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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Wood – One Response to Carbon Sequestration

Infographic: Putting Forests to Work

Infographic: Putting Forests to Work

One has to watch assertions. Even though well-intentioned, they can sometimes be misleading. So, it was that I questioned one such assertion regarding a particular detail in what was overall a good presentation. The assertion was “Products made of wood currently capture 70 million metric tons of CO2 from the air annually.” I wanted to know how that was possible and said via email “An assertion in your graphic seems not entirely ‘possible’ to me, could you please explain, elaborate or clarify ?” I noted that we are “forest-friendly” saying – “We steward a 500 acre forest in Missouri.” and that “I understand that using wood would keep the tree from potentially decaying and thereby releasing the carbon it has sequestered.”

I won’t say that the response was entirely informative but I was referred to a couple of links –

You can find more details about forests and climate on our website: https://www.forestfoundation.org/forests-and-climate-change

And specifically read about the statistic you mention here (recommendation #2): https://www.forestfoundation.org/read-our-recommendations. The calculations have been verified by several different folks, including U.S. Forest Service researchers.

Thanks so much for your interest.

So, I thought I would explore around this for my blog today. What was confusing to me was that it seemed to be saying “dead” wood in the form of “products” could actually pull CO2 from the air. I do question that. So, let us take a look at the link that she suggested would explain that. Here is what Recommendation # 2 says specifically –

“2) Promote Forest Products:

Forest products, such as lumber, store carbon throughout their lifecycle. Nationwide, forest products already store 71 million metric tons of CO2 annually. There are many opportunities to strengthen markets for forest products. Measures such as these could reduce emissions by an additional 21.1 million metric tons of CO2, or 0.3% of annual U.S. greenhouse gas emissions, equivalent to emissions from 5.5 coal plants in one year.”

So, when they say “capture”, they actually mean “store”. Not that it continues to pull carbon from the air after it becomes a product. Now, I do not intend what I have said to be interpreted to mean that I think the American Forest Foundation had any intention of misleading anyone. Still “capture” “from the air annually” could easily be interpreted by the casual reader as meaning that their purchase of a wood product – that the house, table, bowl and chair are actively removing CO2 from the air.

Damage in Missouri from 2009 Derecho

Damage in Missouri form 2009 Derecho

Still, I do know that we once thought that we would never cut a tree. Then, along came the extreme storms where our big trees were taken down 3 or 4 years in a 5 year period. A tree decaying naturally, while adding to the soil which is not in itself a bad thing, is also releasing it’s carbon. So, selectively logging our forest, in a careful un-even aged management by a state forester’s selections, does provide wood for products and prevents some trees that might be lost in storms from releasing their carbon (removed as CO2 from the air). And we have also performed some salvage logging after a storm for the very same reason.

Recommendation # 1 suggested “Provide Sound Data and Science: Accurate, up-to-date information is needed to manage forests for the greatest carbon benefit, understand the conditions and trends of forest carbon stocks, and to address climate-driven stressors on forests. Supporting existing inventory efforts, research and applied science partnerships to understand and address threats …”

About a decade ago, we discovered “mystery trees” at the edge of our property. To be honest, at first the only explanation we could come up with was a bit disturbing. Someone was going deep into our forest to perform disturbing rituals or to hide evidence from some criminal activity. Nothing much happened there for a decade but periodically, we would go back to see if there had been any change. This year, we saw that the odd marks that had been put on the trees had been “refreshed” and felt invaded and threatened all over again.

FIA Tree Marking

To rescue our sense of security, came an answer from our Missouri Dept of Conservation state forester. She said – “Your mystery is actually a forestry thing.

There is a program (and has been since around the 1960’s) called the Forest Inventory and Analysis (FIA) project, where random plots were chosen throughout Missouri’s forests (regardless of landowner) to be surveyed. Permanent plots were established and are re-measured every 5-7 years. If the trees are cut, then that is recorded also. This program is a way of establishing the growth or decline of Missouri’s forests.

