Another one bites the dust, nature conquers bioengineering — again

And another one bites the dust. Corn rootworms, once the scourge of corn growers, stymied by corn engineered to produce Bt toxin (a crystalline toxin that basically pokes holes in the guts of these worms) are back. No matter how you feel about bioengineering, this is bad news because it can only lead to increased pesticide use.

In his book Lords of the Harvest Journalist Daniel Charles chronicled the early days of Monsanto’s genetic engineering feats.  In the beginning, wrote Charles, bioengineers saw themselves as green “revolutionaries”.  These were scientists who had come of age during the 1970s and who viewed biology, such as it was, as the answer to agriculture’s chemical addiction.  Fears of genetics gone awry aside, biotech could help reign in the large scale use of toxic pesticides. A case in point were plants engineered to express Bt toxin, a pesticide borrowed from Bacillus thuringiensis. Strains of the soil dwelling bacteria (a relative of anthrax bacteria) secrete toxin lethal to certain species of caterpillar, moth, and nematode pests of crops like cotton, corn and potato. Eliminating the need for industrial chemicals, the bacteria have been an “organic” farmer’s friend since the 1920s. For bioengineers, identification of the Bt toxin gene was an opportunity to improve upon nature. Isolated in the early 1980s its discovery, writes Charles, was “too perfect a target for the fledgling biotechnology industry to ignore.”

File:Bt plants.png

Bt toxins present in peanut leaves (bottom image) protect it from extensive damage caused by Lesser Cornstalk Borer larvae (top image).Jan Suszkiw (November 1999.). “Tifton, Georgia: A Peanut Pest Showdown”. Agricultural Research magazine. Archived from the original on 12 October 2008. Retrieved 2008-11-23.

By the end of the decade, the first generation of gene jockeys from Monsanto and elsewhere had figured out how to cut and paste the Bt toxin gene into laboratory plants. Today the crystalline toxin is expressed in corn, cotton and potato crops grown in the US and around the globe. Today there is controversy over the potential for toxicity to nontarget species and resistance is evolving in target species.  But, if pesticide reduction was the goal of Monsanto’s early bioengineers, Bt was a shining example.

Well aware that insects might one day render Bt engineered crops useless by evolving resistance, growers were required to incorporate a block of non-Bt crops where Bt sensitive insects can flourish. A “refuge” of sorts so that sensitive genes continue circulating in the insect populations essentially diluting the influence of resistance.

File:Western corn rootworm.jpg

Western corn rootworm

Unfortunately an idea is only as good as its execution. Refuges were a good idea. But as Brandon Keim explains in his article Voracious worm evolves to eat biotech corn, refuge requirements were lacking, as was the intent of too many growers who ignored the requirement. And as with Roundup resistant crops, the benefits of engineering failed – loved to death by users who, rather than rotating crops to disrupt pest populations kept the pressure on planting in this case, Bt corn after Bt corn after Bt corn. Resistance was inevitable.

[Adapted from Unnatural Evolution: how we are changing the world gene by gene by E. Monosson]

For more see Field Evolved Resistance by Western Corn Rootworm to Multiple Bacillus thuringiensis toxins in transgenic maize by Gassmann et al. PNAS 2014.

Changing the world gene by gene

Here’s the skinny: evolution is happening all the time, all around us. Living things are like one roiling mass of DNA. OK, so that’s a little over the top. But DNA is far more dynamic than once believed, and our use of toxic chemicals — from antibiotics to pesticides — is making this abundantly clear. Ever since some distant ancestor realized that life could be snuffed out by way of mineral, animal or vegetable poisons, humans have been in the business of killing off those deemed pests – human or otherwise. Once we figured out how to synthesize poisons in the laboratory – we ramped up this business of killing off whatever we didn’t like or need.  Antibiotics, weed, mosquito, lice and rat killing chemicals – for better or worse made us the so-called masters of our local environments.  Until we weren’t.  Today we live in a world of resistance: resistant staph, strep and syphilis; mosquitos, lice and bedbugs; even rats and mice. What do all of these species have in common? Rapid evolution in response to our chemical poisons. Evolution isn’t just for museum dioramas it is a part of our everyday life. It is ongoing all the time, all around us.  One gene here, another there – selected under pressure from killer chemicals.  Too often our response is to up the dose.  More antibiotic; more pesticide. Ironically, that’s just the kind of push that highly evolvable species need. When we threaten pigweed or staphylococcus or lice with eradication, we are challenging them to evolve or die. Too often they simply evolve. But we can change the equation. Use less rather than more and reduce the pressure; alternate with nonchemical approaches; turn an evolved resistance into a weakness; or even in some cases practice some Kumbaya and learn how to live with rather than annihilate whatever is bugging us.  We can no longer afford to ignore evolution. Rather than risk heading off into a near future hilled with Super Bugs whether pest or pathogen, we can change our ways now. We can reduce our evolutionary footprint.

