HOPE IN SCIENCE

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It’s impossible to ignore all of the discouraging stories in the news these days, but there are also stories of great hope, including in the various fields of science. Here are a few recent ones:

In October 2017 a couple of teenage Cystic Fibrosis patients in the UK who’d been given double lung transplants developed bacterial infections that didn’t respond to any of the drugs available.

A University of Pittsburgh micro­biologist named Graham Hatfull had been gathering the world’s largest collection of bacteriophages—viruses that prey solely on bacteria—more than 15,000 of them, so a colleague at London’s Great Ormond Street Hospital called him up. Although Hatfull’s team couldn’t save one of the patients, they were able to identify four phages that would attack the other patient’s infection once they were “activated” via some genetic modification. That patient is slowly recovering. The drawback is that this method is ultra-specific—it involves tailoring a cure for each individual patient. As bacteria and viruses become more drug-resistant, this development offers hope, though it needs to be greatly improved in efficiency to be practical on any larger scale. And there are an estimated nonillion phages that haven’t yet been discovered and catalogued (a US nonillion is a 1 followed by 30 zeroes). Other top-level medical science facilities are now exploring this territory.

With climate change threatening to make some dry areas of the planet even drier, and with industry and agriculture’s voracious appetite for water, the need to reclaim industrial waste water and even produce drinkable water from the oceans will become increasingly urgent. Now some researchers from Columbia University have developed a process called Temperature Swing Solvent Extraction which involves mixing amine solvents with heavily-salted water at room temperature. The solvent-and-water is lighter than the salts and can be extracted, and then higher temperatures separate the solvent from the pure water. Experiments show that up to 98.4% of the salt can be removed, which is comparable to reverse osmosis. But this new process requires relatively little energy and produces very high water recoverability compared to current desalination methods. If it can be scaled up, it could be a real lifesaver in the world of the future.

Researchers who call themselves agroecologists are promoting more natural ways of growing crops. This approach not only nourishes soil, which makes it more productive and its crops more nutritious, but by helping the microorganisms in the soil to flourish, it also helps to absorb carbon dioxide and water vapour from the air at a much greater rate than scientists thought possible. CO2 and water vapour are two of the most prevalent greenhouse gases driving global climate change. Plants soak up carbon and share it with the microbes in soil, which helps the soil retain water. Scientists warn that, although reducing the amount of CO2 we produce is absolutely necessary, it’s no longer enough to ward off serious climate effects. So we need to find ways to remove excess carbon and water from the atmosphere, and the methods of agroecology could be very effective in doing this. Plus it reduces dependence on chemical fertilizers and pesticides while making food more nutritious. Sounds like a big win in my book.

In a similar story, though on a much smaller scale, astronauts on the International Space Station will be testing an algae bioreactor—a contraption that will use the CO2 the crew exhales to grow algae which can be used as food. On one level, this could be a great help for long space voyages and colonies on other planets, but it has often been proposed that large algae farms here on Earth, perhaps on the oceans, could be an abundant source of food while, again, removing a lot of unwanted carbon dioxide from the atmosphere.

All of these stories offer much-needed hope in trying times. Science fiction has been coming up with ideas similar to these, and many more, for decades, as authors imagine the exploration and exploitation of outer space. Science is constantly proving that radical ideas can be turned into reality, and I would argue that science fiction provides the fertile imaginative “soil” from which harvests of new scientific developments spring.

Examples like these also reinforce my belief that hopeful and optimistic SF is still not only defensible, but perfectly sensible. We can’t ignore the potential hazards of human technology and growth, but we also have a duty to promote science as a force for good.

It truly is, when we make it so.

CAN WE RESTORE THE SPECIES WE'RE MAKING EXTINCT?

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For 20,000 years and more the skies of North America darkened Spring and Fall with the migration of from three to five billion birds. They were called passenger pigeons. Deforestation and hunting through the 1800’s changed that. In 1914 the last passenger pigeon died at the Cincinnati Zoo.