I worked on this crew when I was just out of college. They are supposed to contact the landowners before accessing the property, but sometimes if they cannot get hold of them, they have been known to slip in and re-measure old plots. This project is run by the US Forest Service (research branch), and I believe they are still based out of the Salem office.

The layout of the plot is a central circle usually marked at the center with re-bar. Then there are three other circles around the main circle ( I forget how far away). There are witness trees marked to help locate the main plot center.

Nothing sinister, but they definitely should have talked to the landowner at some point.”

Living Forest Components

Living Forest Components

We did some additional research and while never definitely confirming our plot was part of that, we were told by a USDA Forest Service employee that “From your description of the marking this does sound like a Forest Inventory Research plot.” That did reassure us and we don’t mind being a “research” subject. They even have a Forest Carbon Estimation based upon their work. They indicate there that “US forests and associated industries currently provide the largest annual reduction of CO2 emissions of any land use in our Nation. Reliable estimates of this ecosystem service is essential to our society.”

EPA Forest Wood Sequestration

EPA Forest Wood Sequestration

Regarding the chart above, TreeHugger author John Laumer shared a few thoughts – “The total US forest-carbon pie can not increase significantly, inside a decade, based on organic growth. Some uses of one or more slices can reduce the total carbon stored in a few years, however. Individual slices can be increased to make up for decreases elsewhere.I begin with above-ground biomass in the USA, and brainstorm from the graphic, clockwise, discussing the millions of metric tons carbon in storage and possible tradeoffs.”

It is nice to know that “Once you put wood in any form into a landfill (64 MMT/7%), the carbon stays there for decades, maybe centuries. Recycling and re-use keeps the carbon roughly the same: stored. Conversely, diverting wood from the landfill to a biomass burner, whether for building heat of electricity generation or both, pulls that carbon out of the storage pie.”

Laumer also suggests – “You can make wood a more common building material – LEED buildings often do – diverting carbon from the above ground slice and into the wood products slice, keeping the carbon locked up (37 MMT/4%). If wood is imported, above ground slice stays as it is. If harvested locally it goes down. Only way to keep the pie size constant in global terms is to require replanting regardless of source.”

I really like the point he makes, “Dead wood is 37 MMT/4% and likely rising rapidly in the USA due to the pine bark beetle and other invasive Asian insects. Given our metaphorical habit of ‘getting rid of the dead wood’ I suspect there will always proposals afoot to log dead wood, either for product manufacture or for burning. Arguably, manufacturing is the better option as it keeps carbon in storage longer; but, to the extent that living disease-resistant trees are planted to replace the dead wood, use of dead wood as biofuel or as ethanol feedstock displaces fossil fuels and is thus a second place ‘good’.”

And I especially appreciate “balance”, which the author brings in at the end of his piece – “If a politician favors logging to bring jobs and expand the tax base, he’ll cite a study that only measures above ground living biomass. If an environmental interest favors wilderness preservation, they’ll add up all the slices they can, which is objectively sensible, but which leads observers wondering if anyone is ‘right’.”

Forest Light

I do love trees, no doubt about it. However, I also believe that humans are part of what is “natural” to this planet and that we are here to be thinking entities. We can be those thinking entities in ways that benefit the planet. We once believed in a hands-off forest. We changed our minds and decided to be stewards participating in a considered forest management process. That isn’t always the easiest path, when one loves trees. Yet, it is my hope, that a healthy vital forest is another way of expressing my love for the trees. And yep, I hug a tree fairly often. It feels awesome.

~ Information Resources

American Forest Foundation – “Infographic: Putting Forests to Work” – https://www.forestfoundation.org/infographic-putting-forests-to-work#.U7CAdrdOXL8

American Forest Foundation – Recommendation # 2 – https://www.forestfoundation.org/read-our-recommendations

USDA Forest Service – “Forest Inventory and Analysis National Program” – http://www.fia.fs.fed.us/

USDA Forest Service – “Forest Carbon Estimation” – http://www.fia.fs.fed.us/Forest%20Carbon/default.asp

“Forest Carbon Management: Let’s Brainstorm The Trade-offs” by John Laumer posted at TreeHugger.com on Dec 15, 2009 – http://www.treehugger.com/corporate-responsibility/forest-carbon-management-lets-brainstorm-the-trade-offs.html

