Tag Archives: viruses

Reading a virus like a book

Teaching grammar and syntax to artificial intelligence (AI) algorithms (specifically natural language processing (NLP) algorithms) has helped researchers understand and predict viral mutations more speedily. This facility is especially useful at a time when the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus seems to be mutating into more easily transmissible variants.

Will Douglas Heaven’s Jan. 14, 2021 article for the Massachusetts Institute of Technology’s MIT Technology Review describes the work that links AI, grammar, and mutating viruses (Note: Links have been removed),

Galileo once observed that nature is written in math. Biology might be written in words. Natural-language processing (NLP) algorithms are now able to generate protein sequences and predict virus mutations, including key changes that help the coronavirus evade the immune system.

The key insight making this possible is that many properties of biological systems can be interpreted in terms of words and sentences. “We’re learning the language of evolution,” says Bonnie Berger, a computational biologist at the Massachusetts Institute of Technology [MIT].

In the last few years, a handful of researchers—including teams from geneticist George Church’s [Professor of Health Sciences and Technology at Harvard University and MIT, etc.] lab and Salesforce [emphasis mine]—have shown that protein sequences and genetic codes can be modeled using NLP techniques.

In a study published in Science today, Berger and her colleagues pull several of these strands together and use NLP to predict mutations that allow viruses to avoid being detected by antibodies in the human immune system, a process known as viral immune escape. The basic idea is that the interpretation of a virus by an immune system is analogous to the interpretation of a sentence by a human.

Berger’s team uses two different linguistic concepts: grammar and semantics (or meaning). The genetic or evolutionary fitness of a virus—characteristics such as how good it is at infecting a host—can be interpreted in terms of grammatical correctness. A successful, infectious virus is grammatically correct; an unsuccessful one is not.

Similarly, mutations of a virus can be interpreted in terms of semantics. Mutations that make a virus appear different to things in its environment—such as changes in its surface proteins that make it invisible to certain antibodies—have altered its meaning. Viruses with different mutations can have different meanings, and a virus with a different meaning may need different antibodies to read it.

Instead of millions of sentences, they trained the NLP model on thousands of genetic sequences taken from three different viruses: 45,000 unique sequences for a strain of influenza, 60,000 for a strain of HIV, and between 3,000 and 4,000 for a strain of Sars-Cov-2, the virus that causes covid-19. “There’s less data for the coronavirus because there’s been less surveillance,” says Brian Hie, a graduate student at MIT, who built the models.

The overall aim of the approach is to identify mutations that might let a virus escape an immune system without making it less infectious—that is, mutations that change a virus’s meaning without making it grammatically incorrect.

But it’s also just the beginning. Treating genetic mutations as changes in meaning could be applied in different ways across biology. “A good analogy can go a long way,” says Bryson [Bryan Bryson, a biologist at MIT].

If you have time, I recommend reading Heaven’s Jan. 14, 2021 article in its entirety as it’s well written with clear explanations. As for the article’s mentions of George Church and Salesforce, the former could be expected while the latter is not (by me, I speak for no one else).

I find it fascinating that a company which describes itself (from What is Salesforce?) as providing “… customer relationship management, or CRM. It gives all your departments — including marketing, sales, commerce, and service — a shared view of your customers … ” seems to be conducting investigations into one (or more?) areas of biology.

For those who’d like to dive into the science as described in Heaven’s article, here’s a link to and a citation for the paper,

Learning the language of viral evolution and escape by Brian Hie, Ellen D. Zhong, Bonnie Berger, Bryan Bryson. Science 15 Jan 2021: Vol. 371, Issue 6526, pp. 284-288 DOI: 10.1126/science.abd7331

This paper appears to be open access (or it is, at least for now).

There is also a preprint version available on bioRxiv, which is an open access repository.