The American bison once numbered as high as 30 million. By 1889 humans had reduced their population to about a thousand animals. Fortunately, some humans found reasons to reverse that trend and there now might be as many as half a million bison living on the continent.

We have the ability to destroy the animals, birds, reptiles, and fish with which we share the planet like no other species in history, but we also have the power to stop the destruction, and are now even learning to bring species back.

There have been five mass extinctions on Earth beginning with the end of the Ordovician Era 444 million years ago that saw the end of 86% of all life forms at the time. You’re more likely to think of the last one, the end of the Cretaceous Period 66 million years ago that saw the demise of the dinosaurs. Most of those extinctions have been blamed on sudden climate change, including the asteroid strike that wiped out Dino and his buddies. It takes millions of years for the number of species to reach pre-disaster levels. And, needless to say, those are replacements—the original creatures are gone for good.

Now, many scientists believe we’re undergoing a 6th extinction event, this time caused by…guess who?

The passenger pigeons and the dodo are just two of the 140 bird species, 34 types of amphibian, and at least 77 mammals that scientists say have become extinct since the year 1500, thanks to human activity, especially the destruction of their habitat. Those are the ones we know about. There are still a lot of species, especially insects, reptiles, and amphibians, that have never been classified and could very well be gone before we ever know about them. Some estimates suggest the planet loses hundreds of species a year. And as our powers to shape the environment grow, intentional and not, the rate of extinctions is quickly rising. The International Union for the Conservation of Nature recently predicted that virtually all species currently considered critically endangered and more than two-thirds of endangered species will be gone within the next century. Scientists from Aarhus University in Denmark have calculated that it would take up to 5 million years of evolution to return the planet’s diversity to current levels, and 7 million years to return it to what it was before modern humans showed up and began our path of destruction.

Is there hope? Of course there is. We can curb our out-of-control consumption and stop so much habitat destruction, razing of rainforests, scouring the bottom of the oceans, and spewing plastic and pollution everywhere. Will we? Well, that’s a whole other question.

What about the species already gone, and those it’s likely too late to save? That’s where human technology can actually have a positive side. There are a number of exciting initiatives that point the way to a brighter future.

I’ve mentioned the Svalbard Global Seed Vault in Norway in previous blogs. Built ten years ago to preserve and protect the world’s plant diversity from disaster, it’s reputed to contain a million different varieties now. Seeds evolved to remain dormant when required, so they store pretty well. But what about animals and birds? Projects like the Frozen Ark in Nottingham, UK and the Australian Frozen Zoo in Victoria are working to preserve large collections of frozen DNA from the creatures of the world. That has its challenges certainly. So what if you didn’t have to physically preserve the DNA? For some years now it’s been possible to sequence DNA—transcribe the whole chemical code that determines a species (and an individual’s) cellular makeup. The UK’s Natural History Museum, Royal Botanic Gardens and Wellcome Sanger Institute have joined together in the Darwin Tree of Life Project to sequence Britain’s 66,000 species of animals, plants, protozoa and fungi. Harvard University and other partners around the world are undertaking similar initiatives in the hope that the genetic codes of one-and-a-half million species will eventually be mapped.

Mind you, all of that is like having the full blueprints of a house without the tools or materials to actually build it. We don’t have the technology to recreate plants or animals from scratch like building a Lego set from the instructions. But one day we will.

In Melbourne, Australia, an American scientist named Ben Novak has been working to recreate passenger pigeons by engineering the DNA of ordinary rock pigeons. A team at Harvard is attempting to produce a woolly mammoth by splicing mammoth DNA into the genome of Asian elephants. The tool they use is called CRISPR-Cas9, a combination of repeating RNA (to use as a guide) and the protein Cas9, which allows scientists to basically “cut and paste” DNA in existing sequences. Inserting DNA from an extinct species into the genome of a genetic relative species is how the fictional dinosaurs were created in Jurassic Park (though if anyone’s trying to do that in real life, they’re not admitting it!)

