This is the third post in a series reviewing basic concepts in genomics. The first one was titled “How Many Genes Does a Person Have?” and the second was “How do Genomes Vary, Person to Person?” This is a breezy summary of the Sanger method of DNA sequencing. I plan to cover short-read massively parallel (which is occasionally still called “next-gen”), and long-read single molecule (which should never under any circumstances be called “next-next-gen”) in subsequent posts.

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Opposites Attract

Before getting started, I would like to pause for a quick digression on the importance of the attraction between opposites, at least as far as DNA sequence is concerned. It is hard to overstate the utility and power of the highly specific affinity between complementary strands of nucleic acids. This attraction, combined with the sheer intuition-defying number of molecules present in even very small reaction volumes, can come to seem like a magical, near-universal tool to manipulate DNA.

For example, we often want to grab a strand of DNA at some particular location. As discussed in previous posts, the concept of “location” is slippery in genomics. There is no such thing as a coordinate system on the chromosomes, at least as far as the underlying biology is concerned. Instead, we settle for a location relative to some highly conserved sequence of nucleotides.

To go fishing for the DNA near such a location, we construct (or, more commonly, buy) an oligonucleotide (oligo for short) that spells out the reverse complement of the desired sequence. The oligo serves as a bait or a primer that will very selectively latch on to its target. The primer is attached to some molecular chemistry that allows us to hold it back when everything else is washed away. We add the bait to the DNA and raise the temperature until the paired strands separate or denature, making room for the interloper to cut in. After a bit of time and agitation, we lower the temperature again. Raising and then lowering the temperature to open and close the strands of DNA and allow some reaction to take place is called thermal cycling.

The uncanny affinity of DNA for its mate-paired sequence, combined with the remarkable and counterintuitively consistent behavior of truly vast numbers of molecules, means that when we wash away everything that did not take the bait, we are left with a highly purified solution of all and only the DNA containing a match to our desired sequence.

To me, at least, this is pretty remarkable. We’re talking about a technique that can find a very specific needle – some particular substring of DNA – in a haystack of 3.2 billion letters. The remarkable power of exponential math means that we only need an oligo of between 18 and 22 letters to accurately isolate most locations in the human genome, though of course repetitive and low-complexity sequences are always problematic.

I started on the computational side of things, and it took years before I developed any intuition whatsoever about what was easy vs. hard in the lab, and the subtle ways that laboratory realities show up as biases and even errors in downstream data.

Sanger Sequencing

Sanger sequencing, after Frederick Sanger – whose team developed it in the late 70s – is one of the original methods for determining the sequence for a DNA molecule. There are a number of variations on the theme, but they all share a common core:

• Make a bunch of copies of some particular chunk of DNA, varying in length from one to about a thousand nucleotides
• Tag or label the molecules somehow so we can identify the final nucleotide (C, G, A, or T)
• Sort the molecules, shortest to longest, physically spreading them out on a gel or in a capillary tube
• Read the terminal nucleotides, shortest substrings first.

We accomplish the first two steps (making sub-strings of all possible lengths and identifying the terminal residue) with modified nucleotide precursors called di-deoxy (ddNTP) rather than the regular deoxy (dNTP) version that makes ordinary DNA. Because of its slightly different structure, ddNTP serves as a terminator and blocks any further nucleotides (either ddNTP or dNTP) from being added to the strand. Once a DNA molecule takes up a ddNTP rather than a dNTP, it becomes fixed in length (at that particular replication site), regardless of the availability of additional raw materials.

We use a mix of dNTP and ddNTP, setting the relative abundances so that approximately one in a thousand replication events will incorporate a ddNTP and stop. It is conceptually simple (though of course there are always details) to run the replication reaction until we have the desired mix of lengths, all of them terminated by a synthetic ddNTP.

Early versions of the Sanger method used radioactive labeling, which made the DNA molecules visible but did not allow observers to distinguish between the nucleotides. The synthetic C, G, A, and T molecules were run as four separate reactions and spread out as four distinct lanes of a rectangular gel, creating the classic “ladder” representation that has become visually synonymous with genomics.

Fluorescent ddNTPs that emit photons when illuminated with a laser were a later innovation. Fluorescent molecules can be created such that different ddNTP molecules shine at different frequencies, which allowed the reactions to be mixed together and sorted in a single capillary tube. Beyond reducing the amount of radioactive isotopes needing to be pipetted around the lab (nearly always a good thing), this allowed substantially reduced the reaction volumes which allowed increases in speed and automation.