Non-viral ocular gene therapy with gold nanoparticles and femtosecond lasers

I love the stylistic choice the writer made (pay special attention to the second paragraph) when producing this November 19, 2018 Polytechnique Montréal news release (also on EurekAlert),

A scientific breakthrough by Professor Michel Meunier of Polytechnique Montréal and his collaborators offers hope for people with glaucoma, retinitis or macular degeneration.

In January 2009, the life of engineer Michel Meunier, a professor at Polytechnique Montréal, changed dramatically. Like others, he had observed that the extremely short pulse of a femtosecond laser (0.000000000000001 second) could make nanometre-sized holes appear in silicon when it was covered by gold nanoparticles. But this researcher, recognized internationally for his skills in laser and nanotechnology, decided to go a step further with what was then just a laboratory curiosity. He wondered if it was possible to go from silicon to living matter, from inorganic to organic. Could the gold nanoparticles and the femtosecond laser, this “light scalpel,” reproduce the same phenomenon with living cells?

A very pretty image illustrating the work,

Caption: Gold nanoparticles, which act like “nanolenses,” concentrate the energy produced by the extremely short pulse of a femtosecond laser to create a nanoscale incision on the surface of the eye’s retina cells. This technology, which preserves cell integrity, can be used to effectively inject drugs or genes into specific areas of the eye, offering new hope to people with glaucoma, retinitis or macular degeneration. Credit and Copyright: Polytechnique Montréal

The news release goes on to describe the technology in more detail,

Professor Meunier started working on cells in vitro in his Polytechnique laboratory. The challenge was to make a nanometric incision in the cells’ extracellular membrane without damaging it. Using gold nanoparticles that acted as “nanolenses,” Professor Meunier realized that it was possible to concentrate the light energy coming from the laser at a wavelength of 800 nanometres. Since there is very little energy absorption by the cells at this wavelength, their integrity is preserved. Mission accomplished!

Based on this finding, Professor Meunier decided to work on cells in vivo, cells that are part of a complex living cell structure, such as the eye for example.

The eye and the light scalpel

In April 2012, Professor Meunier met Przemyslaw Sapieha, an internationally renowned eye specialist, particularly recognized for his work on the retina. “Mike”, as he goes by, is a professor in the Department of Ophthalmology at Université de Montréal and a researcher at Centre intégré universitaire de santé et de services sociaux (CIUSSS) de l’Est-de-l’Île-de-Montréal. He immediately saw the potential of this new technology and everything that could be done in the eye if you could block the ripple effect that occurs following a trigger that leads to glaucoma or macular degeneration, for example, by injecting drugs, proteins or even genes.

Using a femtosecond laser to treat the eye–a highly specialized and fragile organ–is very complex, however. The eye is part of the central nervous system, and therefore many of the cells or families of cells that compose it are neurons. And when a neuron dies, it does not regenerate like other cells do. Mike Sapieha’s first task was therefore to ensure that a femtosecond laser could be used on one or several neurons without affecting them. This is what is referred to as “proof of concept.”

Proof of concept

Mike and Michel called on biochemistry researcher Ariel Wilson, an expert in eye structures and vision mechanisms, as well as Professor Santiago Costantino and his team from the Department of Ophthalmology at Université de Montréal and the CIUSSS de l’Est-de-l’Île-de-Montréal for their expertise in biophotonics. The team first decided to work on healthy cells, because they are better understood than sick cells. They injected gold nanoparticles combined with antibodies to target specific neuronal cells in the eye, and then waited for the nanoparticles to settle around the various neurons or families of neurons, such as the retina. Following the bright flash generated by the femtosecond laser, the expected phenomenon occurred: small holes appeared in the cells of the eye’s retina, making it possible to effectively inject drugs or genes in specific areas of the eye. It was another victory for Michel Meunier and his collaborators, with these conclusive results now opening the path to new treatments.

The key feature of the technology developed by the researchers from Polytechnique and CIUSSS de l’Est-de-l’Île-de-Montréal is its extreme precision. With the use of functionalized gold nanoparticles, the light scalpel makes it possible to precisely locate the family of cells where the doctor will have to intervene.

