Tag Archives: biotechnology

The lab leak hypothesis is dead. Long live the lab leak hypothesis!

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The lab leak hypothesis is back baby! Well, there is no new scientific evidence. But the U.S. “intelligence community” has now reported that it is officially split on the issue, with some agencies favoring the hypothesis. Snopes has a good explainer. The intelligence agencies’ main argument seems to be that…there is no new scientific evidence. So do the scientists and intelligence community even disagree? Or is there a science communication problem here? The scientists may be saying a natural origin is more likely than not, but the evidence is not so strong that they are willing to completely reject other hypotheses. The intelligence agencies meanwhile may have a much lower bar in terms of uncertainty, and they have an axe to grind with China. I haven’t forgotten their “intelligence assessment” of Iraq’s weapons of mass destruction, on which there was unanimous agreement.

It seems to me there are some different flavors of the lab leak hypothesis though. We know the Wuhan lab was working with bat viruses. We know they at least applied for funding at some point for genetic engineering experiments on bat viruses, because a U.S. organization was a party to that and it has been made public. We know their safety standards have been criticized. So…a lab researcher or employee could have been exposed and infected by a naturally occurring virus that was being studied there. Or they could have been exposed and infected by a genetically engineered virus that was being studied there. If the latter happened, that genetically engineered virus could have been under study for legitimate medical and public health reasons, even safety standards were inadequate. Or, maybe this is a biowarfare laboratory run by Dr. Evil. Nobody does bioweapons research by international treaty, and I just assume everybody including the United States does it.

If the problem is not the existence of adequate safety standards, but their implementation and enforcement, there are fairly obvious things that could be done to minimize the risk of a future lab leak. Training, inspections, accountability. Something akin to the IAEA’s nuclear weapons inspection regime could work. It would be in everyone’s best interests to agree and follow this course of action, right?

February 2023 in Review

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Sorry to all my faithful readers worldwide (who I could undoubtedly count with the fingers of one hand with some left over) for my lengthy posting gap. Anyway, let’s have a look at what I was thinking about in February.

Most frightening and/or depressing story: Pfizer says they are not doing gain of function research on potential extinction viruses. But they totally could if they wanted to. And this at a time when the “lab leak hypothesis” is peeking out from the headlines again. I also became concerned about bird flu, then managed to convince myself that maybe it is not a huge risk at the moment, but definitely a significant risk over time.

Most hopeful story: Jimmy Carter is still alive as I write this. The vision for peace he laid out in his 2002 Nobel Peace Prize acceptance speech is well worth a read today. “To suggest that war can prevent war is a base play on words and a despicable form of warmongering. The objective of any who sincerely believe in peace clearly must be to exhaust every honorable recourse in the effort to save the peace. The world has had ample evidence that war begets only conditions that beget further war.”

Most interesting story, that was not particularly frightening or hopeful, or perhaps was a mixture of both: It was slim pickings this month, but Jupiter affects the Sun’s orbit, just a little bit.

January 2023 in Review

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We’re now 1/12th of the way through 2023. Is this really the fabulous science fiction future we were promised? Well, at least the Earth is not a smoking ruin, at least most parts of it.

Most frightening and/or depressing story: How about a roundup of awful things, like the corrupt illegitimate U.S. Supreme Court, ongoing grisly wars, the CIA killed JFK after all (?), nuclear proliferation, ethnic cleansing, mass incarceration, Guantanamo Bay, and all talk no walk on climate change? And let’s hope there is a special circle of hell waiting for propaganda artists who worked for Exxon.

Most hopeful story: Bill Gates says a gene therapy-based cure for HIV could be 10-15 years away.

Most interesting story, that was not particularly frightening or hopeful, or perhaps was a mixture of both: Genetically engineered beating pig hearts have been sown into dead human bodies. More than once.

Pfizer and “gain of function” research

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This Pfizer press release just confirms that the technology to make genetically engineered viruses is widespread:

we have conducted research where the original SARS-CoV-2 virus has been used to express the spike protein from new variants of concern. This work is undertaken once a new variant of concern has been identified by public health authorities. This research provides a way for us to rapidly assess the ability of an existing vaccine to induce antibodies that neutralize a newly identified variant of concern…

In a limited number of cases when a full virus does not contain any known gain of function mutations, such virus may be engineered to enable the assessment of antiviral activity in cells. In addition, in vitro resistance selection experiments are undertaken in cells incubated with SARS-CoV-2 and nirmatrelvir in our secure Biosafety level 3 (BSL3) laboratory to assess whether the main protease can mutate to yield resistant strains of the virus.  It is important to note that these studies are required by U.S. and global regulators for all antiviral products and are carried out by many companies and academic institutions in the U.S. and around the world.