The vast majority of modern Sanger sequencing uses this technique, DNA molecules are terminated by fluorescent synthetic nucleotides and sorted by weight in capillary tubes. Most labs use a workhorse of an instrument called the ABI (for Applied Biosystems) 3730 that integrates and automates most of this process.

The length limitation, where we can only read about a thousand base pairs (though realistically it’s closer to 850), is derived from the shrinking ratio between the weight of a single nucleotide and total weight of the DNA molecule as the chain grows longer. Eventually, sorting by weight doesn’t spread the molecules out far enough to tell one position from the next. Read length is one of the most important properties that differentiates the various sequencing technologies.

While Sanger sequencing is incredibly powerful and still used every day all over the world, it has some significant limitations, particularly at scale. The read length of ~850bp (base pairs) means that it would take several million reactions to read through the 3.2 billion locations on the genome. If we want to interrogate some particular region we need to construct or buy custom oligos to bait it out. If we choose to “shotgun” sequence instead – grabbing at random and using computational techniques to stitch things together – we need to do highly redundant reactions to achieve good coverage.

Finally, despite fitting in a capillary tube, the volumes of material required per-molecule in Sanger sequencing become unwieldy at genomic scales. An old engineering mentor of mine was fond of saying that even very small things in your design become big and important when they happen thousands of times per second. Even if we were able to get down to a single instance of each DNA substring per reaction (we cannot), Sanger sequencing would still require hundreds of nucleotides at each location to be interrogated – which turns out to be expensive and inefficient.

My next posts will explore higher throughput techniques, focusing on illumina’s short-read sequencing by synthesis technology and long-read single molecule technologies like those used in Pacific Biosciences and Oxford Nanopore.

This is the second post in a series where I review and explore some basic concepts and confounders in genomics. The first one was titled “How Many Genes Does a Person Have?”

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Until quite recently, genetic variation was described in terms of difference from a human reference, of which there have been 38 major versions. The 39^th version of the human reference has been indefinitely postponed while the scientific community grapples with the fact that the observed diversity of human genetics does not map well to any single linear reference. Beyond the fact that a simplistic model is inadequate to represent the data, the concept of a “normal” or “reference” genome is problematic and can lead to sloppy, incorrect thinking. Early genomic datasets were heavily biased towards people of European descent. This meant that genetic variation was, practically speaking, being defined in terms of divergence from the white population.

So, we’re on a bit of a pause with the whole idea of a human reference. However, genomes do differ between individuals and across populations and we need to be able to talk about the differences. Here are a few major categories of variation.

Single Nucleotide Polymorphisms (SNPs) (pronounced “snips”)are loci where we encounter different nucleotides in the “same” location on a chromosome. Eliding over the question of what exactly is meant by “the same location,” we might see a G rather than an T there. If a SNP is in a protein coding region and the change does not result in any changes to the amino acid sequence encoded by the DNA, then it is referred to as a silent or synonymous substitution. The ratio of nonsynonymous to synonymous mutations is one of the key metrics used in calculating rates of evolutionary change and generations of divergence between populations.

Admittedly, I’m indulging in a bit of hyperbole when I call out genomic location as a challenge with SNPs. Practically speaking, the location of most SNPs is defined in terms of highly conserved sequences that surround them. The Lightning project from Arvados expands on this concept, using reliable sequence “tags” as signposts to localize more variable features, independent of any reference.

Insertions and Deletions (InDels): are loci where a stretch of DNA is present in some individuals and absent in others. All indels can be represented as either an insertion or a deletion – depending on whether we choose to anchor on the larger or the smaller sequence of DNA. Frameshift mutations are indels within exons where the change is not a multiple of three nucleotides in length. Frameshifts disrupt the three letter code used in translation from RNA to protein, which can have significant biological impacts. Things get messy when the inserted segment contains additional variation that also needs to be represented. Biologists have developed conventions for handling these cases, but it is important to remember is that there are multiple correct ways to describe the same underlying variability.

Inversions happen when a stretch of DNA is written backwards, swapping the two strands for a while before swapping back. Copy Number Variations (CNV) occur when a sequence of nucleotides repeats a variable number of times. Inversions and CNVs are both considered  structural variants (SV), and can be difficult to identify beyond a certain scale when using certain DNA sequencing technologies.

SNPs where naturally paired nucleotides are swapped (G/C or A/T) could be described as single base inversions. Nobody talks that way, but it’s not incorrect.

So how much do we vary?