Over the next few weeks and months, as I wrap up the next book project Unnatural Evolution (to be published by Island Press) about the effects of rapid evolution on our lives stay tuned for selected examples, or whatever happens to pop up in the news re: rapid evolution!  

Bumfuzzled by Epigenetics

Ding Dongs

While there is absolutely no scientific evidence is it possible that all those Ding Dongs I scarfed down in middle school could possible affect my future grandchildren?

This week at our local Toastmaster’s meeting the word of the day was bumfuzzeled. The challenge is to use it as much as possible that night.  As I struggled to give my two minute “Table Topic” an impromptu presentation about the paint color Tart Green – it was enough just to try and tell an entertaining story let alone work in a new word. But, as I write about epigenetics I can say without artifice that I am truly bumfuzzeled.

Thanks to genomics, we know that we are not solely the product of our genes but also of nature and nurture (and increasingly a whole slew of bacteria, viruses and who knows what else – but that’s another story). Epigenetics, altered gene expression caused by an environmental influence is a part of this new understanding. In this context, the nature and nurture environment can include stress, temperature, nutrition, even toxic chemicals. All of which have been shown, under certain conditions, to reach right in and jiggle the genetic code – causing certain genes to be turned on, or off.

Just as silent pauses in music influence how we hear a song or melody, genes too can be either silenced or turned on to great effect. What’s more, some epigenetic changes don’t just influence the expression of our own DNA, but can influence our children’s and our grandchildren’s gene expression. This is pretty wild if you think about it. There are several ways this can happen. One way is for molecular tags (methyl groups) to be added to the DNA, like pins in a clock timer – telling DNA when to turn off.

An increasing body of literature suggests that epigenetic influences may last a generation or two or even more depending on the species (in some plants epigenetic tags may stick for several generations).  For example studies are showing that a grandparent’s nutritional experience can influence their grandchildren’s health; possibly through epigenetic changes.  Biologically, and hypothetically, this sort of makes sense. If you have been struggling to make that Saber Tooth stew stretch, it may be a good thing to produce metabolically thrifty descendants.  But some toxic chemicals too can influence subsequent generations;not only the grandchildren but the great grands as well. Granted these studies to date have used concentrations of chemicals not relevant in the real world – but they certainly are suggestive. Could we inadvertently be jiggling the DNA of future generations with our modern day chemicals?

Where will this take us? I think about all the Yodels and Ding Dongs that I consumed back in the day, combining a sugar high with poor nutrition and quite possibly toxic chemicals. What if they influence future generations? Is this why my daughter craves an all white diet? What of her kids? Its enough to make one shudder. This is purely hypothetical of course. Scientists have not linked Ding Dongs to disease in grandchildren – though I wouldn’t be all that surprised if they did.

But you see where I’m going.  Epigenetics raises fascinating questions. And in the context of my current project (rapid evolution in a chemical world), one in particular looms large. Are epigenetic changes relevant to evolution? And can they be caused by environmental exposures to industrial age chemicals? If my diet influences my grandchildren and perhaps beyond –could my generation’s poor choices from diet, to climate change to toxic chemicals – influence human evolution?

There certainly is quite a bit of excitement about the prospect. Here are biologists David Crews and Andrea Gore writing about the topic: “Epigenetics is the next epoch in evolutionary theory, as these mechanisms alter heritability and force us to confront classical genetic ways of viewing the environment.” Psychology Today ran this headline, A Revolution in Evolution: a return to Lamarck?  While others get excited that Some Evolution May Not Depend on Genes. When it comes to evolution, it’s like Epigenetics is the new Black!

