Biological and artificial neurons

Biological neurons

A biological neuron (nerve cell) is an electrically excitable cell that processes and transmits information through electrical and chemical signals. A chemical signal occurs via a synapse, a specialized connection with other cells. Neurons connect to each other to form neural networks. Neurons are the core components of the nervous system, which includes the brain, spinal cord, and peripheral ganglia. There are different types of neurons: sensory neurons, motor neurons and interneurons.

A typical neuron possesses a soma (perkaryon or cyton = cell body with nucleus), dendrites and an axon. Neurons do not undergo cell division.

Neurons

Neuron (Wikipedia)

Dendrites are thin structures that arise from the cell body, branching multiple times and giving rise to a complex dendritic tree. An axon is a special cellular extension that arises from the cell body and travels for long distances (as far as 1 meter in humans). The cell body of a neuron gives rise to multiple dendrites, but never to more than one axon, although the axon may branch hundreds of times before it terminates. The axon terminal contains synapses, specialized structures where neurotransmitter chemicals are released to communicate with target neurons. At the majority of synapses, signals are sent from the axon of one neuron to a dendrite of another, however there are a lot of exceptions.

All neurons are electrically excitable, maintaining voltage gradients across their membranes by means of metabolically driven ion (sodium, potassium, chloride, calcium) pumps. Changes in the cross-membrane voltage can alter the function of voltage-dependent ion channels. Each time the electrical potential inside the soma reaches a certain threshold, an all-or-none electrochemical pulse called an action potential is fired, which travels rapidly along the cell’s axon, and activates synaptic connections with other cells when it arrives.

Artificial neurons

An artificial neuron is a mathematical function conceived as an abstraction of biological neurons. The artificial neuron receives one or more inputs (representing the dendrites) and sums them to produce an output (representing the axon). Usually the sums of each node are weighted, and the sum is passed through a non-linear function known as an activation function or transfer function.

The first artificial neuron was the Threshold Logic Unit (TLU) first proposed by Warren McCulloch and Walter Pitts in 1943. This model is still the standard of reference in the field of neural networks and called a McCulloch–Pitts neuron. However, artificial neurons of simple types, such as the McCulloch–Pitts model, are sometimes characterized as caricature models, in that they are intended to reflect one or more neurophysiological observations, but without regard to realism.

In the 1980s computer scientist Carver Mead, who is widely regarded as the father of neuromorphic computing, demonstrated that sub-threshold CMOS circuits behave in a similar way to the ion-channel proteins in cell membranes. Ion channels, which shuttle electrically charged sodium and potassium atoms into and out of cells, are responsible for creating action potentials. Using sub-threshold domains mimicks action potentials with little power consumption.

At the Neuromorphic Cognitive Systems Institute of Neuroinformatics of the University of Zurich and ETH Zurich, a research group leaded by Giacomo Indiveri is currently developing, using the sub-threshold-domain principle, neuromorphic chips that have hundreds of artificial neurons and thousands of synapses between those neurons.

Volunteer Computing

Volunteer computing is an arrangement in which people (volunteers) provide computing resources to projects which use the resources to do distributed computing and/or storage. Distributed computing is a field of computer science that studies distributed systems. A distributed system is a software system in which components, located on networked computers, communicate and coordinate their actions by passing messages.

Neural networks are very good candidates for simulation by distributed computing systems because of their inherent parallelism and beacuse its simulation is a very time consuming process, due to the complex iterative process involved.

The first volunteer computing project was the Great Internet Mersenne Prime Search, which was started in January 1996. The term volunteer computing was coined by Luis F. G. Sarmenta, the developer of Bayanihan.

The Berkeley Open Infrastructure for Network Computing (BOINC) is the most widely-used middleware system for volunteer computing. It offers client software for Windows, Mac OS X, Linux, and other Unix variants. The project was founded at the University of California, Berkeley Space Sciences Laboratory, funded by the National Science Foundation. Other systems are XtremWebXgrid and Grid MP.

Volunteer computing systems must deal with the following problems, related to correctness :

  • Volunteers are unaccountable and essentially anonymous
  • Some volunteer computers occasionally malfunction and return incorrect results
  • Some volunteers intentionally return incorrect results or claim excessive credit for results

A list of distributed computing projects is provided at Wikipedia. Links to a few selected BOINC volunteer computing projects are listed below :

OpenWorm Caenorhabditis elegans

Last update : September 4, 2024

OpenWorm aims to build the first comprehensive computational model of the Caenorhabditis elegans (often called C. elegans, even if this term is a species abbreviation), a free-living, transparent nematode (roundworm), about 1 mm in length, that lives in temperate soil environments. With only a thousand cells, it solves basic problems such as feeding, mate-finding and predator avoidance.