So with all of these efforts to preserve and some day recreate plants and animals, we could theoretically re-introduce forms of life to our planet after they’re gone, or even take them to a new planet somewhere and reform that world in Earth’s image to some degree. That’s very hopeful. Does it excuse us for causing these extinctions in the first place? Absolutely not!

Surely it would be so much better to get our ravenous impulses under control and actually share our beautiful planet with the other species that belong here just as much as we do.

ADAPTING HUMANS TO OTHER PLANETS, PART TWO

In my last post I speculated about how we might adapt ourselves to the environments of other planets rather than trying to terraform them or forever be confined to enclosed settlements and space suits. I used Mars as an example of an “earthlike” planet we might consider colonizing.

A Mars-type planet would be an easy challenge compared to others like Venus. The Venusian atmosphere is also mostly carbon dioxide but the air pressure at the surface is ninety times that of Earth, like being a thousand meters deep in the ocean. We know that fish and other creatures can exist at those depths, and some whales can dive even deeper for a time—so it’s not inconceivable that our bodies could be adapted for it (maybe even encouraged to grow a hard shell?) But again, we wouldn’t be breathing—air at that pressure is basically a fluid. We’d have to get oxygen and/or energy another way. And Venus is hot—hotter than Mercury—about 460 C at the surface. If there is any part that might be relatively hospitable to humans it would be the upper atmosphere, about fifty kilometers high, where the temperature and pressure are nearly Earth-normal. There are obstacles though: winds over 300 kilometers per hour and clouds full of sulphuric acid!

OK, so maybe Venus-like worlds will be beyond biological adaptations and require either full space suits or at least extensive mechanical adaptations.

Gas giant planets don’t hold much attraction as homes-away-from-home, but many of their moons might. With a tough enough skin and a metabolism that uses chemosynthesis instead of air-breathing, maybe we could survive in a near-vacuum, but it’s hard to imagine that we could ever adapt our bodies to temperatures that can freeze water as hard as granite. On Jupiter’s moon Europa, for example, the temperature at the equator (you know, the beach resort zone) averages about -160 C. Where there is a possibility of survival, however, is under the icy surface in an ocean of water. Someday we may create humans who can function as aquatic creatures, in which case our own planet’s oceans will provide a vast amount of space to explore and inhabit.

There’s a chance that we’ll discover planets elsewhere that are almost identical to Earth and already support life. In that event, our problem will be that some of the life, particularly microorganisms, could be utterly hostile to humans. Deadly germs or bacteria. Then we’ll need to either adapt our immune systems to cope with the pathogens, or adapt our whole bodies to co-exist with the alien organisms (although, to be accurate, we’ll be the aliens).

I haven’t even touched on the whole area of technological enhancements to the human body—turning us into partly-cybernetic organisms, or cyborgs. Maybe in another blog someday. And, of course, there are huge philosophical and ethical questions involved whenever the question of bio-engineered humans is raised. Is it too big a risk? If such genetic engineering had to occur at an early age or even at the fetal stage, could we make such decisions for our children? Most of all, how much can you change someone before they’re no longer human? We don’t mind the idea of fictional superheroes transformed by a radioactive spider bite or gamma radiation—the reality might evoke feelings that are quite different.

For now, I’m content to leave this as an exercise of the imagination, but the time will come when we achieve the capability for such things. I hope we’ll have resolved our questions about it by then.

COULD HUMANS BE ADAPTED TO OTHER PLANETS?

In a recent post I mentioned that there are huge amounts of water elsewhere in the solar system—much more than actually exists on Earth. And when scientists assess the potential of other star systems to host life, the foremost yardstick they use is the presence of water, especially liquid water. Where there’s liquid water, there could be life that we would recognize. So a planet orbiting its sun in the so-called “Goldilocks zone” (not too hot, not too cold) might have liquid water and thus be capable of supporting life. Maybe.