Yet as fascinating as many of these studies are, until we know more about the process we ought to proceed with some caution.

Think about it. One some level, it could certainly be beneficial to have this kind of genetic flexibility. Say if I were to move to the arctic wouldn’t it be great if my kids or grand kids were better adapted than I? Maybe stouter bodies or a little more insulation — they’d surely be grateful. But what if my kid decided southern Florida was more to her liking. So she moves there and starts a family. Would her kids be mal-adapted, thanks to me? Of course assuming there is still enough juice to power up the A/C in ten or fifteen years, the grand kids will survive. But consider the plight of wilder animals. While the ability to survive dramatic temperature shifts is a good thing – permanent change in response to temperature in an unpredictable world isn’t. Here is evolutionary biologist Jerry Coyne:

…if the DNA code changed unpredictably back and forth each generation, natural selection and evolution wouldn’t work.  Second, there are also epigenetic changes that are induced not by the DNA sequence but by the environment. Temperature, starvation, and other environmental factors can cause methylation of the DNA as well.  The thing is, though, that such changes, because they’re rarely passed on to future generations, cannot serve as the basis of evolutionary change.  Such changes constitute true Lamarckian inheritance, i.e., the inheritance of acquired characteristics.

And lots of studies show us that Lamarckian inheritance doesn’t operate. Changes that are induced by the environment, or the organism’s “striving,” can’t somehow get incorporated into the DNA.…. My conclusion: if epigenetic changes are involved in an evolutionary adaptation, they must be coded for in the DNA rather than acquired from the environment alone…

So…. those Ding Dongs those of us of a certain age consumed in high school? Clearly not a great choice. But, even if they were to leave behind epigenetic marks influencing the health of my children’s children let’s hope that Coyne has it right. That they won’t change the course of human evolution; we’re leaving enough of a mess behind as it is, we don’t need to be messing with their genetic inheritance as well.

Human evolution in response to pollution? Fact or fiction?

File:PBB Protein ESR1 image.png

From Wikipedia: Estrogen receptor

As I am nearing the closing chapter (I hope) of my book on rapid evolution in a chemical world – I am struggling to understand what this means for humans. If you search rapid evolution and humans, you will find all sorts of excitement in the popular press about how traits enabling humans to drink milk, or tolerate low oxygen or malaria, Evolved Rapidly! Or, Humans, we are still evolving! (All this, despite David Attenborough’s opinion.) It’s all very interesting but in the scheme of things, these traits are estimated to have evolved over the past several thousand years. Talk about relativity! That may well be fast for us long-lived, low fecundity species, but what does it mean for humans in today’s fast-paced world? And, since I’m focused on industrial age chemicals – what does it mean in the context of chemical exposures? Is there a chance we could be responding to industrial age chemicals?

An increasing number of studies are emerging supporting the idea that even in contemporary time frames – human populations can indeed evolve. That is, over a hundred or so years. This is just fascinating. For the past year even as I’ve written about Darwin’s finches evolving within a generation or two, the great majority of this book has focused on other species from bugs to minnows — highly fecund species that have adapted over the course of fifty or perhaps twenty-five generations. At twenty-five years a pop for humans, that would be somewhere around 1000 years give or take.

This is a time frames that trivializes chemical exposures, stretching well beyond the lifetime of most industrial-age chemicals (except for long-lived radioisotopes). As bad as we are with chemical management and regulation, we eventually figure out which are particularly egregious and rein them in. It may take decades to recognize our folly– as with organochlorines – but eventually we get it right. So even if any chemicals were to impose a powerful selective pressures, most likely they would be gone within a generation or two.Maybe industrial age chemicals just aren’t all that relevant to the question of human evolution? (Barring any discussion of epigenetics that’s a post for another day, for now check out this video, where as one participant says “everyone has their definition”.)

But what if the pressure was pervasive, reaching across large swaths of a population? And what if it hit us where it really hurt, reproduction?

