Natural movement of genes between unrelated species? Yeah, it happens all over.

One of the memes of the movement against genetic engineering is that transgenic activity is somehow unnatural, but it turns out that interspecies gene transfer is not only natural, but can be critical to species survival.

And there are in nature lots of examples of it. 

(Image: Emerald elysia, Elysia chlorotica, an animal with plant genes that allow it to conduct photosynthesis. Credit: Sidney K. Pierce, used with permission.)

Examples include plant genes finding their way into animals, viruses into human DNA, bacteria into insects, hornworts into ferns and lots more.

Researchers recently have looked into the green sea slug, which is able to get energy from photosynthesis because takes up genetic material from algae and inserts them into its own. That allows the slug, known as the Emerald elysia, to conduct photosynthesis, like a plant does. 

"There is no way on earth that genes from an alga should work inside an animal cell, and yet here, they do,” said study co-author Sidney K. Pierce of University of South Florida and University of Maryland, College Park. “They allow the animal to rely on sunshine for its nutrition. So if something happens to their food source, they have a way of not starving to death until they find more algae to eat."

The slug in this situation takes on a bright green color, from the plant chlorophyll in its genetic makeup.

The process of passing genetic material from one species to another without involving normal reproduction is sometimes called horizontal or lateral gene transfer. Researchers say this is fairly common among single-celled organisms, but is also found in higher forms of life, including plants, insects, and even humans.

The adzuki bean weevil has in its genome genetic material from the bacterium Wolbachia.  And it turns out that Wolbachia have been able to insert their genetic material into any number of other species as well. One fruit fly species has the entire Wolbachia gene package in its own DNA.

And the authors of this paper report on gene transfers going the other way, from plants into bacteria and fungi. They report that it’s not accidental, and acts as a competitive advantage. 

Writes co-author Nikolas Nikolaidis: “Our study reveals a rare phenomenon in molecular evolution where plant genes have been transferred to simple organisms like fungi and bacteria. The protein products of these genes are weakening the plant cell wall allowing plants to grow. In the case of bacteria and fungi, these proteins are related with the ability of these species to colonize plant roots and their virulence as plant pathogens. Our study suggests that by using proteins acquired from their hosts bacteria and fungi have found new adaptive ways to utilize their hosts resources and maybe become more advanced pathogens.”

Viruses  are famous gene transfer agents. They swap genes among themselves through horizontal gene transfer, but also insert parts of their genetic code between and into unrelated species.

“Viruses also carry out natural "genetic engineering": a virus may incorporate some genetic material from its host as it is replicating, and transfer this genetic information to a new host, even to a host unrelated to the previous host,” says a report, Introduction to the Viruses, from the University of California at Berkeley. 

It was long assumed that this couldn’t happen, but it turns out it happens a lot. The concept of mobile genetic elements, which move readily between even distant species, is discussed in last month’s issue of The Scientist. 

The whole discussion throws traditional concepts of Darwinian evolution into question, which is discussed in this paper by Eugene V Koonin and Yuri I Wolf    at the National Institutes of Health. 

Even the human genome is full of material borrowed from unrelated species, which we now pass on genetically from one generation to the next. Our brains contain viruses that got into our genome millions of years ago, and now are fundamental parts of us. They change the way our brains work, and maybe they make us smarter.  

‘Now it seems our own genome is a patchwork of raw genetic material coming from different places with different histories – that to me is very profound,” said Cedric Feschotte of the University of Utah in this article in the online journal Aeon. 

“Standard theory says that mutations are supposed to happen within a species’s own genome, not come from somewhere else entirely. We now know that the appearance of new genes does not necessarily result from tweaks to native DNA, but might instead represent the arrival of far-flung visitors,” writes Ferris Jabr, the author of that report in Aeon.

© Jan TenBruggencate 2015

Tuna, marlin, even birds seeing elevated mercury levels: Asian coal plants likely to blame

Pollution from human sources—like coal plants—is impacting oceans and marine life in worrisome ways. 

A variety of research papers has reported increased levels of toxic mercury in ocean water and marine life, in Hawaiian tuna,in South Pacific Wandering albatross and in other species.

(Image: Yellowfin tuna jumping. Credit: NOAA Fisheries image by Ken Neil.)

