Friday Spider

Oh my. Oh my oh my. While I was out at our climate strike event, I had to, naturally enough, prowl around for spiders, and there she was, hanging out behind the door of the men’s restroom at Green River Park, a stunning beauty, a classic Steatoda borealis, her body all dark and gleaming in confident repose. She’s perfect.

She walks in beauty, like the night
Of cloudless climes and starry skies,
And all that’s best of dark and bright
Meets in her aspect and her eyes;
Thus mellow’d to that tender light
Which Heaven to gaudy day denies.
One shade the more, one ray the less,
Had half impair’d the nameless grace
Which waves in every raven tress
Or softly lightens o’er her face,
Where thoughts serenely sweet express
How pure, how dear their dwelling-place.
And on that cheek and o’er that brow
So soft, so calm, yet eloquent,
The smiles that win, the tints that glow,
But tell of days in goodness spent,—
A mind at peace with all below,
A heart whose love is innocent.

Where’s Brienne?

We go from the sublime to the hideous. When we were doing our routine check for egg sacs the other day, we discovered that Brienne had produced a nice one for us, deep in the elaborate network of webbing she had built in her box. It’s the pale oval on the lower left in this photo.

But…no Brienne. She had disappeared. Look below the egg sac above — there’s a tangled mess below it. I zoomed in on it. It’s an ogre’s nest, apparently.

Ick. Dead flies, bits of dead cricket carapace, all strung together with thick, ropey cables of webbing. Spiders make multiple kinds of web, you know, and these spiders will make cables of web silk that are remarkably tough and hard even for humans to break. I tugged at these with forceps, and nope, they aren’t going anywhere, shy of ripping out the whole structure and possibly injuring its occupant.

Yeah, Brienne is hiding deep inside, the dark shadow near the center of the nest.

These animals always surprise me. They’ve got a complex range of behaviors, and I have no idea what triggered this strange construction. The other spiders in the colony aren’t doing it. I’ve seen a few examples of spiders cobbling together debris into shelters, but it’s not universal, and usually they aren’t this thickly armored and enclosed.

Next they’re going to start assembling tools and weapons, and then you’d better look out.

Dramatic wars begin with a grievous setback that makes everyone desperate to fight back, right?

I isolated myself in a coffee shop, buckled down, and pounded straight through my grading. I got it done! Early even! The students…well, umm, there were some rough spots. The mean was about 65%, brought down by one specific page where they had to do some math, and it was a massacre. I was imagining that page soaked in blood, with more pouring out of my wicked pen, and was getting a little uneasy. I know what we’re going to be going over in the next class!

Now, though, I get to go home, where my wife has some chore involving the picket fence I’m supposed to do, but once that’s over, I’ve got to honor the completion of one onerous task (if not the outcome).

I’m thinking I’ll sit back and read the new Joe Abercrombie, A Little Hatred. It seems appropriate, very grim-dark, with lots of close-fought bloody battles. For that 65%, you know, which is barely passing and means half the class is getting Ds or worse so far.

(The title does not reflect my feelings towards the students, who are my brave compatriots in the struggle to master cell biology.)

Now I’m making housecalls

I got a call from campus Medical Services today — they’ve been invaded by spiders lately, and were wondering if they should be concerned. So I scurried over, because I’m wondering what exciting kind of spider they’ve found…although also I predicted exactly what it would be, and I was right.

They had a squashed specimen, and it was Agelenopsis, a grass spider, just like the one captured here in the science building the other day. I told them they were perfectly safe, these aren’t going to bite anyone, and they aren’t at all venomous to humans, but I guess they need to keep on smacking them, since they are a medical clinic and it wouldn’t do to have spiders everywhere. The problem is that this time of year the males are horny, and they’re wandering everywhere looking for mates. Also, they had an exterminator come by yesterday and spray all the vegetation outside, so all the nearby females are probably dead and they’re getting desperate.

I also checked out ceilings and corners, and I’m sorry to say our medical services office is stunningly pristine, with no cobwebs anywhere. Darn.

