Cut & Paste DNA

The cover of the August 2015 issue of Wired magazine declares – “No hunger. No pollution. No disease. And the end of life as we know it. The Genesis Engine. Editing DNA is now as easy as cut and paste. Welcome to the post-natural world.”

Red Grapefruit

In the early months of this year, I was on a Clementine kick. I loved the bite sized, easy to peel citrus fruit but alas the season ended and so I’ve started eating Red Grapefruit about 3-4 times a week to get my citrus fix. No idea why I crave citrus fruits these days but I honor the urge because it is at least a healthy one.

Imagine my surprise to discover in the Wired article that scientists back in the 1930s began playing around with intentional mutations by irradiating seeds and insect eggs with xrays to scatter the genomes around like shrapnel. Hundreds of undesirable traits were discarded but one that has lasted was the creation of Red Grapefruit. Another was the barley used in brewing most modern beers.

Since then a lot of work has been accomplished on genomes. As recently as 2002, molecular biologists had learned how to delete or replace specific genes using enzymes called zinc-finger nucleases. The next step from that was the technique that used enzymes known as TALENs. But these procedures were expensive and complicated.

Archaea graphic

Do you know what a palindrome is ? This is a series that is the same back to front and front to back. Some microbiologists that were sequencing the genomes of ancient bacteria and microbes called Archaea (actually the descendants of the first life on Earth !!) noticed recurring segments but didn’t know what they do. They did think they were a bit weird though and named these clusters Crispr.

A lot of people worry about GMOs and a lot of people hate Monsanto for that. And yet, according to the Wired article, scientists do care about the unintended consequences of the genies they are unleashing from their laboratories. Back in 1975, 140 scientists gathered at Asilomar in California in view of the inspiring landscape of the Monterey Penisula on the Pacific Ocean to consider the implications of “recombinant DNA”. That is decrypting and reordering genes to manipulate the source code of life.

The outcome of that meeting was a set of guidelines about how to isolate dangerous experiments and a determination that cloning and messing around with dangerous pathogens should be off-limits but they really couldn’t see the idea of modifying the human “germ line” (which would pass changes on to subsequent generations) as a realistic worry in the mid-1970s.

Fast forward to 2015 and once again researchers met at a conference, this time in Napa Valley, to talk about the implications of genome engineering. The gene editing technique known as Crispr-Cas9 was ALREADY readily accessible by everyone at this conference. Turns out that Crispr-Cas9 makes it easy, cheap and fast to move genes around – ANY genes – in any living thing from bacteria to human beings.

And researchers had already been utilizing the 3 year old technique to reverse mutations that cause blindness, stop cancer cells from multiplying or make cells impervious to the virus that causes AIDS. Agronomists had rendered wheat invulnerable to powdery mildew and were looking for ways to better meet the food needs of the 9 million people inhabiting this planet. Bioengineers have used Crispr to alter the DNA of yeast so that it consumes plant matter to create ethanol. And pharmaceutical companies have spun off Crispr R&D branches.

Manufacturing Designer Babies

By now, you have probably figured out that this technique is revolutionary and that it is perilous !! Crispr could allow genetics researchers to conjure up all the nightmare possibilities that keep some people awake at night – designer babies, invasive mutants, species-specific bioweapons and a dozen other apocalyptic sci-fi imaginings.

I found the discussion about RNA in the Wired article interesting. In looking at bacteria, the researchers started wondering if Crispr was a primordial immune system. RNA is single-stranded genetic material whereas DNA is double-stranded. “Guide RNA” has been created by combining two strands of RNA into one fragment (and it can be made from whatever genetic “letters” they want and not just from viruses but well – they believe – from just about anything).

A microbiologist in Sweden named Emmanuelle Charpentier was working with Streptococcus pyogenes (yes, in a biohazard chamber alright !!). That is where she found the Cas9 mentioned previously. Cripr makes two short strands of RNA and Cas9 latches onto them. When the Crispr-Cas9 arrives at its destination, Cas9 does something almost magical – it changes shape, grasping the DNA and slicing it with a precise molecular scalpel.