Having successfully demonstrated proof of concept, Professor Meunier and his team filed a patent application in the United States. This tremendous work was also the subject of a paper reviewed by an impressive reading committee and published in the renowned journal Nano Letters in October 2018.

While there is still a lot of research to be done–at least 10 years’ worth, first on animals and then on humans–this technology could make all the difference in an aging population suffering from eye deterioration for which there are still no effective long-term treatments. It also has the advantage of avoiding the use of viruses commonly employed in gene therapy. These researchers are looking at applications of this technology in all eye diseases, but more particularly in glaucoma, retinitis and macular degeneration.

This light scalpel is unprecedented.

Here’s a link to and a citation for the paper,

In Vivo Laser-Mediated Retinal Ganglion Cell Optoporation Using KV1.1 Conjugated Gold Nanoparticles by Ariel M. Wilson, Javier Mazzaferri, Éric Bergeron, Sergiy Patskovsky, Paule Marcoux-Valiquette, Santiago Costantino, Przemyslaw Sapieha, Michel Meunier. Nano Lett.201818116981-6988 DOI: https://doi.org/10.1021/acs.nanolett.8b02896 Publication Date: October 4, 2018  Copyright © 2018 American Chemical Society

This paper is behind a paywall.

Removing viruses from water with a ‘mille-feuille’ filter

Mille-feuille is a pastry and it’s name translates to ‘a thousand leaves’, which hints at how a ‘mille-feuille’ nanofilter is constructed. From a May 18, 2016 news item on Nanowerk,

A simple paper sheet made by scientists at Uppsala University can improve the quality of life for millions of people by removing resistant viruses from water. The sheet, made of cellulose nanofibers, is called the mille-feuille filter as it has a unique layered internal architecture resembling that of the French puff pastry mille-feuille (Eng. thousand leaves).

Caption: The sheet made of cellulose nanofibers in the mille-feuille filter which can remove resistant viruses from water. Research led by Albert Mihranyan, Professor of Nanotechnology at Uppsala University, Image by Simon Gustafsson. Credit: Simon Gustafsson

Caption: The sheet made of cellulose nanofibers in the mille-feuille filter which can remove resistant viruses from water. Research led by Albert Mihranyan, Professor of Nanotechnology at Uppsala University, Image by Simon Gustafsson. Credit: Simon Gustafsson

A May 18, 2016 Uppsala University (Sweden) press release on EurekAlert, which originated the news item, expands on the theme,

With a filter material directly from nature, and by using simple production methods, we believe that our filter paper can become the affordable global water filtration solution and help save lives. Our goal is to develop a filter paper that can remove even the toughest viruses from water as easily as brewing coffee’, says Albert Mihranyan, Professor of Nanotechnology at Uppsala University, who heads the study.

Access to safe drinking water is among the UN’s Sustainable Development Goals. More than 748 million people lack access to safe drinking water and basic sanitation. Water-borne infections are among the global causes for mortality, especially in children under age of five, and viruses are among the most notorious water-borne infectious microorganisms. They can be both extremely resistant to disinfection and difficult to remove by filtration due to their small size.

Today we heavily rely on chemical disinfectants, such as chlorine, which may produce toxic by-products depending on water quality. Filtration is a very effective, robust, energy-efficient, and inert method of producing drinking water as it physically removes the microorganisms from water rather than inactivates them. But the high price of efficient filters is limiting their use today.

‘Safe drinking water is a problem not only in the low-income countries. Massive viral outbreaks have also occurred in Europe in the past, including Sweden, continues Mihranyan referring to the massive viral outbreak in Lilla Edet municipality in Sweden in 2008, when more than 2400 people or almost 20% of the local population got infected with Norovirus due to poor water. ‘ Cellulose is one of the most common filtering media used in daily life from tea-bags to vacuum cleaners. However, the general-purpose filter paper has too large pores to remove viruses. In 2014, the group has described for the first time a paper filter that can remove large size viruses, such as influenza virus.