There’s a reason they call software ‘viruses’

Also acutely relevant to the problem I just described is this article by Bruce Schneier, who explains how the problems of computer and software security are very similar to those in biological engineering.

Programmers write software through trial and error. Because computer systems are so complex and there is no real theory of software, programmers repeatedly test the code they write until it works properly. This makes sense, because both the cost of getting it wrong and the ease of trying again is so low. There are even jokes about this: a programmer would diagnose a car crash by putting another car in the same situation and seeing if it happens again.

Even finished code still has problems. Again due to the complexity of modern software systems, “works properly” doesn’t mean that it’s perfectly correct. Modern software is full of bugs — thousands of software flaws — that occasionally affect performance or security. That’s why any piece of software you use is regularly updated; the developers are still fixing bugs, even after the software is released.

Bioengineering will be largely the same: writing biological code will have these same reliability properties. Unfortunately, the software solution of making lots of mistakes and fixing them as you go doesn’t work in biology.

In nature, a similar type of trial and error is handled by “the survival of the fittest” and occurs slowly over many generations. But human-generated code from scratch doesn’t have that kind of correction mechanism. Inadvertent or intentional release of these newly coded “programs” may result in pathogens of expanded host range (just think swine flu) or organisms that wreck delicate ecological balances.

We can’t release “gene patches” to correct errors introduced when tinkering with genomes! I can imagine that someday being an issue — by analogy, going in for dialysis is kind of like a routine software management problem. But no one likes having to do dialysis, it’s a symptom of an underlying problem that is just being patched superficially, not fixed, and modifying genomes can introduce new concerns. I wonder how often software updates create new problems that weren’t present in previous versions? 100%?

I don’t think we think enough about the potential for disaster in genetic engineering, because we are enthusiastic about the potential for great good. We need a balance. It would be helpful for those most optimistic about gene modification to have more consideration for the dangers by, for instance, talking to software security experts.

Opportunities for mischief and malfeasance often occur when expertise is siloed, fields intersect only at the margins, and when the gathered knowledge of small, expert groups doesn’t make its way into the larger body of practitioners who have important contributions to make.

Good starts have been made by biologists, security agencies, and governance experts. But these efforts have tended to be siloed, in either the biological and digital spheres of influence, classified and solely within the military, or exchanged only among a very small set of investigators.

What we need is more opportunities for integration between the two disciplines. We need to share information and experiences, classified and unclassified. We have tools among our digital and biological communities to identify and mitigate biological risks, and those to write and deploy secure computer systems.

I’m optimistic about the future of genetic engineering, but I still cringe when I see some ‘bio-hacker’ inject themselves with some home-brewed cocktail of gene fragments that they think will improve their genome, but is more likely to do nothing or make them sick. I get the same feeling when I see someone stick a flash drive into the USB port of some random public terminal. I hope they’re going to practice good data hygiene and quarantine that widget before they put it in their work computer! (They probably won’t.)

Life, could you stop finding a way already?

It was a cunning plan. All these mosquitos are carrying terrible diseases like dengue fever and Zika, so what if we fired back and gave the mosquitos terrible genetic diseases that decimated their populations? That would serve them right and also reduce their affliction of human populations.

Scientists made it so. They genetically modified swarms of mosquitos to carry a lethal gene, called the OX513A strain, and released them into the Brazilian wilderness to breed with, and taint the precious germ plasm of the native mosquitos.

In an attempt to control the mosquito-borne diseases yellow fever, dengue, chikungunya, and Zika fevers, a strain of transgenically modified Aedes aegypti mosquitoes containing a dominant lethal gene has been developed by a commercial company, Oxitec Ltd. If lethality is complete, releasing this strain should only reduce population size and not affect the genetics of the target populations. Approximately 450 thousand males of this strain were released each week for 27 months in Jacobina, Bahia, Brazil.

Wow. That’s almost 50 million genetically diseased male mosquitos. I hope the scientists said, “Fly, my pretties!” when they dispatched them on their devious mission.