OpenWorm background

Research into the molecular and developmental biology of C. elegans was begun in 1974 by Nobel prize laureate Sydney Brenner and it has since been used extensively as a model organism for development biology. Sydney Brenner founded the Molecular Sciences Institute in Berkeley, California.

Caenorhabditis elegans (Wikipedia)

Caenorhabditis elegans (Wikipedia)

The basic anatomy of C. elegans includes a mouth, pharynx, intestine, gonad, and collagenous cuticle. C. elegans has two sexes: hermaphrodites and males (0.05%).

C. elegans is one of the simplest organisms with a nervous system. In the hermaphrodite, this comprises 302 neurons whose pattern of connectivity (connectome) has been completely mapped and shown to be a small-world network. C. elegans was also the first multicellular organism to have its genome completely sequenced. The genome consists of six chromosomes (named I, II, III, IV, V and X) and a mitochondrial genome. The sequence was first published in 1998 with regular updates, because DNA sequencing is not an error-free process. The latest version released in the WormBase () is WS238.

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, Lincoln Stein of the Ontario Institute for Cancer Research, and John Spieth of the Washington University Genome Sequencing Center. Richard Durbin served as a principal investigator until 2010.

Additional informations about C. elegans are available at the following links :

  • WormBook – a free online compendium of all aspects of C. elegans biology
  • WormAtlas – an online database for behavioral and structural anatomy of C. elegans
  • WormClassroom – an education portal for C. elegans
  • WormImagethousands of unpublished electron micrographs and associated data
  • WormWeb.org – an interactive cell lineage and neural network
  • Cell Exlorer – a 3D visualization tool for the structural anatomy of C. elegans
  • C. elegans movies

OpenWorm open source project

Despite being extremely well studied in biology, the C. elegans still eludes a deep, principled understanding of its biology. The OpenWorm project uses a bottom-up approach, aimed at observing the worm behaviour emerge from a simulation of data derived from scientific experiments carried out over the past decade. To do so, the data available in the scientific community is incorporated into OpenWorm software models.

An open-source simulation platform called Geppetto is used by the OpenWorm Project to run these different models together. An OpenWorm Browser enables ready access to a cell-by-cell 3D representation of the nematode C. elegans in a WebGL enabled browser. The 3d browser was created with the help of the Google Labs Body Browser team. The browser has also been ported to an iOS app to support the project. All the code produced in the OpenWorm project is Open Source and available on GitHub.

The OpenWorm project was realized by a highly motivated group of individuals who believe in Open Science.

The early core team members of the OpenWorm project were :

Bibliography

Neuromorphic computing

neuromorphic computing by Spike Gerrell

credit : Spike Gerrell for the Economist

Neuromorphic computing is a concept developed by Carver Mead, describing the use of very-large-scale integration (VLSI) systems containing electronic analog circuits to mimic neuro-biological architectures present in the nervous system. Carver Mead is a key pioneer of modern microelectronics.

Today the term neuromorphic is used to describe analog, digital, and mixed-mode analog/digital VLSI and software systems that implement models of neural systems. Neuromorphic computing is a new interdisciplinary discipline that takes inspiration from biology, physics, mathematics, computer science and engineering to design artificial neural systems and autonomous robots, whose physical architecture and design principles are based on those of biological nervous systems.

The goal is to make computers more like brains and to design computers that have  features that brains have and computers do not have up to now :

  • low power consumption (human brains use about 20 watts)
  • fault tolerance (brains lose neurons all time without impact)
  • lack of need to be programmed (brains learn and change)

An important property of a real brain is that each neuron has tens of thousands of synaptic connections with other neurons, which form a sort of small-world network. Many neuromorphic chips use what is called a cross-bar architecture, a dense grid of wires, each of which is connected to a neuron at the periphery of the grid, to create this small-world network. Other chips employs what is called synaptic time multiplexing.

The Economist published a few days ago a great article “Neuromorphic computing – The machine of a new soul” with illustrations from the London-based illustrator Spike Gerrell.