For Hawai`i residents, reports are of increasing levels of mercury in yellowfin tuna or ahi are deeply concerning.

There did not seem to be increasing levels through the turn of the century. A 2003 study looked at mercury in Hawaiian ahi during a 27-year span from 1971 to 1998. It found no change during that period in Hawaiian-caught yellowfin, with respect to methylmercury levels. 

But studies from 1998 to 2008 saw steady increases, according to a newly published review of previous studies.

“The authors found that the concentration of mercury in these fish currently is increasing at a rate of at least 3.8% per year. This rate of increase is consistent with a model of anthropogenic forcing on the mercury cycle in the North Pacific Ocean and suggests that fish mercury concentrations are keeping pace with current loading increases to the ocean,” the authors wrote.

Where's all that mercury coming from? It has been well-tracked, and most comes from Asia--China, Japan and Korea appear to be primary sources, according to this report from 2009.

What to do about it?

“Future increases in mercury in yellowfin tuna and other fishes can be avoided by reductions in atmospheric mercury emissions from point sources,” wrote the authors of the paper that found annual 3.8 percent increases in yellowfin.

A little information about methylmercury, the most toxic form of the silver metal.

“The organic form of Hg (mercury), methylmercury, is of greatest concern because it is a potent neurotoxin and because it accounts for > 95% of the Hg in fish,” says a report, “Methylmercury in Marine Ecosystems: Spatial Patterns and Processes of Production, Bioaccumulation, and Biomagnification.”  More on human impacts later in this article.

A 2013 study in the journal Nature Geoscience, by a team that includes Hawai`i researchers, had already suggested things were changing. 

It looked at nine species of marine fish that feed at different levels. It appears that the toxic methylmercury is formed by microbes that attach themselves to particles containing regular mercury, that fall onto the ocean from the atmosphere. It is formed, the paper says, “by methylating microbes that live on sinking particles.”

In theory, as more mercury from the stacks of Chinese and other Asian coal-fired plants blows out over the Pacific, it dumps more mercury on the ocean. That mercury is converted into methylmercury by marine microbes, and is taken up in the oceanic food chain.

"This study reinforces the links between mercury emitted from Asian countries and the fish that we catch off Hawaii and consume in this country," said the paper’s lead author, Joel Blum.

Since methylmercury is more prevalent in deeper water, it makes sense that deeper-feeding fish would have higher levels. And they do.

"We found that predatory fish that feed at deeper depths in the open ocean, like opah and swordfish, have higher mercury concentrations than those that feed in waters near the surface, like mahi-mahi and yellowfin tuna," said Brian Popp, a University of Hawaii at Mānoa geology and geophysics professor. He was quoted in a 2013 report.

 What's interesting there, of course, is that ahi are comparatively shallow feeders. If they're getting higher levels of methylmercury, that is perhaps an indication that the levels are far higher than they once were.

And as you might expect, mercury levels ARE up. This US Geological Survey study found mercury levels up 30 percent in the Pacific in the past 20 years. It projects another 50 percent increase by 2050. 

There's lots of data on this. Here's a paper from the journal Global Geochemical Cycles.

A report on the Wandering albatross, the bird with the longest wingspan in the world—from 8 to nearly 12 feet—finds increasing levels of mercury, cadmium and persistent organic pollutants in the birds.

While adult survival seems to be unaffected, the paper reports that the pollutants are “negatively impacted long-term breeding probability, hatching and fledging probabilities.”

Some of the pollutants, like PCB and DDT, are long-banned but still persist in the environment. Others like mercury may be associated with coal-fired power and industrial plants.

What this means to humans who eat marine life depends on the person. Methylmercury is highly toxic, but is most toxic to fetuses and infants—individuals with developing brains. It is less of a threat to adult males and adult women who will not become pregnant and are not breastfeeding infants.

The Hawai`i Department of Health factsheet on eating marine fish can be found here.

The U.S. Environmental Protection Agency says “women of child-bearing age are the population of greatest concern. Children of women exposed to relatively high levels of methylmercury during pregnancy are at greater risk for a variety of developmental and learning disorders.”

And it’s not just ahi. Here is what the U.S. Food and DrugAdministration says about eating fish, specifically for women and children:

“Do not eat Shark, Swordfish, King Mackerel, or Tilefish because they contain high levels of mercury.

