Gene Drives Reversible?

NYTimes magazine has an article on gene drives, discussing the positives and negatives.  Lots of concerns about negatives, particularly outside the scientific community.

In reading it I wondered:  if I understand correctly, the gene drive consists of a genetic package which says: "if you find gene A, replace it with gene B and Crispr package X."  So a gene drive spreads a gene throughout the population while also spreading the Crispr package needed to replace A by B.

So what did I wonder?  Whether a gene drive isn't reversible, just do: "if you find gene B, replace it with gene A and Crispr package X"

Of course, it turns out any layman speculation I might have is out-of-date, witness this 2015 piece.

CRISPR and Cassava

Tamar Haspel tweeted a link to this article on using CRISPR in cassava.  Part of the key was making cassava flower reliably and early, so regular breeding and cross-matching techniques could be employed down the line.  (Cassava feeds a lot of people (is a billion a lot--I think so) but has been hard to improve because it didn't flower regularly.)

The article goes on to comment on the barriers to CRISPR being erected in other areas of the world.

CRISPR is near and dear to my heart, though it's been around for just a few years, because I identified it early as an interesting technique, though just today have I added a label for it (using "genetic modification" before). 

You're Not Who You Were a Second Ago

Been reading Jennifer Doudna's Crack in Creation.  She's one of the scientists involved in the creation and development of CRISPR, the tool used to edit DNA without importing genes from other species. 

Towards the end she has this sentence: "Every person experience roughly one million mutations per second..."  If I understood her book, there's a natural process to correct those mutations, a process which CRISPR adapts.

A Position on GMO's

Tamar Haspel expressed her agreement with a Mark Lynas speech, which he summarizes here:

So that’s my peace plan. To recap:

1. Environmentalists accept the science of GMO safety, and scientists in return need to accept that politics matter in how scientific innovations are deployed.
2. We drop national GMO bans and instead allow fully informed choices to be made by consumers in the marketplace via rigorous labelling and full traceability.
3. We all get over the Monsanto obsession but make a much more serious effort to start getting off the chemical treadmill and moving farming onto more sound ecological principles.
4. We agree to support public sector and non-corporate uses of genetic engineering where these can clearly contribute to environmental sustainability and the public interest.
5. We support all forms of agriculture that aim to find ways towards greater sustainability. Let a hundred flowers bloom.
6. We stop the name-calling. Let’s avoid using the term anti-science in particular. Anti-GMO activists are not opposing the scientific method in general, they are opposing a particular technological innovation.
7. Let’s make ethical objections to genetic engineering explicit and in the process recognise real-world tradeoffs about where we do and don’t use this technology.

CRISPR: Once Again

Here's a piece on various advances in science the use of CRISPR (editing out genes) will enable in 2017 and future years.

I've been doing regular posts noting the rapid advances in using the method.  My first notice was about 20 months ago, when  I noticed it bypassed the usual objections to genetic modification. Maybe it's time for me to keep quiet, rather than trying to impress with my prescience? 

Times and GMO's--II

I blogged previously about the NYTimes article on GMO's,  Tyler Cowen links to another approach--the writer arguing that farmers are making rational decisions on which seeds to buy, which must mean that GMO seeds have advantages over nonGMO.

The Times and GMO Crops--Something Screwy

NYTimes has a front page article on the usage of GMO crops: comparing the yields and herbicide usage between US/Canada and Europe.  Not sure how I got this referral, but this commentary post 
seems quite on the point, pointing out some of the problems in the article.

One thing I haven't seen discussed; perhaps it's too elementary for these writers to explain, but it's straight line graph of yields. Turns out the Times sticks its graphics in a separate url--I've stolen it here:


The arrow points to the place where GMO's come into play and the graph covers early 80's to 2015 I think.  What I don't understand is what the lines represent.   If they show the average increase/decrease in national yield each year, each would be a jagged line, with an upward slope.  So it must be some average over the time period.  But obviously an average over the whole time period won't show any change for GMO adoption in the middle of the period.  It might be an average over the whole period for Western Europe and two averages for US/Canada--one up to the adoption of GMO's and one after, but it's certainly not labeled that way nor explained.