Small size viruses have been much harder to get rid of, as they are extremely resistant to physical and chemical inactivation. A successful filter should not only remove viruses but also feature high flow, low fouling, and long life-time, which makes advanced filters very expensive to develop. Now, with the breakthrough achieved using the mille-feuille filter the long awaited shift to affordable advanced filtration solutions may at last become a reality. Another application of the filter includes production of therapeutic proteins and vaccines.

Here’s a link to and a citation for the paper,

Mille-feuille paper: a novel type of filter architecture for advanced virus separation applications by Simon Gustafsson, Pascal Lordat, Tobias Hanrieder, Marcel Asper,  Oliver Schaeferb, and Albert Mihranyan, Mater. Horiz., 2016, Advance Article DOI: 10.1039/C6MH00090H First published online 18 May 2016

This paper is behind a paywall.

Nanotechnology-enabled cleansers in Turkish baths

This item about Turkish baths came to me via Chinese news agency Xinhua. In a March 10, 2016 news item on ShanghaiDaily.com,

It is very common to take a bath, yet it is quite a different experience to bathe in Istanbul’s famed hamams, or bath houses.

Bathing in a hamam is similar to that of a sauna, but is more closely related to ancient Greek and ancient Roman bathing practices, and it involves services like washing, aromatherapy oil massage, reflexology, Indian head massage and facial clay mask.

Both tourists and local Turks alike are fans of Turkish baths, said Banu Cagdas, the owner of Cagaloglu.

As customers are flocking and their number growing, hygiene appears to be the most important issue for Turkish baths.

“Visually there is nothing,” said Cagdas. “It looks like every corner is clean and no one can see the germs and viruses with the naked eye.”

Generally, Turkish baths have been using the traditional ways to maintain the state of hygiene, like bleach.

“The sterilization with bleach, especially a long-lasting sterilization, is very difficult to achieve,” Cagdas said, noting that after two hours of the cleaning, micro-organisms and bacteria start to reproduce again due to the warm and humid environment.

Fungal infections are among the most common diseases in Turkish baths. “Then comes all kind of genital diseases,” said Cagdas.

The team is turning to a cleaning agent developed by Turkish engineers from Sabanci University in Istanbul. The product, the result of five-year efforts based on nanotechnology, is called Antimics.

Antimics can stunt the production of germs, viruses, bacteria and fungi.

“We have been applying the solution to Cagaloglu bath once a month and we observe the rate of bacterium has been dropping each time even further,” Menceoglu told Xinhua.

She explained that Antimics enables the bath’s surface to be covered with a tiny antimicrobial coating and “no single microbe, virus or bacterium can hold on to after the application.”

“Every time we do the cleaning we witness that the bacteria level has been dropping drastically,” she said.

In addition, the eco-friendly new product is not harmful to humans, as opposed to the traditional disinfectant detergents that contain chemicals.

It is possible to get more information about the product (Antimic Nanotego Facebook page and on antimic.com) but you do need Turkish language reading skills.

Touchless displays with 2D nanosheets and sweat

Swiping touchscreens with your finger has become a dominant means of accessing information in many applications but there is at least one problem associated with this action. From an Oct. 2, 2015 news item on phys.org,

While touchscreens are practical, touchless displays would be even more so. That’s because, despite touchscreens having enabled the smartphone’s advance into our lives and being essential for us to be able to use cash dispensers or ticket machines, they do have certain disadvantages. Touchscreens suffer from mechanical wear over time and are a transmission path for bacteria and viruses. To avoid these problems, scientists at Stuttgart’s Max Planck Institute for Solid State Research and LMU Munich have now developed nanostructures that change their electrical and even their optical properties as soon as a finger comes anywhere near them.

