outside the body and the actual sound sensed by the fetus.

In recent developments, there are now unique tools that are capable of analyzing the travel of sounds inside such a complex system as the human body. There are several ultrasound operations made today in a non-invasive manner, that heat up and destroy malignant tissue inside the body using sound-waves. However, analysis of sounds in the audible range, which has a much lower frequency than ultrasound, is much trickier. Nevertheless, advanced numerical tools that solve the wave equation in random and inhomogeneous media (which is the human body), exist today.

The project I'm suggesting involves a unique combination of imaging tools, advanced numerical sound-propagation tools and inverse problem analysis. I'll explain the steps toward the goal, which is to play the fetus sound in-utero that are identical, from a neuronal perspective, to sounds she will hear when she is born.

1.      Produce high definition imaging of the entire abdomen, with all organs and positions. This can be done in a non-invasive non-radiative manner using MRI and ultrasound. The output of this stage is a clear 3D map of the organs inside the mother's belly, including the position of the fetus.

2.      Use advance numerical tools, with the unique 3D map of the body, to understand, predict and invert the propagation of sound in such a complex medium. In other words, one can now know what the fetus senses when we make sounds outside the uterus, but more importantly one can know which sounds to produce outside in order for the fetus to hear what we want.

3.      Given the fetus developmental age, augmented by its 3D map, one can ascertain the level of auditory processing occurring prior to auditory neurons firing. In earlier ages, there is virtually no processing, whereas in later developmental stages the inner and outer ear are already there and influence the distortion of sounds dramatically.

4.      Given the inverse transform, i.e. which sounds to produce in order for the fetus to hear what we want, and given the fetus's auditory processing, we can now decide which sounds to produce, outside the body, for the fetus to "hear" sounds that are similar to those that it will hear after it is born.

This project is based on a huge assumption, and have some moral issues: should we even try to produce sounds in-utero that are not natural to the development of the fetus? I believe that the brain is a learning organ and that everything "thrown" at it, it will learn and adapt. I thus believe that if we make sounds such that the developing brain "hears" similarly to those that it will hear later on, after delivery, then I think that it will learn much faster to recognize sounds, voices and other auditory cues when it is a new born baby.

The Morphing Room

She entered her home after a long day. The single-room apartment looked completely bare, with no furniture of any kind, nor closets, tables or any possessions. However, she walked slowly to her favorite spot and simply said "chair, please". The floor rose to meet her descending body in a caressing embrace; several hexagonal columns, ending in small inflatable cushions rose from the floor in a three-dimensional arrangement she so admired. They created a chair under her and she finally relaxed. "A glass of wine, please" she said and an opening appeared in one of the walls, two feet above the floor. A small robot holding a glass of wine began to come out, and was met by an ascending column of hexagonals, which formed a straight path from the opening to the newly formed chair. The robot gracefully rolled on the path and upon reaching the chair's location, was raised to the chair's height by the last few hexagonals. She took the glass, murmuring an absent minded "thank you" and sipped her wine. Several minutes of relaxation were interrupted by a knock on the door. She placed her wine on the raised hexagonal and went to the door, whereupon her chair slowly receded to the floor. She opened the door and saw her friend smiling "am I too early?" "No, you're just on time". They both entered and the host said "two chairs and a table, please". An arranged of two chairs rose from the floor, adjacent to one of the walls, whereupon a slab came out of the wall between them, forming a comfortable corner. "Do you want to drink something before we begin?" she asked. "Just water, please". Another opening appeared in the wall and a path from it to the table formed just as a small robot rolled on it with a clear glass of water. The visitor, not yet accustomed to The Morphing Room was a little surprised and dropped the glass of water, which shattered on the floor. "I am so sorry", she said, "I'll help clean it up". "No need" her host smiled. All the hexagonals in the vicinity of the shattered glass descended to the floor, creating a flat surface. From an opening on the floor level came out a small robot and cleaned the floor, returning to another opening with the glass remnants. Another opening appeared and another robot came and wiped the water from the floor. After three minutes, the floor was clean and the hexagonals resumed their three dimensional arrangement prior to the incident. Another glass of water appeared and the visitor took it and drank. "Let's start" her host suggested. The table lit up and they worked on the work-table for some hours, sometimes interrupting their work with an order of a beverage or a snack. After they finished the visitor rose and said "I think we got it now, what do you think?" "I agree. Let's meet tomorrow again to finalize things." They embraced and the visitor left, accompanied by the reshaping of the room to its bare shape once more. During their goodbyes, several small robots appeared from the floor-level openings and cleared all the now-flat floors in a graceful easy dance. When she finally closed the door behind her friend, she was very tired. "Bed, please" she said and the usual arrangement of hexagonals of her soft bed rose from the floor the exact height she liked. From one of the openings a folded blanket came via another robot and was laid on the bed. She took it while the path leading the robot back to its niche descended to the floor. The lights dimmed and she quickly fell asleep.

---

The Morphing Room is based on the concept of a changing floor that can meet the three dimensional needs of its occupants. The floor is made of height-adjustable components that can shift and create a three dimensional shape at will and recede back to the floor when it is no longer needed. Another important consequence of this arrangement is that simple robotic helpers can be incorporated into the room. Their locomotion can be completely limited to two dimensions with no obstacles, a task easily achieved today. Their third dimension movement is performed by the coordinating floor and obstacles are usually removed either by the descending floor or by other robots. This enables very simple robotics to operate, clean and help the occupant of the room in whatever they need. Furthermore, the walls become completely accessible in all heights since the floor makes it accessible.

Technology. The basic ingredients of The Morphing Room is an array of hexagonals that must fulfill the following requirements:

1.      Rise and descend quickly to any desirable height: this can be done either by electric or hydraulic pistons below the floor level.

