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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Unavoidably Cynical

BPA Free is a load of BS

One would think that common sense could have eliminated this possibility before it even got started. Seeing so many acquaintances receive a cancer diagnosis and watching some of those die, I have come to believe that the excessive number of man-made chemicals that now dominate our environment plays at least some role in what seems like ever increasing numbers of people thus afflicted. A Science News article from April 4, 2015 caught my eye as I was wondering what I might write about today. The headline read –

“Doubts grow over BPA replacement – Bisphenol S poses the same health risks, researchers suggest” by Beth Mole in the Earth & Environment section.

The illustration that accompanies the article compares the two noting their similar chemical structure and that both have the SAME hormone-disrupting effects on animal cells.

BPA BPS comparison

So manufacturers have been able to honestly claim “BPA FREE” but that reassurance seems to have been deceptively unfair to consumers. One would think the chemists should have known better. I simply am not able to trust the chemical industry in general any more. Of course, I know chemicals are important and necessary and that some are even “natural” and “organic” (and I can “trust” those to be what they are at least). Just this past week I posted a reply from my Missouri R Senator Roy Blunt that was mighty slow in coming, and as politicians are wont to do uses a lot of words that look good but don’t really say all that much, as a comment on another blog here – “What Happened to Good Intentions ?” published here on Feb 2nd of this year.

BPA Free Seal

The author of the Science News piece concludes that “Chemical tweaks aren’t enough to tame a possibly dangerous component of plastics, two new studies suggest”. The difference between BPA and BPS are in how the ring structures are linked together – by a carbon atom attached to two methyl groups for BPA and by a sulfur atom attached to two oxygen atoms for BPS. BPS has been used as a replacement for BPA in paper receipts since concerns about cashiers and waiters handling these so frequently arose. Regrettably, even back in 2012, 81% of people who were tested had detectable amounts of BPS in their urine.

Most likely it was the least expensive approach to growing consumer boycott’s of containers using BPA. One of the studies goes so far as to admit – “. . . products labeled ‘BPA-free’, such as baby bottles, are not as free of health risks as consumer might expect.” What’s there to worry about ? Researchers found that BPS, just like BPA, can boost heart rates and spur irregular heartbeats in female rats. Heart cells in male rats block certain estrogen signals – it’s known if that would hold true with humans. A pharmacologist involved in the heart study commented that the two chemicals “are nearly indistinguishable, if not identical”, in their effects.

A separate study found that BPS, just like BPA, can alter brain development and behavior in zebrafish. Embryonic fish exposed to levels of BPS similar to the low levels of BPA found in nearby waterways were hyperactive and zooming around their tanks in circles. BPA exposure in humans has been linked to behavioral changes that include hyperactivity.

Previous reports had already reported the same estrogen mimicking effects with BPS as with BPA in both humans and other animals. Three years ago Mercola.com published warnings about BPS in an article posted online (see Information Resources at the end of this blog). While the potential human health hazards of BPS’s estrogen-mimicking effects remain unknown – BPA has been linked to obesity, cardiovascular disease, cancer, infertility, neurological problems and asthma. And there is more troubling news – even though the Food and Drug Administration banned the use of BPA in baby bottles in 2012, there are few other restrictions on its use in the United States and the use of BPS is not restricted at all at this time.

Without naming BPS, the Environmental Defense Fund notes on its “Four Reasons ‘BPA-free’ won’t protect you” page – “When BPA is removed, it’s often replaced with a similarly dangerous chemical. This is known as ‘regrettable substitution’, and there’s no one charged with ensuring replacements are any safer.” And the EDF goes on to note – “Regrettable substitution is a problem not just for BPA, but thousands of chemicals.” because “. . . the Toxic Substances Control Act, is nearly 40 years old and ineffective. Unlike prescription drugs, companies can sell and use chemicals without showing they’re safe.” You can sign a petition about that at the link for the EDF in the Information Resources section at the end of this blog.

Tomatoes in Amber Glass

Dr Mercola suggested – “If you’re interested in avoiding any number of chemical toxins leaching into your food and beverages, choose glass over plastic, especially when it comes to products that will come into contact with food or beverages, or those intended for pregnant women, infants and children. This applies to canned goods as well, which are a major source of BPA (and possibly other chemicals) exposure, so whenever you can, choose jarred goods over canned goods, or opt for fresh instead. Another good idea is to ditch plastic teething toys for your little ones and choose natural wood or fabric varieties instead.”

Another possibility is to buy as much as you can in aseptic packaging. Tetra Pak offers a diagram of their package materials, very simple like “basic ingredients” – polyethylene, aluminum and paperboard.

Tetra Pak diagram

Tetra Pak diagram

Dr Mercola did admit – “To be fair, you probably can no longer completely eliminate your exposure to BPA, BPS and similar toxins (since they’re likely in our air, water, and food, too) but you can certainly reduce your exposure dramatically by making informed choices like those described above.” Remember – back in 2012, 81% of those tested were already “positive” for the presence of both BPA and BPS – sadly.

~ Information Resources

“Doubts grow over BPA replacement – Bisphenol S poses the same health risks, researchers suggest” by Beth Mole posted March 9, 2015 at ScienceNews.org – https://www.sciencenews.org/article/replacement-toxic-chemical-plastics-receipts-may-be-just-toxic?mode=topic&context=65

“What Happened to Good Intentions ?” by Deborah Hart Yemm posted Feb 2, 2015 at What’s New in Eco-Materials – Exploring the Complexities of Environmental Choices – http://wp.me/p3XHLm-bS

“Four reasons ‘BPA-free’ won’t protect you – Plus: What you can do to make sure hazardous chemicals are properly regulated” at the Environmental Defense Fund website – http://www.edf.org/health/four-reasons-bpa-free-wont-protect-you

“BPA-Free Products Still Contain Bisphenols of Equal Toxicity” posted by Dr Mercol on June 20, 2012 at Mercola.com – http://articles.mercola.com/sites/articles/archive/2012/06/20/bpa-free-plastic-still-toxic.aspx

“NEW – Amber Glass Jars of EDEN® Organic Tomatoes & Sauces” – http://www.edenfoods.com/articles/view.php?articles_id=191

Tetra Pak Packaging Materials, Aseptic Carton – http://www.tetrapak.com/packaging/materials

“7 Companies You Can Trust to Use BPA-Free Cans” by A K Streeter at treehugger.com posted March 2, 2010 – http://www.treehugger.com/green-food/7-companies-you-can-trust-to-use-bpa-free-cans.html (author’s comment – I’m not sure that “trust” is an appropriate word any more . . .)

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

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