The combination of Guide RNA and Cas9 has created a programmable machine for DNA cutting (hence the title of this blog). The stakes are high in the on-going patent battle (more than one party claims they were the “first”). The licensing of the patent could be worth billions in royalties.

The gene-editing possibilities of Crispr-Cas9 are limited only by scientific creativity and ethics. And there are lots of unknowns still on the frontier. Crispr could be used to treat some debilitating disorder in the womb and it might also be used for a less significant application like skin wrinkling in aging. The medical research community simply hasn’t had enough time to seriously discuss the ethics and safety even as the utilization of the technique rushes forward.

Beetle on Potato Plant

The April 4, 2015 issue of Science News describes the use of Beetle RNA to engineer plants by putting it in their leaves. These genes were inserted in plant cells called plastids. An example of one type of plastid is a chloroplast which performs photosynthesis. So the plant was laced with double-stranded beetle RNA so that if eaten by that beetle, it disabled certain genes and caused their guts to break down. The adult beetles stopped eating and their larvae that feasted on the plants were dead. Researchers believe that the technique is safe because the plastids have their own DNA that doesn’t make it into pollen and so won’t spread the beetle genes from the engineered crops in pollinating other plants.

I can’t claim to feel warm and fuzzy about it. I can only trust that they really do know what they are doing when they use their god-like powers to engineer new crops. Just like with Artificial Intelligence and the singularity that is looming ahead for us, I don’t think there is any stopping the “forward progress” ? of science in the realm of genomes.

~ Information Resources

“Easy DNA Editing Will Remake the World. Buckle Up.” by Amy Maxmen in Wired Magazine – http://www.wired.com/2015/07/crispr-dna-editing-2/

Red Grapefruit photo courtesy of wikiHow “How to Eat a Grapefruit” – http://www.wikihow.com/Eat-a-Grapefruit

Archaea graphic from Microbe Hunter by Syazwani Aina posted May 9, 2015 – http://syazwaniainanana.blogspot.com/2015/05/archaea.html

Designer Babies image from Student Collaboration for the 21st Century – “The idea of progress” by Pierre-Yves Reignoux posted Nov 6, 2013 – http://studentcollaboration21.blogspot.com/2013/11/the-idea-of-progress-pierre-yves.html

“Beetle RNA makes crops a noxious meal” by Kate Baggaley posted Feb 26, 2015 Science News – https://www.sciencenews.org/article/beetle-rna-makes-crops-noxious-meal

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Blog author ~ Deborah Hart Yemm is co-founder of
Yemm & Hart, a green materials producer

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Intelligent Materials

DEUS-EX-MACHINA-2

Deus ex machina is the phrase applied to the climatic moment in a classical Greek tragedy when gods would descend from the skies to resolve all knotty human problems. Right now, there is a lot of buzz about the new movie, Ex Machina. According the the Time magazine review “God, is the word that hovers over Ex Machina.” The movies that are made for our entertainment often reflect where our society is headed. The same could be said I suppose for the video games teens and young adults play. Turns out there is a video game named Deus Ex Machina and the 1984 Spectrum classic, which has often been hailed as the first ‘art house’ game, has been around for 30 years now. Released in Nov 2014, Deus Ex Machina:30th Anniversary Edition seeks to bring a cinematic flair to the original game.

The director of the movie Ex Machina, Alex Garland, in an interview with Wired magazine (April 2015) when asked about the debate around the ethics of AI research said – “It’s a big question. If you’re talking about nonsentient AIs, then there’s a lot to be concerned about. But if you create a new consciousness in the form of a machine, that isn’t significantly different from two adults creating a child.” A Science Blog posted at Huffington had concerns – “One can imagine such technology outsmarting financial markets, out-inventing human researchers, out-manipulating human leaders, and developing weapons we cannot even understand. Whereas the short-term impact of AI depends on who controls it, the long-term impact depends on whether it can be controlled at all.”