Here’s what a touchless screen looks like when tracking,

Touchless colour change: A nanostructure containing alternating layers of phosphatoantimonate nanosheets and oxide ... [more] © Advanced Materials 2015/MPI for Solid State Research

Touchless colour change: A nanostructure containing alternating layers of phosphatoantimonate nanosheets and oxide … [more]
© Advanced Materials 2015/MPI for Solid State Research

An Oct. 1, 2015 Max Planck Institute press release, which originated the news item, gives technical details,

A touchless display may be able to capitalize on a human trait which is of vital importance, although sometimes unwanted: This is the fact that our body sweats – and is constantly emitting water molecules through tiny pores in the skin. Scientists of the Nanochemistry group led by Bettina Lotsch at the Max Planck Institute for Solid State Research in Stuttgart and the LMU Munich have now been able to visualize the transpiration of a finger with a special moisture sensor which reacts as soon as an object – like an index finger – approaches its surface, without touching it. The increasing humidity is converted into an electrical signal or translated into a colour change, thus enabling it to be measured.

Phosphatoantimonic acid is what enables it to do this. This acid is a crystalline solid at room temperature with a structure made up of antimony, phosphorous, oxygen and hydrogen atoms. “It’s long been known to scientists that this material is able to take up water and swells considerably in the process,” explained Pirmin Ganter, doctoral student at the Max Planck Institute for Solid State Research and the Chemistry Department at LMU Munich. This water uptake also changes the properties of the material. For instance, its electrical conductivity increases as the number of stored water molecules rises. This is what enables it to serve as a measure of ambient moisture.

A sandwich nanomaterial structure exposed to moisture also changes its colour

However, the scientists aren’t so interested in developing a new moisture sensor. What they really want is to use it in touchless displays. “Because these sensors react in a very local manner to any increase in moisture, it is quite conceivable that this sort of material with moisture-dependent properties could also be used for touchless displays and monitors,” said Ganter. Touchless screens of this kind would require nothing more than a finger to get near the display to change their electrical or optical properties – and with them the input signal – at a specific point on the display.

Taking phosphatoantimonate nanosheets as their basis, the Stuttgart scientists then developed a photonic nanostructure which reacts to the moisture by changing colour. “If this was built into a monitor, the users would then receive visible feedback to  their finger motion” explained Katalin Szendrei, also a doctoral student in Bettina Lotsch’s group. To this end, the scientists created a multilayer sandwich material with alternating layers of ultrathin phosphatoantimonate nanosheets and silicon dioxide (SiO2) or titanium dioxide nanoparticles (TiO2). Comprising more than ten layers, the stack ultimately reached a height of little more than one millionth of a metre.

For one thing, the colour of the sandwich material can be set via the thickness of the layers. And for another, the colour of the sandwich changes if the scientists increase the relative humidity in the immediate surroundings of the material, for instance by moving a finger towards the screen. “The reason for this lies in the storage of water molecules between the phosphatoantimonate layers, which makes the layers swell considerably,” explained Katalin Szendrei. “A change in the thickness of the layers in this process is accompanied by a change in the colour of the sensor – produced in a similar way to what gives colour to a butterfly wing or in mother-of-pearl.”

The material reacts to the humidity change within a few milliseconds

This is a property that is fundamentally well known and characteristic of so-called photonic crystals. But scientists had never before observed such a large colour change as they now have in the lab in Stuttgart. “The colour of the nanostructure turns from blue to red when a finger gets near, for example. In this way, the colour can be tuned through the whole of the visible spectrum depending on the amount of water vapour taken up,” stressed Bettina Lotsch.

The scientists’ new approach is not only captivating because of the striking colour change. What’s also important is the fact that the material reacts to the change in humidity within a few milliseconds – literally in the blink of an eye. Previously reported materials normally took several seconds or more to respond. That is much too slow for practical applications. And there’s another thing that other materials couldn’t always do: The sandwich structure consisting of phosphatoantimonate nanosheets and oxide nanoparticles is highly stable from a chemical perspective and responds selectively to water vapour.