It worked for a while. Mosquito numbers dropped. But then…

Genetic sampling from the target population six, 12, and 27–30 months after releases commenced provides clear evidence that portions of the transgenic strain genome have been incorporated into the target population. Evidently, rare viable hybrid offspring between the release strain and the Jacobina population are sufficiently robust to be able to reproduce in nature.

Uh-oh. Is anyone surprised?

Our data clearly show that release of the OX513A has led to significant transfer of its genome (introgression) into the natural Jacobina population of Ae. aegypti. The degree of introgression is not trivial. Depending on sample and criterion used to define unambiguous introgression, from about 10% to 60% of all individuals have some OX513A genome

They don’t know what effects these other genes will have on the mosquitos.

It is not known what impacts introgression from a transgenic strain of Ae. aegypti has on traits of importance to disease control and transmission. We tested OX513A and Jacobina before releases for infection rates by one strain each of the dengue and Zika viruses and found no significant differences. However, this is for just one strain of each virus under laboratory conditions; under field conditions for other viruses the effects may be different. Also, introgression may introduce other relevant genes such as for insecticide resistance. The release strain, OX513A, was derived from a laboratory strain originally from Cuba, then outcrossed to a Mexican population. The three populations forming the tri-hybrid population now in Jacobina (Cuba/Mexico/Brazil) are genetically quite distinct, very likely resulting in a more robust population than the pre-release population due to hybrid vigor.

Before their experiment, there was one known population of Ae. aegypti around Jacobina, and they understood the genetic properties of those animals and could predict the salutary effect of introducing their lethal gene there. Unfortunately for their clever plan, the mosquito vector used to introduce that gene also had all those other mosquito genes, which have also been introduced into the region, and now they have become three genetically distinct mosquito populations, and their response to the ‘lethal’ gene has become complex and unpredictable. Yikes. Unintended consequences are entirely predictable, not in detail, of course, but the general chaos is.

You know what else is predictable? This.

Oxitec, the company responsible for developing the GM mosquito strain discussed in this article, has contacted New Atlas claiming that the report cited in this article contains “false, speculative and unsubstantiated claims and statements about Oxitec’s mosquito technology.” Oxitec says it is currently working with the journal publishers, Nature Research, to remove or update the article, which now carries a disclaimer.

Clearly, it is the scientists who exposed this problem, not the corporation that released transgenic mosquitos, that have Meddled with the Primal Forces of Nature.

You have meddled with the primal forces of nature, Mr. Beale, and I won’t have it, is that clear?! You think you have merely stopped a business deal — that is not the case! The Arabs have taken billions of dollars out of this country, and now they must put it back. It is ebb and flow, tidal gravity, it is ecological balance! You are an old man who thinks in terms of nations and peoples. There are no nations! There are no peoples! There are no Russians. There are no Arabs! There are no third worlds! There is no West! There is only one holistic system of systems, one vast and immune, interwoven, interacting, multi-variate, multi-national dominion of dollars! petro-dollars, electro-dollars, multi-dollars!, Reichmarks, rubles, rin, pounds and shekels! It is the international system of currency that determines the totality of life on this planet! That is the natural order of things today! That is the atomic, subatomic and galactic structure of things today! And you have meddled with the primal forces of nature, and you will atone!

Let’s be clear here. The scientists behind OX513A haven’t created a monster, the humans of Jacobina don’t have to flee for their lives, they haven’t done something that creates immediate medical issues. No, what they’ve done is increased the genetic diversity of the mosquito population and made the problem of controlling them more complex for future management.

Benjamin R. Evans, Panayiota Kotsakiozi, Andre Luis Costa-da-Silva, Rafaella Sayuri Ioshino, Luiza Garziera, Michele C. Pedrosa, Aldo Malavasi, Jair F. Virginio, Margareth L. Capurro & Jeffrey R. Powell (2019) Scientific Reportsvolume 9, Article number: 13047.