Some neuromorphic computing reletad projects are listed below :

Neuromorphic computing is dominated by European researchers rather than American ones. The following links provide additional informations about neuromorphic computing related institutions and topics :

Artificial General Intelligence

Last update : August 7, 2013

Artificial General Intelligence (AGI) is an emerging research field aiming at the building of thinking machines; that is, general-purpose systems with intelligence comparable to that of the human mind (and perhaps ultimately well beyond human general intelligence). While this was the original goal of Artificial Intelligence (AI), the mainstream of AI research has turned toward domain-dependent and problem-specific solutions; therefore it has become necessary to use a new name to indicate research that still pursues the Grand AI Dream. Similar labels for this kind of research include Strong AI, Human-level AI, etc. Other AI researchers prefer the term of Synthetic Intelligence.

The research on AGI is interdisciplinary, focused on whole systems and includes scientific and philosophical investigation and software engineering.

Artificial General Intelligence Research Institute

The term AGI was first used by Mark Avrum Gubrud in November 1997. Fifty years after the launch of the Artificial Intelligence Project in Dartmouth in 1956, Ben Goertzel, Phil Goetz, Pei Wang and Bruce Klein organized the first Artificial General Intelligence Research Institute (AGIRI) workshop in May 2006 to bridge the gap between narrow AI and general-purpose AI. The AGI Research Institute was founded in 2001 with the mission to foster the creation of powerful and ethically positive Artificial General Intelligence. The institute is sponsored by Novamente LLC.

The aspects of Artificial General Intelligence are explained by Pei Wang and Ben Goertzel  in the introduction of their book Advances in Artificial General Intelligence (IOS Press, 2007).

The first conference on Artificial General Intelligence (AGI-08) was organized by AGIRI in March 2008 in Memphis, Tennessee, USA, in association with the Association for the Advancement of Artificial Intelligence (AAAI).

Artificial General Intelligence Society

Ben Goertzel, Pei Wang, Joscha Bach and others founded in September 2011 the Artificial General Intelligence Society (AGI society), a nonprofit organization with the following goals:

  • promote the study of artificial general intelligence (AGI), and the design of AGI systems
  • facilitate co-operation and communication among those interested in the study and pursuit of AGI
  • hold conferences and meetings for the communication of knowledge concerning AGI
  • produce publications regarding AGI research and development
  • publicize and disseminate by other means knowledge and views concerning AGI

The organization of the annual Artificial General Intelligence conference series, which was started in 2008 by AGIRI, has been taken over by the AGI society. The next conference (AGI-2013) will be held in Beijing, China, July 31 – August 3, 2013.

Some additional informations about AGI are available at the following links :

More links are provided in the updated post about Artificial Intelligence.

A look inside mice brains

A team of researchers at the Stanford University, lead by Mark Schnitzer, an associate professor of biology and applied physics, planted tiny probes inside mice brains to detect what were essentially mouse memories. The study was published February 10, 2013, in the online edition of Nature Neuroscience.

inside mice brains

Read a mouse’s mind

The experiment involved the insertion of a needlelike microscope into the hippocampus of the mice brains. The microscope detected cellular activity and broadcast digital images through a cell phone camera sensor that fit like a hat over the heads of the critters as they were running around. Over the course of a month, the scientists were able to document patterns of activity in about 1000 neurons of the mice brains where they store long-term information. To get the results, an engineered gene was injected into the mice brains so that their proteins were sensitive to calcium ions. That caused the magnified cells to light up on the computer screen in flashes of green fluorescence when the neurons were activated.

Three students, who worked on the project, have formed a startup company called Inscopix, and they plan to sell the technology to neuroscience researchers.

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More informations are available at the news website of Stanford University.

Synthetic Biology

Synthetic biology is the design and construction of new biological parts, devices, and systems, and the re-design of existing, natural biological systems for useful purposes. It combines biology and engineering with a focus on Biotechnology.

Synthetic biologists focus on finding how life works (the origin of life) or how to use it to benefit society, including the approach of biology by inserting man-made DNA into a living cell and the approach of chemistry by working on gene synthesis as an extension of synthetic chemistry.

The website syntheticbiology.org, originally started by a group of students, faculty and staff from MIT and Harvard, now regroups all individuals, groups and labs from various institutions who are committed to engineering biology in an open and ethical manner. The site is hosted on OpenWetWare and can be edited by all members of the Synthetic Biology community.

An exciting synthetic biology project was recently funded succesfully on Kickstarter : Glowing Plants: Natural Lighting with no Electricity. A few days ago, without explanation, Kickstarter quietly altered its guidelines for project creators, introducing a new term that bans creators from giving away genetically-modified organisms (GMOs) as rewards to their online backers (see the post Kickstarter bans project creators from giving away genetically-modified organisms edited by Duncan Geere at The Verge website).