2.      Strong enough to support the weight of a person: this can be done with today's reinforced plastic materials.

3.      Modifiable endpoint to allow for either hard or soft endings: this can be done by inflatable cushions, whose air can pass in the middle of the hexagonal.

The walls are also an important part of The Morphing Room. They are composed of many compartments, each responsible for a different function, e.g. refrigerator, cupboard, closet, garbage, etc. They can be laid out in any arrangement, since height is of no importance, but to facilitate its function.

An assembly of helper robots are also an important, yet not mandatory, part of The Morphing Room. The room facilitates the use of simpler robots, since the environment changes to accommodate simpler navigation and reachability for the robots. They should be divided to two basic types, namely, graspers for bringing things and cleaners that clean the floor (and only the floor, since all else can become a floor). While more complex robots can facilitate more complex dynamics, e.g. quadcopters can have a truly three-dimensional maneuverability, they are not necessary in The Morphing Room.

 To conclude, The Morphing Room is a new design for a malleable room in which the floor can change its shape to accommodate the requirements of its inhabitant. The floor also facilitates accessibility to all heights of specially designed walls and enables an entourage of simple robots to keep it serviceable and clean.

Indexing the Brain

For the last two decades, Human Brain Mapping (HBM) research has flourished, generating tens of thousands of research papers that describe the anatomical and functional structure of the human brain. This is mainly accredited to the infiltration of fMRI research to every branch related to neuroscience, from cognition, to decision making, neuro-economics, as well as sensory perception and motor actions and planning. There is a huge amount of data out there that is hardly indexed, and the number of fMRI papers is increasing every year.

I believe that current technological tools, mainly web scraping, crawlers and natural language processing (NLP) tools, have reached a point that one can create an automatic tool that "reads" all these papers and aggregate them in a single database according to anatomical as well as functional structure.

In order to understand how to implement this project, as well as how to use its products, a short explanation on fRMI research is in order. A typical research begins with an experimental design, where the most basic one is composed of two conditions, for example presenting the subject with a picture of either a house or a face. Then the experiment begins inside the fMRI research and is repeated many times per subject, as well as on many subjects, in order to get a statistically significant result. Such a result is usually described as: "area A was more active under condition X than condition Y". This result thus suggests that area A is somehow involved in processing condition X. For example, it was shown that an area called the Fusiform Gyrus is more active when seeing faces than when seeing houses and this result (with many others) suggests that the Fusiform Gyrus area is involved in processing visual aspects of faces.

An example Abstract of an fMRI research paper (quite old):

"Using functional magnetic resonance imaging (fMRI), we found an area in the fusiform gyrus in 12 of the 15 subjects tested that was significantly more active when the subjects viewed faces than when they viewed assorted common objects. This face activation was used to define a specific region of interest individually for each subject, within which several new tests of face specificity were run. In each of five subjects tested, the predefined candidate “face area” also responded significantly more strongly to passive viewing of (1) intact than scrambled two-tone faces, (2) full front-view face photos than front-view photos of houses, and (in a different set of five subjects) (3) three-quarter-view face photos (with hair concealed) than photos of human hands; it also responded more strongly during (4) a consecutive matching task performed on three-quarter-view faces versus hands. Our technique of running multiple tests applied to the same region defined functionally within individual subjects provides a solution to two common problems in functional imaging: (1) the requirement to correct for multiple statistical comparisons and (2) the inevitable ambiguity in the interpretation of any study in which only two or three conditions are compared. Our data allow us to reject alternative accounts of the function of the fusiform face area (area “FF”) that appeal to visual attention, subordinate-level classification, or general processing of any animate or human forms, demonstrating that this region is selectively involved in the perception of faces." From: Nancy Kanwisher, Josh McDermott, and Marvin M. Chun, "The Fusiform Face Area: A Module in Human Extrastriate Cortex Specialized for Face Perception". The Journal of Neuroscience, 1 June 1997, 17(11):4302-4311

The first sentence has all the relevant information for the project: an area "fusiform gyrus" and condition "subjects viewed faces than when they viewed assorted common objects".

Furthermore, most papers have fMRI images that show the exact area of activation, as well as standard 3D coordinates within the brain call Talaraich coordinates. The project should thus first create an indexed database of papers according to their coordinates and/or function/condition; then using NLP tools to extract the meaning of the area from many such papers. The product is thus a tool for future researchers that can query such a database for a specific area they discover in their own research and get not only proper citations for their papers (which is important), but also a suggestion for the meaning of the areas they discovered. If it works, the tool can be even more powerful; usually each experiment results in several areas that are active, because more recent experiments are much more complex and examine higher cognitive functions (e.g. neuroeconomics). Hence, the tool can actually suggest a reconstruction of the experiment all by itself. How? Given the active areas, the tool knows and connects, via NLP and extensions, what function each area performs and can integrate all of these into a hypothesis of the experiment that gave such activation. This is a huge step in human brain mapping research and neuroscience in general: it is akin to reading the inner as well as outer environment of a person, solely from an fMRI scan (a little different from recent "thought reading" experiments, which focus on much finer details).

How to implement this project?

1.      Crawlers in the internet can search specific sites of neuroscience-related journals (not that many) and automatically scan for specific keywords: fMRI, subjects, research, etc.

2.      Once a candidate paper is found, the relevant areas are searched for (again, not that many); or searching for Talaraich coordinates inside the paper.

3.      Milestone: An indexed 3D map/database of human brain papers.

4.      Scanning all papers in the database for a description of the experiment/condition.

5.      Using state-of-the-art NLP tools to extract and index database of conditions/experiments such that there would be overlap between papers.

6.      Milestone: An indexed 3D map/database of the human brain function.