“Eat up to 12 ounces (2 average meals) a week of a variety of fish and shellfish that are lower in mercury.

“Five of the most commonly eaten fish that are low in mercury are shrimp, canned light tuna, salmon, pollock, and catfish.

“Another commonly eaten fish, albacore ("white") tuna has more mercury than canned light tuna. So, when choosing your two meals of fish and shellfish, you may eat up to 6 ounces (one average meal) of albacore tuna per week.

“Check local advisories about the safety of fish caught by family and friends in your local lakes, rivers, and coastal areas. If no advice is available, eat up to 6 ounces (one average meal) per week of fish you catch from local waters, but don't consume any other fish during that week.

“Follow these same recommendations when feeding fish and shellfish to your young child, but serve smaller portions.”

© Jan TenBruggencate 2015

No consensus on genetic engineering safety? Depends on your definition of consensus.

Opponents of genetic engineering are cheering a peer-reviewed survey that has found 300 self-selected folks willing to say they don’t think there’s consensus on the safety of the technology.

The paper has been out for a couple of years, but press coverage keeps coming out in the anti-GMO field. It’s of interest to Hawai`i both because of the power of the genetic engineering furor in the Islands, and because a co-author is Vandana Shiva, the anti-GMO diva who recently spoke in the Capitol rotunda during the opening day of the Hawai`i State Legislature.

There are lots of problems with that paper’s claims, including that much bigger groups claim the science of genetic engineering is pretty well settled and that GM foods are safe to eat.

One of them, the Pew Research Center, in collaboration with the respected American Association for the Advancement of Science, last week (Jan. 29, 2015) published its survey, which found that of 3,700 scientists queried, 88 percent said GMO food is safe to eat. 

If you read the no-consensus study, several things leap out. Not the least of them is that several of the authors walked into the study with a background in attacking the genetic engineering industry.

One of the authors is anti-GMO activist Vandana Shiva, who famously asserts credentials as a scientist but whose degree is in arts and humanities. Her own bio says she is “trained as a physicist,” specializing in quantum theory, which has little to do with agriculture, chemistry, genetic engineering and epidemiology. 

Co-author Ricarda Steinbrecher holds the opinion that “Genetic Engineering is a test tube science and is prematurely applied in food production.”

Co-author Philip Bereano is described as “engaged activist concerning genetically modified (GM) foods.” 

Co-author Eva Novotny, in a letter to The Guardian newspaper, argues in an article headlined “Pro-GM scientists should admit defeat and redirect their talents,” and that “corporate control must be dismantled.” 

There’s a fascinating “pot calling the kettle black” issue, as this internal circle of like-minded anti-GMO stakeholders in its paper uses this language: 

“Decisions on the future of our food and agriculture should not be based on misleading and misrepresentative claims by an internal circle of likeminded stakeholders that a ‘scientific consensus’ exists on GMO safety.”

Then there is the issue of the paper’s content.

First, it’s not an original scientific paper at all. Rather, it’s a summary of a study on the activist website of the European Network of Scientists for Social and Environmental Responsibility. ENSSER's own website says it is focused on “the negative impacts of new technologies and their products.” 

It is clear that some of the concerns are not about genetic engineering but about genetic engineering for pesticide resistance. It argues that “some reviews and individual studies have associated them with increased herbicide use.”

The 300 scientists are self-selected, and haven't necessarily done any research on the subject: The ENSSER website asks you to write in and sign up. Interestingly, there are lots of doctors, but also lots of veterinarians and foresters, a land planner, and a bunch of folks whose expertise is unlisted. One says he is an official of the controversial Club of Rome.

And the fundamental question: The paper argues that there is no consensus on GMO food safety. It says there isn’t consensus on the grounds that there are studies that disagree with that conclusion.

This raises the core issue: What does consensus mean?  

There is the problem. If you go to Webster, it means two different things, depending on who’s using it: unanimity and majority. I used the Merriam Webster's Collegiate Dictionary, 10th Edition.

So, the 300-scientist paper is absolutely right if consensus means unanimous agreement; clearly if one person disagrees, you don’t have that. This climate change denial website argues that it's not consensus unless "all scientists of any stature believe." That's a pretty tough standard, by which you might have trouble getting consensus around the existence of gravity.