A 2016 paper in the journal “Genome Biology” claimed that “typical” human genomes differ from the reference at between 4 and 5 million out of our 3.2 billion loci – leaving 99.9% of our nucleotides in common. Most of these variants, around 99% of the 0.1%, are shared with a substantial fraction of the human population – though the specific makeup varies. This layered and complex commonality is at the root of the mathematical problem with using a single reference. Of the 40,000 to 200,000 variants that have not yet been seen in very many other people, between 40 and 80 are “de-novo” variants that were not inherited from either parent. Out of those 40 to 80, we only expect a couple to be nonsynonymous mutations within an exon.

So we vary a lot, or a little, or not very much at all, depending on how you choose to look at it.

Somebody recently asked me, innocently enough, “how many genes are there in the human genome?” As one does in these situations, I answered a slightly different question: We are made up of about 20,000 unique proteins. This sufficed to move the conversation along, but I found myself wondering what an honest answer would look like.

The 23 chromosomes of the human genome can be thought of as an ordered string of approximately 3.2 billion (3.2 x 10⁹) nucleotides. Our genome is diploid, which means that we have two similar but non-identical instances of each chromosome in most cells. The sex chromosomes are an exception – chromosomal females have a pair of the larger X chromosomes, while chromosomal males have one X and one much smaller Y. In people with multiple X chromosomes, all but one is disabled at random on a cell-by-cell basis early in development. This “X chromosome inactivation” means that we are all functionally haploid for the X chromosome within any given cell.

Loci that exist on both instances of a chromosome are either the same (homozygous) or different (heterozygous). Loci that occur on only one chromosome are referred to as hemizygous. This can occur when an entire chromosome is haploid (as with ‘Y’), or when a stretch of DNA appears on one chromosome but is absent on the other. The latter situation can lead to multiple representations of the same underlying biology depending on whether we choose to describe it as an ‘insertion’ or a ‘deletion.’

A single DNA molecule is made up of two strands wrapped around each other to form a double helix. This double helix structure is not the chromosomal pairing described above. DNA strands are directional, and the paired strands of a single DNA molecule proceed in opposite directions. One end of a strand is called 5’ (“five prime”), and its opposite is 3’ (“three prime”). These names refer to which specific carbon atom is bound to the adjacent nucleotide. Biological operations like replication and transcription proceed in the 5’ to 3’ direction, and DNA sequences are conventionally written out in that same order.

Each locus in a chromosome consists of a pair of nucleotides, one per strand. The two strands contain the same information, but running in opposite directions and coded as the reverse complement of the other – Guanine (G) swapped with Cytosine (C) and Adenine (A) swapped with Thymine (T). While each strand is directional, the double stranded molecule is not. Neither strand has priority over the other. This means that there are at least two valid representations for the DNA sequence found at any location on a chromosome.

The best understood mechanism of genetic action is codified in the fundamental dogma articulated by Watson and Crick:  Portions of the dual stranded DNA in the nucleus are transcribed into single stranded RNA; RNA transcripts move from the nucleus into the cytoplasm, where they are translated by the ribosomes into a series of amino acids; this amino acid chain then folds up into a protein. We refer to the portions of the nuclear DNA that eventually code for the amino acids in proteins as the protein coding or simply the coding regions.

The coding sequence for a particular protein is not a continuous stretch of chromosomal DNA. Coding regions, or exons, are interspersed with non-coding regions called introns. The protein coding regions of RNA are spliced together during transcription into a single strand that omits the introns.  In addition to introns, which are non-coding regions within genes, there is also substantial intergenic DNA that is not part of any protein at all. Introns and intergenic regions have important, sequence-specific functions, despite not being transcribed or translated, including regulating the rate of transcription of nearby protein coding regions.

In addition to the messenger, or mRNA, described above – other sorts of untranslated transcripts exist (utRNA) which never wind up contributing their sequence to amino acid chains: Transfer RNA (tRNA) supports protein synthesis; ribosomal RNA (rRNA) is coded by the ribosomal genome – a circular chromosome in the cytoplasm; and micro RNAs (miRNAs) play a significant role in gene regulation. There is also diversity within the mRNA transcripts coding for a single protein. Splice variants occur when exons are omitted during transcription or removed later in a post-transcriptional splicing event. There are even reverse transcriptase proteins that, fundamental dogma notwithstanding, write RNA sequences back into the nuclear DNA in living cells. These are the mechanism of action behind retrotransposons (colloquially known as “jumping genes”), telomere repair, HIV, certain cancer-associated viruses, and of course gene editing technologies like CRISPR.