Here’s a fun hypothetical really, JUST a hypothetical.  Consider a chemical or group of chemicals that act upon reproductive output – not so hard to do considering the apparent wealth of industrial age chemicals that do so. Perhaps they interact with estrogen receptors. They might be subtle, not shutting down reproduction, but just making it that much more difficult to conceive. What if, rather than a scenario like PD James’ Children of Men (where sperm went downhill fast,) women’s estrogen receptors instead evolved just enough to “ignore” estrogen binding plastics and plasticizers or other chemicals that might influence fertility and fecundity? It’s a totally fascinating mental exercise. Because if that were to happen, given all the other stuff estrogen does – the trade offs would be anyone’s guess. Hopefully that is all this will ever be, an interesting mental exercise. But given the fast pace of human evolution – and this brave new chemical world we are creating, you just never know.

Antibiotic resistant bacteria caught in flagrante delicto in wastewater treatment plants

File:Sewer Plant.jpg

A sewage treatment plant, not THE sewage treatment plant

I’ve been writing about antibiotic resistance from the perspective of rapid evolution. That totally drug resistant bacteria exist is scary enough. Now we find that even in places like sewage treatment plants designed to destroy the buggers, they are happily breeding away.

A report out of Rice University this week describes research revealing survival and reproduction of resistant bacteria at two wastewater treatment plants in China. Just the prospect resistant bacteria breeding in sewage plants meant to disinfect water is disturbing enough but there’s more. Because bacteria are incredibly promiscuous, they are sharing their resistance genes via plasmids with other bacteria inside and outside of the plant.

Here is quote from Rice University’s Press Release (Pedro Alvarez led the study and is one of the authors of the report):

“We often think about sewage treatment plants as a way to protect us, to get rid of all of these disease-causing constituents in wastewater. But it turns out these microbes are growing. They’re eating sewage, so they proliferate. In one wastewater treatment plant, we had four to five of these superbugs coming out for every one that came in.”

See more at: http://news.rice.edu/2013/12/16/superbugs-found-breeding-in-sewage-plants/#sthash.v8pUsF1g.dpuf

Quote of the Day

This morning driving back from Boston, there was an NPR story about the right to home school. While explaining why homeschooling was a good thing, one of the students said that she was able to study “creationism and the science and biology of it.” Hmmm. As a scientist I have not waded into the creationism/intelligent design morass; but feel a bit like yes, and you can learn that one plus one equals three, but that doesn’t mean its true.

So in light of that sentiment (sort of) here are a couple of quotes from a paper by Russell Powell, The Future of Human Evolution, (British Journal for the Philosophy of Science, 2012) which set the stage for Powell’s argument that ultimately evolution is inevitable even for us humans, when some would say that science and technology have all but brought humans to an evolutionary halt:

“It is widely believed that modern human populations are no longer evolving in biologically interesting ways. The claim, to be more precise, is that evolutionary biological mechanisms, including and especially natural selection, will play a negligible part in any explanation of the future genotypic and phenotypic landscape of the human species.”

“The idea that humans have largely escaped the mechanisms of biological evolution that have governed the history of life for 3.5 billion years is an extraordinary claim.”

In the end writes Russell , “I conclude that properly conceived, biological evolution is a permanent and ineradicable fixture of any species, including Homo sapiens.”  

I am wondering if these kinds of papers made the “science and biology” reading list of the aforementioned home schooler?

Robot Evolution: about as rapid as it gets?

This isn’t exactly evolution in response to chemicals – but could be argued that it is a rapidly evolving system! I wrote this article for AEON Magazine, a thoughtful and interesting online journal; but it touches upon some of the earliest “in silico” and then more recent attempts to understand the processes of evolution.

A quadrupedal robot used to help evolve gaits.  Courtesy Cornell Creative Machines Lab

A quadrupedal robot used to help evolve gaits. Courtesy Cornell Creative Machines Lab

In a laboratory tucked away in a corner of the Cornell University campus, Hod Lipson’s robots are evolving. He has already produced a self-aware robot that is able to gather information about itself as it learns to walk. Like a Toy Story character, it sits in a cubby surrounded by other former laboratory stars. There’s a set of modular cubes, looking like a cross between children’s blocks and the model cartilage one might see at the orthopaedist’s – this particular contraption enjoyed the spotlight in 2005 as one of the world’s first self-replicating robots. And there are cubbies full of odd-shaped plastic sculptures, including some chess pieces that are products of the lab’s 3D printer.