Pfizer

So they aren’t creating genetically engineered bioweapons of mass destruction, but they could if they wanted to. Somebody somewhere probably is. Not the U.S. government, which has no track record of lying or trying to dominate the world, and doesn’t collude with big business entities with the technology to do so.

2022 – a “breakthrough year” for transplanting genetically modified pig organs into people

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Yes, the headline pretty much describes what this Wired article is about. The following things have happened:

  • Pig hearts were genetically modified to reduce their odds of being rejected by human recipients.
  • A genetically engineered pig heart was transplanted into a human being, who lived for 60 days. This was considered a success.
  • Genetically modified pig kidneys were transplanted into a brain-dead person and the body was kept alive(?)/functioning for 77 hours.
  • Genetically engineered pig hearts were transplanted into two “recently deceased” human bodies and kept beating for three days.
  • It’s not clear from the article exactly when this happened, but a genetically modified pig heart was transplanted into a baboon and the baboon lived for over two years.

There are some obvious ethical questions here. The living human beings who took part in these studies were close to death and had no other viable options that would extend their lives, and I would assume that both they and the “recently deceased” individuals consented to the tests. And there are people dying every day because their organs fail before they get to the top of the transplant lists. I suppose I would let them use my recently deceased body in this way if it would help someone else. It seems a bit creepy, but to surgeons a human body is just a machine and they are mechanics. And after they shut down my pig heart or whatever, they could still use my body as a crash dummy. Or could they use dead bodies with functioning organs as crash dummies? There’s a disturbing thought, but if it would save the lives of people with actual brains and loved ones it would not be obviously unethical.

Now if we were writing a science fiction horror story, we could probably think of other places to go with this. Paul Macauley’s 1998 story collection The Invisible Country comes to mind. These are mind-blowing, disturbing stories about mistreatment of genetically engineered baboon-human hybrids who are kept as slaves, prostitutes, and worse. Using a deceased human body with no functioning brain for these purposes would be very creepy but less obviously unethical.

Trends in Ecology and Evolution horizon scan

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This journal does an annual “horizon scan” of of emerging topics and issues. Here are a few that caught my eye:

  • “bio-batteries” – “DNA-enabled biobattery technology uses a set of enzymes coupled to DNA to degrade organic compounds, releasing electrons and generating electricity…Such batteries could theoretically supply power densities in orders of magnitude greater than widely used lithium-ion batteries”. There are also new processes for extracting lithium more sustainably from waste materials. So there is some hope that the resource and waste limitations to scaling up renewable energy can be solved. Thermophotovoltaic cells are a third energy storage technology mentioned.
  • more practical methods of converting human urine to fertilizer – This might not sound like a big deal, but our coastal waters are being choked by nutrients both from treated wastewater and from farm runoff, while the nutrients in the farm runoff are derived from fossil fuels in the case of nitrogen or a mined from finite geological resources in the case of phosphate. Reprocessing urine into fertilizer is almost a no-brainer. And the technology has been known for awhile. The problem has been waste taboos which seem to be extremely ingrained in our psyches. I really want this one to be overcome, but as a wastewater industry insider I have become more cynical about this one over time. Genetic engineering of crops to help them take up nitrogen directly from the atmosphere (which peas and beans can do naturally, but most crops can’t) is also mentioned.
  • A particular pathogen that infects amphibians may be spreading to new areas.
  • European countries are considering new policy/legal frameworks for biodiversity reporting and conservation. This might sound boring, but we have gotten there with conventional pollution and we are getting there with greenhouse gases and renewable energy, while land use and conversation have mostly been left out to date.
  • Artificial intelligence is increasingly being used to try to accelerate drug, chemical, and pesticide research.
  • trash reefs – New ecosystems may actually develop and adapt around ocean garbage patches.

human brain cells in rats

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You wouldn’t necessarily get the idea from this Nature article that it is about implanting human brain cells in rats. But according to this (sensationalized?) article in Axios, that is exactly what it is about. The scientists are doing this to study diseases like autism that they can’t just study by growing human brain cells in a jar (which they have been doing for some time, apparently!).