But the 300-scientist paper is absolutely wrong if you mean majority, because as Pew suggests, a very, very big majority says they’re fine with eating GM products. This climate change site suggests a consensus is a majority.

Who are the PEW AAAS scientists who think eating genetically engineered food is safe? Those polled include 3,748 scientists, including 1,802 in the biological and medical sciences. The rest of them are spread between chemistry, earth sciences, engineering, math and computer sciences, physics and astronomy and social sciences and policy.

They were asked about a range of issues. Seventy nine percent of them feel it’s a major problem that news services don’t distinguish between “well-founded and not well-founded scientific findings.” And 84 percent said it’s a major problem that the general public doesn’t know much about science.

A full 98 percent believe in evolution. Eighty-seven percent believe “the earth is getting warmer mostly because of human activity such as burning fossil fuels.” Ninety-four percent believe climate change is a very or somewhat serious problem. Most favor nuclear power and most oppose fracking. Eighty-six percent believe ALL children should be vaccinated.

And on the issues at hand? Sixty-eight percent say it’s generally safe to eat foods grown with pesticides and 88 percent say it’s generally safe to eat genetically modified foods. That's about 3,300 of the 3,748 polled.

As an afternote, I'll apologize for the number of hyperlinks in this article. I wanted to be sure to attribute the various statements and studies referenced.

© Jan TenBruggencate 2015

Below the bottom of the sea, a third of our planet's biomass breathes sulfate

A massive group of sulfate-breathing microbes, potentially representing a third of all the life on our planet, has been identified living below the ocean floor.

It’s an amazing finding led largely by researchers at the University of Hawai`i, and it adds a whole new wrinkle to the study of how carbon is cycled on and in the planet. 

(To collect samples beneath the seafloor more than a mile and a half below the ocean’s surface, the GeoMicrobe [box at left], developed at the University of Hawaii Manoa, was hooked into the Circulation Obviation Retrofit Kit [CORK] observatory [right]. Credit:  Deep Submergence Group, Woods Hole Oceanographic Institution.)

The finding was reported in the journal Frontiers in Microbiology.

The authors are Alberto Robador, Sean P. Jungbluth, Douglas E. LaRowe, Robert M. Bowers, Michael S. Rappé, Jan P. Amend and the late James P. Cowen. They represent the University of Hawai`i’s NASA Astrobiology Institute, the Hawaii Institute of Marine Biology and the Department of Oceanography at the School of Ocean and Earth Science and Technology, as well as the Department of Earth Sciences and Department of Biological Sciences at the University of Southern California, Los Angeles.

The partnership that led to these discoveries was announced in 2010. 

The team dug two boreholes in the ocean floor, careful to seal them to prevent contamination from ocean water, and collected samples from the vast aquifer that exists under the bottom of the sea.

Why look there? “The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown,” the authors write.

When they went looking, they found there’s lots of biological life there—a wide array of life forms in an area that characteristically does not have enough oxygen to support ocean life as we commonly recognize it. The organisms “breathe” using a process called sulfate reduction.

They are able to use the sulfate-rich water to break down carbon-based material that drops to the ocean floor with the death of marine life—algae, whales, fish and do forth.

“This is the first direct account of microbial activity in these type of environments, and shows the potential of these organisms to respire organic carbon,” said lead author Robador said in a press release.

It’s a good thing they issued the press release, because with due respect to the authors, when they’re writing for each other, it’s not as if most folks can even understand them: 

“Our sulfate-reduction rate measurements and sulfate-reducing microbial community analysis are indicative of the metabolic potential and broad dispersal of organotrophic sulfate-reducing microbial groups along fluid flow paths within deeply buried basaltic crust with significant implications for the marine carbon cycling.”

The researchers used DNA sequencing to study the life forms they found, most of which have not yet been described. 

“It’s a massive biome dominated by microbes that scientists know very little about,” says a University of Hawai`i press release. 

Because there is so much of it, it apparently plays a significant role in the planet’s carbon cycle, and getting a better understanding of it can help us understand how the Earth works.

“This is very exciting work that links rates of microbial activity to novel groups of microorganisms, particularly because we are combining cutting edge molecular biology techniques with samples collected from a part of our planet that is less accessible than outer space,” said University of Hawai`i researcher Jungbluth in another press release.

In the words of the study itself: “Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling.”

© Jan TenBruggencate 2015