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

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Better Plastics & Other Options

Pacific Ocean Plastic Island

Pacific Ocean Plastic Island

A lot of people hate plastics, especially environmentalists. We don’t hate plastics and we are environmentalists. That’s because we take recycled #2, #4 and #5 plastics and recycle them into panels used for construction applications like countertops and restroom partitions as well as some consumer products such as furniture, lamps, cutting boards and clipboards. However, realistically, plastics are winning and that isn’t an entirely good thing and that is where the hate, on the extreme, and the dislike on the more average end of the spectrum comes from. There were a lot fewer plastics in my life as a child growing up in the 60s. And the pioneers that settled our part of Missouri, depended upon glass and metal, and because they had no recycling options but the reuse or melting down they may have done for their own requirements, we continue to find their debris here and there in our forests – for they thought nothing of haphazardly burying their wastes.

Facing realities about plastics – they require fossil fuel production in their manufacture, they mostly are not biodegradable, though some resins can be recycled – some can’t – and the mass of humanity doesn’t (it is estimated that only 1/4 of 1% of the 7 billion lbs of PVC plastic alone is recycled each year in the US – our Flexisurf material DOES recycle some of this waste). That is just one; and it seems that PVC is one of the world’s more common and most toxic plastics.

So, for today’s blog, I went exploring around and found some interesting information about plastic alternatives and research into making more “environmentally friendly” plastics. Some of the alternatives my own family employs because we know that even our own recycling and re-composition-ing of plastics is minor, compared to the total amount of plastic waste that is out there. The best advice for living a sustainable lifestyle is still – reduce, re-use and recycle.

Plastics: Environmental Preference Spectrum  ~ developed by Tom Lent

Plastics: Environmental Preference Spectrum
~ developed by Tom Lent

RESEARCH & DEVELOPMENTS

[1] PDCs (prodegradant concentrates). Adding compounds that may promote oxidation processes to break down plastic into fragments that microorganisms happily gobble up, sounds like a good thing and it reportedly is. So what’s not to like ? They are useful in single-use plastic applications and reportedly result in no harmful residues once the process is completed. However, it is not easy to identify which plastics have these additives and which do not. The consequences for the recycler in today’s processes can be catastrophic, causing a failure in contaminated resins, reducing their lifespan. An example would be irrigation pumps fabricated from recycled polyethylene, when contaminated by PDCs.

[2] Milk Protein. Casein-based plastic is actually an OLD idea, around since a French chemist treated casein with formaldehyde in the 1880s to make a substitute for ivory and tortoiseshell. However, this proved too brittle for applications beyond jewelry. Modern scientists have learned that adding silicate clay that has been frozen into a spongelike material creates a polystyrene-like material that degrades completely at the landfill and is made even less toxic by substituting a glycerine based chemical for formaldehyde.

[3] Chicken Feathers. The disposal of chicken feathers is a BIG waste problem (more than 3 billion lbs per year in the US alone). Chicken feathers are predominantly keratin, which is tough and durable (think hooves and horns). When chicken feathers are processed with a liquid found in nail polish, a plastic is created that is stronger and more resistant to tearing than plastics created from soy or starch. Chicken feathers are definitely a constantly renewing resource. It is also believed that chicken feather plastics will prove biodegradable.

[4] Liquid Wood. A biopolymer that looks, feels and performs much like plastic but is biodegradable. The resource for this plastic is pulp-based lignins, considered a renewable resource. These lignins are a byproduct of paper mills. When mixed with water and exposed to high heat and pressure, they create a modable composite material that is strong and non-toxic. It is believed that this plastic could be recycled with other wood products.

[5] Polycaprolactone (PCL). Synthetic polyesters, while not sourced from renewable resources, are finding a welcome role in biomedical devices and sutures because of their slow but certain degradation. Adding cornstarch to the manufacture of this material reduces it’s cost and it may have future applications in food-contact products.