Given all that, this is the paragraph that really caught my eye:

A current concern, though, is whether organoids might be transplanted to non-human primates. Paşca says there is no need: “It’s not something that we would do or that I would encourage doing.”

Axios

So it could be done then. And what can be done, Somebody somewhere will probably eventually do.

I have a childhood memory of seeing the Rats of Nimh on the big screen and being utterly terrified. By the Rats. Who were supposed to be the good guys in the story.

lobsters are not immortal, or at least only sort of

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From McGill University:

So why do we stop growing, while lobsters don’t? The cells that make up our body are constantly making new cells by dividing. A biological technicality causes us to lose a bit of DNA at the ends of our chromosomes (structures made up of DNA and proteins) after each replication. DNA contains the blueprint for our lives, so in order to make sure we aren’t losing crucial information during these divisions, the long molecules of DNA are protected by shorter segments of DNA at their ends called “telomeres.” An analogy would be the plastic tips on a shoelace that prevent it from unraveling. When a cell multiplies, the only part of the chromosome that is lost is a piece of the telomeres. But as we age, our telomeres get shorter, until they reach a critical point where the cell can no longer replicate without damage to its essential DNA. When this occurs, the cell becomes inactive or dies. Shortening of telomeres is linked to senescence and increased risk of disease. Other contributors to aging include oxidative stress (hence the appeal of antioxidants).

Lobsters have a perpetual supply of telomerase – the enzyme that can restore telomeres, helping cells avoid that fateful end. Humans also have telomerase, just not enough to overcome the constant shortening of telomeres. In fact, telomerase is often found in cancer cells, giving tumours a survival advantage.

Unfortunately for our pal Larry, a large supply of telomerase can be a double-edged sword. Lobsters are still more likely to die with age because their hard-shell exoskeleton moults and has to be regrown. This requires reams of energy, eventually too much. As a result, common causes of death for lobsters are exhaustion, immobility, and shell disease, although the leading cause is still predation.

McGill

The article goes on to say that there are actually some jellyfish that are biologically immortal, meaning they do not age or ever die of old age, although they can be killed.

Given an infinite span of time, the odds of a “biologically immortal” organism being killed would seem to be 100%. So this does not sound like immortality to me in a colloquial sense, But figure out this mystery and come up with a drug to restore our telomeres without causing cancer, and we could live for a long, long time if we are careful. Would our brains hold up more than a century or so?

Interestingly, and this is a frequent point of conversation my son likes to bring up, the Norse gods are “biologically immortal” because they do not age but they can be killed (sorry, Thor fans). But the Greek/Roman gods are truly indestructible. I recall one story where Zeus was cut up into little pieces and put into a bag by another one of the gods. Eventually, somebody let him out and the pieces just assembled themselves together again and he continued being Zeus.

May 2022 in Review

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Most frightening and/or depressing story: The lab leak hypothesis is back, baby! Whether Covid-19 was or was not a lab accident, the technology for accidental or intentional release of engineered plagues has clearly arrived. And also, the world is waking up to a serious food crisis.

Most hopeful story: I came up with (but I am sure I didn’t think of it first) the idea of a 21st century bill of rights. This seems to me like a political big idea somebody could run with. I’ll expand on it at some point, but quick ideas would be to clarify that the right to completely free political speech applies to human beings only and put some bounds on what it means for corporations and other legal entities, and update the 18th century idea of “unlawful search and seizure” to address the privacy/security tradeoffs of our modern world. And there’s that weird “right to bear arms” thing. Instead of arguing about what those words meant in the 18th century, we could figure out what we want them to mean now and then say it clearly. For example, we might decide that people have a right to be free of violence and protected from violence, in return for giving up any right to perpetrate violence. We could figure out if we think people have a right to a minimum standard of living, or housing, or health care, or education. And maybe clean up the voting mess?

Most interesting story, that was not particularly frightening or hopeful, or perhaps was a mixture of both: I found one easily accessible and understandable source of Covid-19 wastewater surveillance data.