This fairly narrow view isn’t so much based on the idea that we only want to meet aliens that look like us (as in most Star Trek episodes) but more because we want to visit places that will present the fewest obstacles to our survival there. Lots of oxygen in the air would be nice. Clean drinking water. Reasonable weather. Gravity that doesn’t make us feel like we’re wearing lead overcoats.

You’ve probably heard news stories about “earthlike” planets being discovered around other stars. That description usually only means that they’re rocky planets instead of gas giants, and they’re not frozen or roasting hot. That’s it. Everything else about them might be far different from Earth—we just don’t know because those planets are too far away. We do know about the planets in our own solar system, and by the above standards Mars would be considered earthlike, except a little cold. But we certainly can’t live there. At least, not yet.

For humans to survive on another planet—in this solar system or any other—there are three ways to do it. The ways that get the most attention are: 1) building habitats (even domed cities) that will protect us from the planet’s hostile elements and enclose a simulated Earth environment; and 2) change the planet’s entire ecosphere into a close approximation of Earth’s—what is called terraforming. Enclosed habitats will always be very restrictive and costly to expand, while terraforming some place like Mars would take thousands of years.

The third option is to change the human body itself in ways that will adapt us to the alien environment.

On Mars that would require quite a few changes. We know that people can adapt to colder climates (especially over a number of generations) but even Mars’ most hospitable climes would require genetic tweaking to rev up our metabolism, increase blood flow, and grow much thicker layers of insulating fat under our skin. We’d have to grow a tougher skin, too, with closable orifices—even skin pores and tear ducts—to prevent the low air pressure from boiling away our bodily fluids. These things aren’t inconceivable as we get better and better at gene splicing—we’d find organisms with those traits here on Earth (perhaps creatures that live in extreme environments) and splice the necessary genes onto our own genome. Even so, a few more mechanical implants might also be in order, like heating coils in our nostrils to warm our inhaled air!

Mars’ atmosphere is mostly carbon dioxide with very little oxygen, so to avoid the need to carry air with us we’d have to either re-engineer our body cells to use some energy source other than oxygen, or get assistance from something that can make the oxygen we need from CO2. Plant life uses photosynthesis to produce food energy from carbon dioxide and water using sunlight (but it’s slow). Creatures that live around deep-sea volcanic vents use chemosynthesis instead, getting their energy, not from sunlight, but from the oxidation of compounds like hydrogen sulphide gas. Giant tube worms, crabs, clams and others are filled with proteobacteria and archaea—some of the earliest life forms on the planet—which replace their usual digestive tracts of stomach, intestines etc. And we know many kinds of algae and bacteria that can produce oxygen from materials in their environment, including the bacteria Methylomirabilis oxyfera which extracts oxygen from nitrates in the river mud where it lives. Since our bodies already carry around hundreds of types of bacteria that help keep us alive, it’s not a huge stretch to believe that a few additional species might help us exist on other worlds.

Mars would be one of the easier planets for us to adapt to. And, of course, there’s the whole ethical question of whether or not we should tinker with the human body to that extent at all. But that topic will have to wait until my next post. In the meantime you can read some other people’s thoughts about this here, here and here.

EDITING THE GENOME

A genetic technology discovered in 2012 made news again this month when some researchers at the Salk Institute’s Gene Expression Laboratory were successful in removing the HIV virus (which causes AIDS) from cells that had been attacked. HIV subverts the cell’s own mechanisms to make copies of itself, and embeds itself in the cell’s DNA. Patients have to keep taking drugs for HIV, because it can crop up again years later. The new technique removes the active HIV within the cell but also “snips” it out of the DNA, suggesting it could provide a permanent cure (though the success rate isn’t 100% yet).