In 2006, Lipson’s Creative Machines Lab pioneered the Fab@home, a low-cost build-your-own 3D printer, available to anyone with internet access. For around $2,500 and some tech know-how, you could make a desktop machine and begin printing three-dimensional objects: an iPod case made of silicon, flowers from icing, a dolls’ house out of spray-cheese. Within a year, the Fab@home site had received 17 million hits and won a 2007 Breakthrough of the Year award fromPopular Mechanics. But really, the printer was just a side project: it was a way to fabricate all the bits necessary for robotic self-replication. The robots and the 3D printer-pieces populating the cubbies are like fossils tracing the evolutionary history of a new kind of organism. ‘I want to evolve something that is life,’ Lipson told me, ‘out of plastic and wires and inanimate materials.’

Upon first meeting, Lipson comes off like a cross between Seth Rogen and Gene Wilder’s Young Frankenstein (minus the wild blond hair). He exudes a youthful kind of curiosity. You can’t miss his passionate desire to understand what makes life tick. And yet, as he seeks to create a self-assembling, self-aware machine that can walk right out of his laboratory, Lipson is aware of the risks. In the corner of his office is a box of new copies of Out of Control by Kevin Kelly. First published in 1994 when Kelly was executive editor of Wired magazine, the book contemplates the seemingly imminent merging of the biological and technological realms — ‘the born and the made’ — and the inevitable unpredictability of such an event. ‘When someone wants to do a PhD in this lab, I give them this book before they commit,’ Lipson told me. ‘As much as we are control freaks when it comes to engineering, where this is going toward is loss of control. The more we automate, the more we don’t know what’s going to come out of it.’

Lipson’s first foray into writing evolvable algorithms for building robots came in 1998, when he was working with Jordan Pollack, professor of computer science at Brandeis University in Massachusetts. As Lipson explained:

We wrote a trivial 10-line algorithm, ran it on big gaming simulator which could put these parts together and test them, put it in a big computer and waited a week. In the beginning nothing happened. We got piles of junk. Then we got beautiful machines. Crazy shapes. Eventually a motor connected to a wire, which caused the motor to vibrate. Then a vibrating piece of junk moved infinitely better than any other… eventually we got machines that crawl. The evolutionary algorithm came up with a design, blueprints that worked for the robot.

The computer-bound creature transferred from the virtual domain to our world by way of a 3D printer. And then it took its first steps. The story splashed across several dozen publications, from The New York Times to Time magazine. In November 2000, Scientific American ran the headline ‘Dawn of a New Species?’ Was this arrangement of rods and wires the machine-world’s equivalent of the primordial cell? Not quite: Lipson’s robot still couldn’t operate without human intervention. ‘We had to snap in the battery,’ he told me, ‘but it was the first time evolution produced physical robots. It was almost apocalyptic. Eventually, I want to print the wires, the batteries, everything. Then evolution will have so much freedom. Evolution will not be constrained.’

In the late 1940s, about five decades before Lipson’s first computer-evolved robot, physicists, math geniuses and pioneering computer scientists at the Institute for Advanced Study at Princeton University were putting the finishing touches to one of the world’s first universal digital computing machines — the MANIAC (‘Mathematical Analyzer, Numerical Integrator, and Computer’). The acronym was apt: one of the computer’s first tasks in 1952 was to advance the human potential for wild destruction by helping to develop the hydrogen bomb. But within that same machine, sharing run-time with calculations for annihilation, a new sort of numeric organism was taking shape. Like flu viruses, they multiplied, mutated, competed and entered into parasitic relationships. And they evolved, in seconds.

These so-called symbioorganisms, self-reproducing entities represented in binary code, were the brainchild of the Norwegian-Italian virologist Nils Barricelli. He wanted to observe evolution in action and, in those pre-genomic days, MANIAC provided a rare opportunity to test and observe the evolutionary process. As the American historian of technology George Dyson writes in his book Turing’s Cathedral (2012), the new computer was effectively assigned two problems: ‘how to destroy life as we know it, and how to create life of unknown forms’. Barricelli ‘had to squeeze his numerical universe into existence between bomb calculations’, working in the wee hours of the night to capture the evolutionary history of his numeric organisms on stacks of punch cards….

For more article see Robot Evolution.

For more about the early days of computing at the IAS see: An Artificially Created Universe.