More informations about synthetic biology are available at the following links :

Kickstarter projects

Last update : October 6, 2018

Kickstarter is a new way to fund creative projects. It’s a crowdfunding platform for everything from films, games, and music to art, design, and technology. Since the launch in 2009, more than 12 million people have pledged over 2.8 Billion dollars, funding more than 118.000 creative projects. Project creators set a funding goal and a deadline. If people like a project, they can pledge money to make it happen. Funding on Kickstarter is all-or-nothing : projects must reach their funding goals to receive any money. To date, 36% of projects have reached their funding goals. Backers are supporting projects to help them come to life, not to profit financially. Instead, project creators offer rewards to thank backers for their support.

A Kickstarter app for mobiles is available at the AppStore.

I am a backer for the following projects :

Kickstarter Account Page

Kickstarter Account Page with backed projects

Here is a list of further projects which I consider very interesting :

Links

Supertoy Teddy and Huggable

Supertoy Teddy

Supertoy Teddy

Supertoy Teddy is the world’s first talking teddy with a mind of its own and the ability to hold real conversations with those who speak to it. It has been developed by Ashley Conlan (CEO of Supertoy Robotics) and Kartsen Fluegge (CEO of Pannous GmbH), the creators of the successful app Jeannie, the Siri style chatbot that has been downloaded over 3 million times on mobile devices.

Supertoy Teddy uses artificial intelligence (AI). A smartphone acts as its brawn and the internet server as its brain. Supertoy Teddy’s robotic mouth moves in synchronization to what it says and inbuilt speakers enhance the volume of its voice. Role play will be added to the Supertoy Teddy and several costumes and dresses will be sold at the online shop.

The robot’s hardware is simple: just an audio in/out interface and a motor for mouth animation. Supertoy Teddy connects via standard audio plug to an iOS or Android device. Asley Conlan suggests putting the phone inside the Supertoy for realism. The magic is in the software, which has evolved from the popular Jeannie chatbot app.

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The creators of Supertoy Teddy have started a Kickstarter campaign for crowdfunding during the funding period July 24, 2013 – August 23, 2013. I am one of the bakers of the project.

Huggable (MIT)

Huggable (MIT)

Huggable is a similar type of robotic companion that has being developed at the MIT Media Lab (Personal Robots Group) for healthcare, education, and social communication applications a few years ago. The early technical development of the Huggable was supported in part by a Microsoft iCampus grant in 2006.

Crowdfunding and crowdsourcing

Last update : September 24, 2013

Crowdfunding is the application of the Crowdsourcing concept to the collection of funds through small contributions from many parties in order to finance a particular project or venture. Crowdsourcing is the practice of obtaining needed services, ideas, or content by soliciting contributions from a large group of people, and especially from an online community, rather than from traditional employees or suppliers.

The First AAAI Conference on Human Computation and Crowdsourcing will be held November 7-9, 2013 in Palm Springs, California, USA.

Crowdfunding is alternately called crowd financing, equity crowdfunding or crowd-sourced fundraising.

An early precursor of the crowdfunding business model was Praenumeration, a common business practice in the 18th century book trade in Germany.

Crowdfunding is not only used to fund a startup company (equity-based crowdfunding), but also to create artworks such as music, theater, dance, films, literature and technology.

Crowdfunding platforms bring together the project initiator and the crowd. They create the necessary organizational systems and conditions for resource integration among all the players to take place. There are over 450 crowdfunding platforms with fundamental differences in the services provided. A comparison of crowd funding services is available at Wikipedia.

Some examples of crowdfunding platforms are listed below :

Since soliciting investments from the general public is often illegal in most countries, unless the opportunity has been filed with an appropriate securities regulatory authority, traditional crowdfunding platforms treat funds as donations. In the U.S. the crowdfunding exemption movement has been successful in 2012 with the passage of the Jumpstart Our Business Startups Act or JOBS Act,  a law intended to encourage funding of small businesses by easing various securities regulations.

In the past capital for startup companies has mainly been provided by business angels (also known as angel investors), in exchange for convertible debt or ownership equity. An increasing number of angel investors organize themselves into angel groups or angel networks to share research and pool their investment capital, as well as to provide advice to their portfolio companies.

Some angel networks in Luxembourg and the Greater Region are listed hereafter :

  • Luxembourg Business Angel Network (LBAN)
  • Seed4Start
  • EBAN (pan-European representative for the early stage investor community)

Here are some links to selected crowdfunding projects :