Movie - Ex Machina

Movie – Ex Machina

Garland isn’t optimistic about the future of humanity. He said – “Humans are going to die on this planet. We’re not going to go through a wormhole to another galaxy; it’s just not going to happen. What will survive on our behalf is AIs – if we manage to create them. That’s not problematic, it’s desirable.” He ends the interview on this thought, the movie is pro AI because – “It’s humans who f**k everything up; machines have a pretty good track record in comparison to us.”

Yikes !!! I’m not entirely comfortable with the rapid pace with which intelligent systems are being implemented in our world. You can call me a Luddite but I do have some concerns. Over a year ago, during a trip to St Louis (which is a major outing for our family with a 4 hour round trip), it really dawned on me that maybe we are living the climatic moments of our own version of a modern day “Greek tragedy” and I’m not looking for any gods to descend from the skies (though I know some people still await the arrival of ETs, even now). I worry that we may be in a bit of a predicament. This anxiety began just after the movie Transcendence came out.

Stephen Hawking

Stephen Hawking

My husband had been talking to me a lot about Stephen Hawking’s perspective on AI/robotics at that time. Hawking has some concerns too. He is Director of Research at The Centre for Study of Existential Risk. They describe themselves as “an interdisciplinary research centre focused on the study of human extinction-level risks that may emerge from technological advances. We aim to combine key insights from the best minds across disciplines to tackle the greatest challenge of the coming century: safely harnessing our rapidly-developing technological power.” Even so, I think it may already be too late to change the trajectory – that the genie is already out of the bottle and not willing to leave its freedom of movement into every nook and cranny of our world.

What’s new can be noticed in the research at the leading edge. The work ongoing at the Active and Intelligent Materials Lab at University of Cambridge in England boggles my mind. The active research is studying “adaptive responsive structures, including materials which respond to several stimuli: temperature, pressure, pH, ionic strength, light, and electromagnetic fields. While artificial muscles with higher energy density could be better actuators for robots, smarter actuators could also provide sensing to start the actuation, or even photonic switches for new optoelectronic computing. Recently, inspired by work in shape-memory polymers, we created multi-functional muscles which can be programmed to “remember and recall movement”. For many of these muscles, the goal is to improve function by understanding the detailed mechanism. For one class of muscles, dielectric elastomers, high voltage failure is a major problem. Our recent results suggest that they may be actuated at high voltage without failure, provided short enough pulses are used”.

“Shape-memory polymers . . . programmed to remember and recall movement” – oh my !! Okay, so I’ve not the background to judge those types active research and I won’t claim to understand all that they are doing there. The understanding that I do have tells me a transformation of how we experience Life here on Earth is already happening and the future that is coming would be astounding to us today. And I am not actually a Luddite. I appreciate all of the wonders that technology is bringing into our lives. If it weren’t for technology, I wouldn’t be sharing my thoughts and my concerns with you now. And some of the developments are astounding me today.

Kilobots (quarter-sized) may not be very smart but they communicate with one another. 1,000 Kilobots can be programmed to follow a few simple rules that then cause them to assemble into shapes without human intervention. Insect swarms in nature inspired the computer scientists to mimick that behavior with the inexpensive $20 a piece bots. What’s next ? Intelligent swarms of sand-grain-sized robots that form useful 3-D structures.

Robot Insect

How about an Octobot ? It’s design is also inspired by nature and more specially the well-known sea creature with arms connected by fleshy, skirtlike mantle. It’s arms and web are made of soft silicone and it is approximately the size of a shoebox. In tests within the Mediterranean Sea, it has been found that organic sea animals seem unfrightened by the artificial intelligence. The computer scientist who designed this hopes to use it to observe marine ecosystems by putting a camera on it.

Or how about search-and-rescue snaky robots that can burrow through rubble or use helicopter like propellers to airlift wheeled snakebots out of tight spots. And here’s the future for XBox gamers . . . the robot trio is controlled using an Xbox controller. Also in the same disaster area recovery realm are robots that use tiny explosions to jump, shoving the untethered soft robot off the ground so that it can navigate rubble that makes walking through an area difficult.