The technique has been called “DNA scissors” because it really targets specific segments of DNA and cuts them out. A lot of DNA has repeat sequences known as CRISPRs with spacer DNA between. Cas proteins are special enzymes able to cut DNA, especially the enzyme Cas9 which can target specific spots in a sequence and make a break. The cell’s repair systems then re-splice the DNA strand with the cut segment removed.

The use of CRISPR-Cas9 technology to remove HIV sounds like fantastic news, but the same method can also be used to target and “edit out” other pieces of DNA just as well. That opens up a whole new can of worms.

There are many human afflictions that have been linked to a specific gene or genetic mutation. Presumably, CRISPR-Cas9 could be used to remove many undesirable bits of DNA and cure a variety of chronic genetic conditions like Cystic Fibrosis or Haemophilia. But the question of what is “undesirable” can be very subjective. HIV is bad, but are exceptionally long limbs also bad? What about freckles? Where is the line drawn? There are serious ethical concerns that this technology will be used for “non-therapeutic” purposes. Think of all the money that’s spent on purely cosmetic medical services, trying to achieve a ridiculous standard of beauty. And, of course, the spectre of engineering “ethnically pure” babies raises its ugly head again.

For another thing, although we’ve learned a lot about genetics in recent decades, there’s a lot more to learn, especially about the interconnectedness of our body systems. Only 2% of human DNA codes for the production of proteins that make our cells. The other 98% of non-coding DNA includes instructions and triggers that direct how the coding DNA behaves. There is still much to know about that.

A “slip of the scissors” could cause errors that might have far-reaching consequences: mutations that might be viable but unwelcome or outright dangerous (X-men-type superhuman abilities notwithstanding). And even if no mistakes are made, our deliberate interventions will almost certainly have long-term repercussions. In one of my novel manuscripts I have extremists use an engineered virus to “snip out” the pieces of the human genome connected to violent behaviour, creating a pacifist race. Some might think that would be a great result, but the consequences of such a thing are unknowable. We might find real cause to regret it. The same could be said about eradicating many conditions we generally consider undesirable. We don’t know the long term consequences. There’s no way we can know them.

Think of DNA as building plans. No-one wants unsightly extra nails sticking out to catch the unwary, but removing the wrong nails in the ridge beam of a peaked roof, a lintel of a doorway, or the top of a staircase could spell disaster.

I’m not against technological progress. But I am very much in favour of being sure we have the knowledge to reverse our tampering before we go ahead and do it.

Let’s know more about where all the nails should go before we start pulling them out and the roof falls in.

BACK TO THE BASICS IN GENETIC ENGINEERING?

At some point in Earth’s history, the first living cell was produced from what’s popularly called a “witches brew” of chemicals in the water of our newborn planet. Then the next big leap was when those first single-cell organisms became multicellular, allowing for specialization of function and the beginnings of the diversity we know today. We’re not sure how that happened, or exactly what triggered it, so for decades chemists have searched for the answer with a wide range of experiments.

Mostly, when we think about evolution, we think in terms of major changes occurring over millions of years, if not billions. Especially a transition as pivotal as from single cells to multicellularity. But now a team of scientists at the University of Minnesota has encouraged cells of simple brewer’s yeast to evolve into multicellular clusters within just two months!

How? By creating conditions that forced it to evolve. Their process is described in a good Wired article here, but essentially the researchers created an environment in which yeast cells that clustered together were given an advantage in reproducing—so that’s exactly what the cells did. Within two months they’d formed permanent multicellular clusters of cells, featuring specialized components and ready to diversify.

The lead researchers suggest that, when we want to produce specialized organisms for industry or medicine, complex genetic engineering might be far more complicated than necessary. We might be better off shaping evolution by doing the job that natural selection has done, but doing it faster. Farmers have done something similar for centuries breeding animals and crops.

To my way of thinking, that method seems a lot less likely to produce unintentional genetic creations that might prove unwelcome or even dangerous.

Sometimes simple is better.