[6] Molasses (PHA Polyesters). Feed sugar to certain types of bacteria and you are producing plastics. These biodegradable plastics closely resemble man-made polypropylenes. They are currently finding applications in packaging, films and injection-molded bottles. Though a high cost of production has slowed the development of these, corn-steeped liquor, molasses and “activated” sludge may one day supply the sugar that these bacteria require to product plastics that are compostable utilizing the same anaerobic workhorse of many biological treatment facilities.

[7] Corn (PLA Polyesters). These plastics are made from lactic acid, produced by fermenting the starches created during the wet milling of corn. Other similarly processed plants are wheat and sugarcane. PLA has enough rigidity to replace polystyrene and PET with the benefit that it decomposes and does not emit toxic fumes when burned. The manufacture of this plastic uses up to 50% less fossil fuels. Blending in starch reduces the cost and increases the biodegradability further. Applications include bottles, bags and film. If scientists can make it stronger and more heat-resistant there may be additional applications in the automotive industry.

Alternatives to Plastic
ALTERNATIVES

[1] Glass. We love glass. For Christmas, our family replaced plastic straws with glass straws. We love the fact that glass doesn’t leach into our food products. Glass is easily recycled and made from sand. It is a renewable resource in every way. But it isn’t easy for us to recycle glass (we have to haul it 50 miles away); and it is bulky and very heavy and can break. Glass can be dangerous and cause bleeding. Stepping on broken glass in waterways is NOT fun and is often banned by officials protecting such recreational resources.

[2] Stainless Steel. It has been around for a long time. We depend upon it for utensils, kitchen sinks, medical uses, teeth, food storage and water bottles. Though corrosion-resistant, the grade matters, including regarding the leaching of metals. It is a mixture of a variety of elements, not always but sometimes used – iron, chromium, carbon, nickle, molybdenum and titanium. Stainless steel is non-magnetic. Keep in mind that stainless steel is one of the most environmentally efficient raw materials available, as well as being recyclable.

[3] Reusable Shopping Bags. We employ cloth and insulated bags on our grocery shopping trips. We also recycle any of the thin plastic bags we do bring home from various retail establishments. Many stores have collection facilities for these. Nothing is uglier than a plastic bag let loose into the environment by its holder. Enough said !!

[4] Choose cardboard and glass for packaging. Look for products that fulfill your needs that do not use plastic in their packaging. This makes the waste materials more eco-friendly by being easier to find recycling options for that waste.

[5] Be a thoughtful consumer. Buy products with careful consideration to their composition and packaging. Online, you can visit “Life Without Plastic“, a website that promotes alternative choices for a wide diversity of products. Alternatives include glass, wood, stainless steel, bamboo, hemp, cotton, wool, khadi, cellulose and recycled paper.

[6] Re-use or recycle. EVERYTHING YOU CAN. Respect and appreciate every resource the planet and the people who inhabit it provide for all of us. Don’t simply be a mindless consumer – give back and respect.

Of course, we wouldn’t wish to dissuade anyone from recycling their plastics – our business depends upon that. However, there is such an abundance of plastics in our modern lives that we can confidently suggest that you broaden your perspectives about plastics beyond simply hating them and consider developments and alternatives as part of your eco-friendly lifestyle mix.

~ Information Resources

“Top 10 Eco-friendly Substitutes for Plastic” by Maria Trimarchi and Vicki M Giuggio posted at How Stuff Works.com – http://science.howstuffworks.com/environmental/green-tech/sustainable/5-plastic-substitutes.htm

“What are some alternatives to traditional plastics ?” posted at Curiosity.com hosted by Discovery – http://curiosity.discovery.com/question/some-alternatives-to-traditional-plastics

“Life without Plastic” – A one-stop shop for safe, high quality, ethically-sourced, Earth-friendly alternatives to plastic products for everyday life – http://www.lifewithoutplastic.com/store/our_products#.U0GE7rdOXL8

There are many reasonable articles at “ReUseIt.com” – this one caught our attention – “Plastic Island – Nasty, Gargantuan & Growing” posted back in August 2008 – http://reusablebags.typepad.com/newsroom/2008/08/plastic-island.html.

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

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