A layer protecting against chemical influences has to let moisture through

The scientists can imagine their materials being used in much more than just future generations of smartphones, tablets or notebooks. “Ultimately, we could see touchless displays also being deployed in many places where people currently have to touch monitors to navigate,” said Bettina Lotsch. For instance in cash dispensers or ticket machines, or even at the weighing scales in the supermarket’s vegetable aisle. Displays in public placesthat are used by many different people would have distinct hygiene benefits if they were touchless.

But before we see them being used in such places, the scientists have a few more challenges to overcome. It’s important, for example, that the nanostructures can be produced economically. To minimize wear, the structures still need to be coated with a protective layer if they’re going to be used in anything like a display. And that, again, has to meet not one but two different requirements: It must protect the moisture-sensitive layers against chemical and mechanical influences. And it must, of course, let the moisture pass through. But the Stuttgart scientists have an idea for how to achieve that already. An idea they are currently starting to put into practice with an additional cooperation partner on board.

Dexter Johnson’s Oct. 2, 2015 posting on his Nanoclast blog (on the IEEE [Institute of Electrical and Electronics Engineers] website) provides some additional context for this research (Note: A link has been removed),

In a world where the “swipe” has become a dominant computer interface method along with moving and clicking the mouse, the question becomes what’s next? For researchers at Stuttgart’s Max Planck Institute for Solid State Research and LMU Munich, Germany, the answer continues to be a swipe, but one in which you don’t actually need to touch the screen with your finger. Researchers call these no-contact computer screens touchless positioning interfaces (TPI).

Here’s a link to and a citation for the paper,

Touchless Optical Finger Motion Tracking Based on 2D Nanosheets with Giant Moisture Responsiveness by Katalin Szendrei, Pirmin Ganter, Olalla Sànchez-Sobrado, Roland Eger, Alexander Kuhn, and Bettina V. Lotsch. Advanced Materials DOI: 10.1002/adma.201503463 Article first published online: 22 SEP 2015

© 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

Protein cages, viruses, and nanoparticles

The Dec. 19, 2012 news release on EurekAlert about a study published by researchers at Aalto University (Finland) describes a project where virus particles are combined with nanoparticles to create new metamaterials,

Scientists from Aalto University, Finland, have succeeded in organising virus particles, protein cages and nanoparticles into crystalline materials. These nanomaterials studied by the Finnish research group are important for applications in sensing, optics, electronics and drug delivery.

… biohybrid superlattices of nanoparticles and proteins would allow the best features of both particle types to be combined. They would comprise the versatility of synthetic nanoparticles and the highly controlled assembly properties of biomolecules.

The gold nanoparticles and viruses adopt a special kind of crystal structure. It does not correspond to any known atomic or molecular crystal structure and it has previously not been observed with nano-sized particles.

Virus particles – the old foes of mankind – can do much more than infect living organisms. Evolution has rendered them with the capability of highly controlled self-assembly properties. Ultimately, by utilising their building blocks we can bring multiple functions to hybrid materials that consist of both living and synthetic matter, Kostiainen [Mauri A. Kostiainen, postdoctoral researcher] trusts.

The article which has been published in Nature Nanotechnology is free,

Electrostatic assembly of binary nanoparticle superlattices using protein cages by Mauri A. Kostiainen, Panu Hiekkataipale, Ari Laiho, Vincent Lemieux, Jani Seitsonen, Janne Ruokolainen & Pierpaolo Ceci in Nature Nanotechnology (2012) doi:10.1038/nnano.2012.220  Published online 16 December 2012

There’s a video demonstrating the assembly,

From the YouTube page, here’s a description of what the video is demonstrating,

Aalto University-led research group shows that CCMV virus or ferritin protein cages can be used to guide the assembly of RNA molecules or iron oxide nanoparticles into three-dimensional binary superlattices. The lattices are formed through tuneable electrostatic interactions with charged gold nanoparticles.