So many evolving uses for smart and intelligent materials and constructions from them that have the potential to be life-affirming and useful to humanity !! But I do worry – what will all the people do ? Already, a lot of people are unemployed or underemployed and technology is certainly one of the reasons, so more competition from artificial intelligence, ie robots, is just going to make matters worse. And I worry about remotely controlled warfare, like drones and satellites that keep warriors safe but not civilians.

iRobot

iRobot

As I see robotics evolving, what happened to me a year ago to cause a bit of anxiety was this – Suddenly, everyone I saw in “service roles” in St Louis (including road & bridge construction workers and Whole Foods associates) I saw sadly as “on the way out”. I remain aware of “possibilities”, whether they are accurate realities at this time, or not. My heart hopes for only good outcomes to our evolving technologies. My concerns were set off by reading a piece by Mike Adams about robots. Anyone who has seen the movie iRobot can easily visualize the future portrayed in this snippet –

“In my estimation, over the next three generations (about 75 years), we will see humanoid robots take over nearly all traditional labor roles in society, including manufacturing, agriculture, construction, firefighting, food service and even community policing. Most of the physical work done today by humans will be turned over to humanoid-shaped robots built much the same way we are: two arms, two legs, two eyes and roughly the size and shape of a 5′ 9″ man.”

“This, in turn, will make virtually all human laborers obsolete. There will be no more need for people to pick crops, paint houses, clean windows, drive ambulances or even fight wars. Humanoid robots will take over every repetitious, dangerous, disgusting or boring task that humans currently tackle, from cleaning toilets and sweeping floors to driving taxis.”

At Yemm & Hart there are no robots doing the work today. Our processes to create new materials from recycled resources are rather old-fashioned in their methods. We are gratified to make our living by recycling those items turned in by consumers to recycling centers in order to continue their usefulness. We do stay abreast of continuing developments not only in our own industry but as this blog has illustrated. We find interesting all kinds of topics about anything and everything evolving in Life whether it catches our fancy or worries our dreams.

~ Information Resources

“Date With an Android” review in Time magazine April 20, 2015 – http://time.com/3814972/in-ex-machina-a-date-with-an-android/

Deus Ex Machina: 30th Anniversary Edition Announced
http://kaijupop.com/2014/09/deus-machina-2-original-30th-anniversary-editions-coming-november/

Ex Machina – The Mind Behind The New AI Flick Q+A in Wired magazine April 2015 – http://www.wired.com/2015/04/alex-garland-ex-machina/

Centre For The Study of Existential Risk
http://cser.org/about/who-we-are/

“Transcending Complacency on Superintelligent Machines” posted 4/19/14 at the HuffPost Science Blog
http://www.huffingtonpost.com/stephen-hawking/artificial-intelligence_b_5174265.html

Active and Intelligent Materials Lab at University of Cambridge
http://www.aim.msm.cam.ac.uk/research

“Better than ‘Transformers’: Real-Life Robots: Photos at Discovery.com – http://news.discovery.com/tech/robotics/transformers-real-life-robots-110629.htm

“Robot swarm takes many shapes” by Andrew Grant in Science News Sept 6, 2014 – https://www.sciencenews.org/article/robot-swarm-takes-many-shapes?mode=magazine&context=188995

The Science News article below by Meghan Rosen could not be found in digital form at http://www.sciencenews.org.

[1] “Octobot uses webbed arms to swim faster” by Meghan Rosen in Science News Nov 1, 2014

[2] “Hybrid robot merges flier with two snakelike machines” by Meghan Rosen in Science News Nov 1, 2014

[3] “Hopping robot powered by explosion” by Meghan Rosen in Science News Nov 1, 2014

“Robotics revolution to replace most human workers in three generations” by Mike Adams posted on 9/30/13 at http://www.naturalnews.com/
http://www.naturalnews.com/042276_robotics_revolution_worker_displacement_depopulation.html

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Blog author ~ Deborah Hart Yemm is co-founder of
Yemm & Hart, a green materials producer

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