The unit of measure is "hectograms per hectare", which is a metric yield measure, like kilograms per square meter.  I read the graph as implying the corn yields for the US and Western Europe are the same, which can't be right. I know damn well corn yields in the US vary greatly, so there's got to be a big difference between countries.  I did a search and found this: "These analyses indicate that Western Europe started with a lower yield than the USA (29,802.17 vs 39,895.57 hectograms/ha) and managed to increase yield much more quickly (1,454.48 vs 1,094.82 hectograms/ha per year) before any use of GM corn by the USA." (The source is some Kiwi's blog working on the same issue back in 2013.  See this post.)

On a football Sunday I've now exhausted my energy on this issue--perhaps more later.

GMO's in Africa

Technology Review has a piece on trials of GMO crops in Tanzania and the possibility African countries are becoming more open to them.  I think this is how change occurs--while humans may resist the new, usually there come times when the advantages of the new outweigh the resistance.

But the example of Japan's resistance to modern firearms cautions that it can take a long time for the advantages to become clear.

Genetics and the Precautionary Principle

Read an article yesterday about concerns over manipulation of the human genome.  Forget where.  Some issues were over correcting genetic problems which cause diseases versus modification of the genome to improve human capacities.  And then you bring in the problem of non-genetic modification: we don't permit performance enhancing drugs in sports, but we no doubt approve of our surgeon drinking a cup of coffee in the morning before she operates on our brain.

Anyhow, it's a deeper subject than I can deal with, but two aspects strike me:

• it's highly likely that benefits from such things will not be equally divided: as usual the rich will get richer (taller, smarter, less disease-ridden, whatever) and the poor won't.
• our discomfort with some of the modifications tends to be higher at the margins.

Accordingly, I'd propose a couple of rules, somewhat similar to the precautionary principle (which can be summarized as: "when in doubt, don't"--not that I like the way it's often been applied.

• before you undertake any modification, determine whether the result will push the existing bounds of  normal human capability.  We don't make a society of Einsteins.
• in undertaking any modification, consciously try to counter the "golden rule" (i.e. the rich get richer).

More on Genetic Modification

Nathanael Johnson's piece at Grist on the complexity of defining GMO's. 

Bottom line: if you can't define it you have difficulty labeling it.

Dehorning Cattle and GMO

We mostly dehorned our dairy cows.  Why?  For safety, both for us (dad) and for the cows.   A cow has a whole lot of strength.  Cows have different personalities: some are affectionate, some are reserved, some are plain nasty.  Pair a nasty cow with horns and you have a risk of a bad injury.  Even a nice cow might injure you; it'd be an accident but still an injury.

So we dehorned our cows.  As soon as we could feel the nubbin of the developing horn we'd apply caustic paste which would burn away the growing point.  It really hurt the calf, but it was for everyone's good.  Kill dad and the cows would go for slaughter.  Keep him healthy and the cows would have more years of life, before going to slaughter. Such is the logic of the dairy farm.

Now CRISPR, gene editing, promises to eliminate that source of pain.  All good to my mind, but it's genetic modification. See this Mother Jones article

CRISPR, I Knew It

This Technology Review article discusses the use of CRISPR to "engineer babies".

And another article says: "Gene drives are just the latest example of the fantastic power of CRISPR editing to alter the DNA of living things,..."  This is in the context of engineering mosquitoes which stop the transmission of the malaria parasite and ensuring they proliferate, raising the possibility of a victory against malaria. But it raises the ethics of changing the biosphere, permanently.

I first posted about CRISPR back in April, which was pretty good of me, though my post was more about the quandary it poses for opponents of genetic modification.  That quandary becomes more severe as we begin to see the potential uses of the technique.

[Updated: An Atlantic article on understanding our genes.--hat tip  Marginal Revolution.]

CRISPR and the Future of Genetic Modification

CRISPR is enabling a lot of "progress".  A quote from a Technology Review piece, predicting CRISPR-ized seeds being available by the end of the decade:

Gutterson said the objectives of plant labs include engineering resistance to blights or to low rainfall by rapidly introducing beneficial gene variants found in other varieties of the same species. Using conventional breeding to move traits can take many years. “It takes a lot of time and is not as precise as we would like,” says Gutterson. “We could very much short-cut that.”

The key question is the attitude that the public and regulators will take to these plants.

Companies hope gene-edited crops could be largely exempted from regulation. Already, the U.S. Department of Agriculture has told several companies that it will not regulate these plants because they don’t contain genes from other species. However, it’s unclear how the European Union or China will approach plants made with the new methods.

As I've been saying, it's going to be hard to reject such plants.