Bravo and thank  you to  Kostiainen who seems to have written the news release and prepared all of the additional materials (image and video). There are university press offices that could take lessons from Kostiainen’s efforts to communicate about the work.

Black Rooster and nanotechnology

The entertainment industry seems to be using nanotechnology as a ready-to-hand narrative device (as per my NEW-GEN Oct. 17, 2011 posting and my Deus Ex: Human Revolution Aug. 18, 2011 posting, amongst others). The latest offering is Patient Zero from Black Rooster Creations. From the Oct. 18, 2011 media release on PRWeb,

Black Rooster Creations has launched its website with a viral campaign and three major book releases written by screenwriter Jim Beck featuring zombies, superheroes, and yes, even bugs.

The first release, Patient Zero, serves as a cautionary tale that mixes old school zombies with new school technology. Narrated by the zombie virus itself, the story follows single father Robert Forrester, who is brought back to life as one of the living dead after a botched experiment involving nanotechnology. [emphasis mine] His transformation is slow, first appearing as a skin rash and advanced arthritis, and he quickly begins to lose control.

Beck stated, “The idea for Patient Zero came to me after ingesting numerous forms of zombie lore and realizing that many of them shared the same basic formula of an unexplained outbreak, followed by a group of people trying to survive. I wanted to tell a more personal story about a single father trying to protect his son and defend their home while coming to grips with his own transformation. I also liked the contrast between zombification and nanotechnology, and telling the story from the point of view of the virus will provide readers with an insight rarely seen in the world of zombies.”

I could be wrong here but I don’t have the impression that this work is well grounded in science still, that doesn’t mean that it won’t be fun. You can go to the Black Rooster Creations website to get more information.

Viruses as manufacturing plants

In her January 2011 TEDx talk at Caltech (California Institute of Technology), MIT (Massachusetts Institute of Technology) Professor Angela Belcher talks about using viruses to grow batteries that don’t require toxic materials for their production or produce toxic materials themselves. It’s similar to biomimicry in that the reference point is nature but rather than trying to simulate nature using synthetic materials this work focuses on tweaking nature so that something like a virus can be used to create something new, e.g., a battery, a solar cell, etc.

 

A Sept. 25, 2011 article by Karen Weintraub on the BBC News website offers further insight into Belcher’s work,

Prof Belcher’s work unites the inanimate world of simple chemicals with proteins made by living creatures, a mash-up of the living and the lifeless.

She is motivated, she says, by a simple question: “How do you give life to non-living things?”

Like the abalone collecting its materials in shallow water and then laying them down like bricks in a wall, Belcher takes basic chemical elements from the natural world: carbon, calcium, silicon, zinc. Then she mixes them with simple, harmless viruses whose genes have been reprogrammed to promote random variations.

The resulting new materials just might address some of our most vexing problems.

The distinctiveness of Prof Belcher’s work, colleagues say, lies in her use of biology to synthesise new materials for such a wide range of uses, to develop an entirely new method for producing entirely novel materials.

“Her methodologies for directing and assembling materials I think will be unique,” says Yet-Ming Chiang, an MIT professor who collaborates with Prof Belcher on battery research. “I think 50 years from now, we’ll look back on biology as an important part of the toolkit in manufacturing… we’ll look back and say this is one of the fundamental tools we developed in this century.”

As I’ve been thinking about life/nonlife (in the context of human enhancement and memristors), this works offers me additional food for thought. Meanwhile, the TEDx talk and the Weintraub article point to some of the vast difference between scientists and lay people (general public). Belcher references life/nonlife quite casually, almost in passing. This could be quite disturbing to folks who believe there’s a distinct difference. The disturbances don’t stop there.