CRISPR and Pets--Micro-pigs

Chinese scientists have used gene editing techniques to modify a small breed of pigs into "micro-pigs" according to this report.  The intent was to make the pigs smaller, therefore cheaper to raise as models for human disease.  They didn't foresee that a nice small pig would have potential as a pet.

IMHO genetic modification is like a horror movie, or Fantasia, where you see the water or other liquid coming under the door, the hero tries to keep it out, or clean it up, succeeding momentarily but ultimately failing.   (Not that I think genetic modification is a threat, per se, but it is change and some changes are mostly irresistable.)

Fake Meat and GMO's

Nicholas Kristof has a piece in the NYTimes describing the progress being made in developing edible fake meat.  It sounds promising.  I've no problems with the effort.

I do wonder though how the food movement and the environmentalists will react if fake meat becomes a reality.  A fake steak would be good for global warming, given the methane production of cattle.  But it seems to me that fake meat should raise all the concerns which the food movement voices in connection with genetically modified organisms.

GMO Seeds and the Chinese Spies (?)

New Republic has a piece on Chinese espionage against US intellectual property, specifically genetically modified seeds.

Think about that: The U.S. Department of Justice and the FBI now contend, in effect, that the theft of genetically modified corn technology is as credible a threat to national security as the spread to nation-states of the technology necessary to deliver and detonate nuclear warheads.

It's a long piece, rehearsing the development of hybrid corn and then GMOs, and touching on farm policy from the New Deal through Earl Butz.  Inevitably such a summary must be incomplete and contain errors, but I'm not up to nitpicking today. 

Growing Meat the New Way

Vox has a long piece on the prospects for lab-grown meat.  In short, progress is being made but it has yet to attract a whole bunch of researchers.

Having just been commenting over on Grist on the prospects for RNA interference (see my post here)
I have to wonder: will the food movement which resists gene modification in their food chain be comfortable with eating man-made meat?

Messing With Plant Genes: the Fourth Way.

If we're counting, there were three ways for humans to mess with plant genes:

1. the time-honored method of selective breeding, picking the good ones from a crop and reproducing them.  The only way approved of by all.
2. direct genetic manipulation in the laboratory, inserting a gene from one species into the germplasm of another species.  This is called GMO, and it is considered bad by many, particularly in Europe, because it creates "unnatural" combinations of genes.  Many believe people must be given the information that they're eating/using such plants.
3. direct genetic manipulation in the laboratory, using CRISPR to remove genetic material from  germplasm.  Not sure that people have made up their minds about this.

Even before we make up our minds about CRISPR, scientists have come up with another way to mess with genes, using "RNA interference".The appeal is that it offers control over genes without modifying a plant’s genome—that is, without creating a GMO. From the piece:

That means sprays might sidestep much of the controversy around agricultural biotechnology. Or so companies hope. What’s certain is that a way to accomplish the goals of genetic engineering without having to develop a GMO could bring commercial rewards. Sprays might be quickly tailored to do battle with an insect infestation or a new type of virus. Not only could this be faster than creating new GM crops, but the gene-silencing effects of RNA interference last only a few days or weeks. That means you might spray on traits such as drought resistance in times of water shortage without affecting the plant’s performance in times of normal rainfall.

I know I don't understand this but the bottom line to me seems to be that the scientists are advancing faster than society is making rules. It's hard to see how those who object to GMO's (no. 2) could object to this.

[Update: Grist weighs in on RNA interference.  Suggests that Monsanto follow Google and change its name.]

GMO Soybeans for Everyone

One of the big accusations against industrial agriculture is the fact that patented seeds must be purchased each year from the seed company.  This is a burden on smaller farms with tighter margins.

But patents are not forever.  It turns out some of Monsanto's GMO patents are expiring.  Technology Review has a report on a seed dealer who took advantage of the fact, selling GMO soybeans no longer under patent.  As the article observes, this means the farmer can use some of his harvest to plant next year.

Dairy and Efficiency and Meat

Nathanael Johnson at Grist has a piece on how to make meat greener.   The answer: be efficient--two quotes.

The average dairy cow in California produces 20,000 pounds of milk a year. But the average dairy cow in Mexico produces only 4,000 pounds of milk a year, while in India it’s just 1,000 pounds. 

The carbon footprint of American milk is 63 percent lower than in 1944, researchers have calculated.

Interesting throughout. (Same piece as the previous post on salmon.)

In the 1950's I think we were doing good at about 12,000 pounds, which was well above average for the county.