In the first place, viruses do not have a good reputation. When you add in the problems with calling your work biotechnology (as Belcher does in her TEDx talk), the stage is set for some interesting possibilities. If that isn’t enough, Belcher’s work comes perilously close to Eric Drexler’s self-assembling nano entities and the spectre of ‘grey’ or ‘green’ goo. It’s been a while since the big scares over genetically modified organisms (GMO), I wonder if scientists have forgotten or perhaps they don’t realize just how much conflicting (and often frightening) information is still being pushed at the general public. As for breaching the life/nonlife boundaries, that could be a whole other mess.

Viruses mine for copper at the University of BC; microscopy at the University of Victoria; the Henry Louis Gates Jr. affair, human nature, & human enhancement

Professor Scott Dunbar at the University of British Columbia’s (Canada) Norman B. Keevil Institute of Mining Engineering needed to partner with colleagues Sue Curtis and Ross MacGillivray from the Centre for Blood Research and the Department of Biochemistry and Molecular Biology after (from the media release on Nanowerk News),

“I read an article about bacteriophage – viruses that infect bacteria – being used to create nanodevices in which proteins on the phage surface are engineered to bind to gold and zinc sulfide,” says Dunbar. “And it struck me: if zinc sulfide, why not copper sulfide? And if so, then it might be possible to use these bio-engineered proteins to separate common economic sulfide minerals from waste during mineral extraction.”

Together the researchers have developed a procedure called “biopanning.” It’s a kind of genetic engineering which could lead to some useful applications.

It turns out that the phage that bind to a mineral do affect the mineral surfaces, causing them to have a different electrical charge than other minerals. The proteins on the phage also form links to each other leading to aggregation of the specific sulfide particles. “The physical and chemical changes caused by phage may be the basis for a highly selective method of mineral separation with better recovery. Another possible application is bioremediation, where metals are removed from contaminated water” says Dunbar.

In other BC news, the University of Victoria (Canada) will be getting a new microscope which senses at subatomic levels. (From the media release on Azonano),

The new microscope-called a Scanning Transmission Electron Holography Microscope (STEHM) — will use an electron beam and holography techniques to observe the inside of materials and their surfaces to an expected resolution as small as one-fiftieth the size of an atom.

This is being done in collaboration with Hitachi High-Technologies which is building the microscope in Japan and installing it at U Vic in late 2010. The microscope will be located in a specially adapted room where work to prepare and calibrate it will continue until it becomes operational sometime in 2011.

After my recent series on robots and human enhancement, I feel moved to comment on the situation in the US vis a vis Henry Louis Gates, Jr. and his arrest by the police officer, James Crowley. It’s reported here and elsewhere that neither the recording of the 911 call nor the concerned neighbour who made the call support Sergeant Crowley’s contention that the two men allegedly breaking into the house were described as ‘black’.

Only the participants know what happened and I don’t fully understand the nuances of race, class, and cultural differences that exist in the US so I can’t comment on anything other than this. It is human to hear what we expect to hear and I have an example from a much less charged situation.

Many years ago, I was transcribing notes from a taped interview (one of my first) for an article that I was writing for a newsletter. As I was transcribing, I noticed that I kept changing words so that the interview subject sounded more like me. They were synonyms but they were my words not his. Over the years I’ve gotten much better at being more exact but I’ve never forgotten how easy it is to insert your pet words (biased or not) when you’re remembering what someone said. Note: I was not in a stressful situation and I could rewind and listen again at my leisure.

I hope that Crowley and Gates, Jr. are able to work this out in some fashion and I really hope that it is done in a way that is respectful to both men and not a rush to a false resolution for the benefit of the cameras. For a more informed discussion of the situation, you may find this essay by Richard Thompson Ford  in Slate helpful. It was written before the recording of the 911 call was made public but I think it still stands.

My reason for mentioning this incident is that human nature tends to assert itself in all kinds of situations including the building of robots and the debates on human enhancement, something I did not mention in my series posted (July 22 – 24, 27, 2009).