None of this answers the original question about how many genes we have, unless you are willing to accept the old “one gene, one protein” mantra, in which case “about 20,000” will suffice. To do better, we need to define what, exactly we mean by “gene.” It would probably also be a good idea to put some thought into which of the phenomena above are within or excluded from “the genome,” lest we leave ourselves open to the usual grab-bag of gotcha questions from the well informed audience.

If Somerville’s city council tries to make moderate cuts to the police budget this year, the Mayor will respond by defunding the crossing guards. He’ll blame the council for making him do it. It’s classic bullying and budgetary hostage taking and it sucks.

In order to make any significant change to the police budget, the council will need to wield their power more like a chainsaw than a scalpel.

I think that they should blow it up. Here’s why.

Our Budget Process

In a normal year, the budget happens like this:

• The Mayor proposes a budget in early June. It comes out as a glossy 200+ page PDF filled with flowery language and slick graphics. Our budget PDFs regularly win awards from something called the “Government Finance Officers Association.”
• The budget package also includes a spreadsheet with organization codes, line items, and dollar amounts. That spreadsheet is the only thing that matters.
• The city council spends 40+ hours in public meetings talking to department heads, trying to understand how the numbers in the spreadsheet match up to the stories in the PDF. Sometimes a bit of dirty laundry gets aired, but mostly it’s just excruciating.
• The council can only cut funds from the spreadsheet. They cannot shift or allocate funds. They certainly cannot cause projects or initiatives to happen — they can only defund particular line items.
• When they make a significant cut, the councilors hold forth at length about what they are trying to achieve by cutting and where the money might be better spent.
• At this point, the Mayor has the option to respond to these pleas by issuing a revised budget increasing other line items. Usually, he does not. The money is simply lost, and property taxes increase a tiny, tiny bit less.
• If the council fails to approve a budget by July 1, then we don’t have a budget. We don’t have funds to pay for stuff. Trash stops being collected. Librarians stop getting paid. At that point, the Mayor blames all of it on the city council for failing to get their job done.
• After the budget is passed, the Mayor does whatever he wants in terms of projects and moves money around to make it happen. No matter how specifically we say that these cuts are supposed to apply to police overtime— the crossing guards wind up getting the axe.

In Somerville, the mayor also has the exclusive use of a communications (AKA public relations and propaganda) department with a budget of $1M per year to spin all of this and crank out those shiny PDFs. Boston, home to eight times more people than Somerville, spends 75% of what we do on comms.

The city council, by contrast, doesn’t even get clerical or legal support. Our city councilors don’t have city issued laptops, which is why two of them do not appear on video on our online meetings. Somehow, this sort of support just never shows up in the budget.

2020 is even worse

As I write these words, it is June 13th and we still do not have a budget proposal. To be fair, things are pretty screwed up right now. Between Covid-19 and mass protests over racial injustice and police violence, 2020 is a mess. Everything is harder than it should be, and everything is late.

While there is an option available to avoid chaos without passing a budget, the Mayor is having none of it. We could approve a 1-month continuing resolution (just like the big kids in Washington!). That would keep things running and give breathing room to sort out the details. The city council has repeatedly requested this option. They have been turned down with a story about how a 1-month budget would make it impossible for businesses to plan.

It’s pretty hard to plan anything with the world on fire, but whatever.

So it’s a high-stakes game of chicken this year. The opening moves are not promising.

Transparency

From the “transparency portal” mentioned in the memo above, it looks like the Mayor is proposing a decrease of $200k in the PERSONAL SERVICES line of the police budget down to $15.9M from $16.1M last year — about 1%.

In the budget, POLICE PERSONAL SERVICES is an “organization code.” This is the practical level at which the city council can control Somerville’s budget. In last year’s budget there were 24 “object codes,” line-items, within this org code. There was $11.8M for salaries, $1.15M for overtime and $430k for crossing guards.

In my previous post, I wrote that transfers in and out of line items need to come before the city council for approval. It turns out that this is not strictly true. The Mayor and his department heads can shift money around within an org code without asking anybody. This makes it damn hard for the city council to exercise any sort of fine grained budgetary control.

The chart below shows what happened in FY19— we brought in $147,807 additional dollars for police overtime ($45k of it from civil asset forfeitures) and spent 99.5% of the total. The crossing guards, on the other hand were underspent by about 25%. We shifted $5,770 of those funds somewhere else.

Anyway, the above 1% cut to an unspecified part of the police budget was accompanied by a PR blast that declared police violence to be a “state of emergency” and committed to all sorts of action that — coincidentally — the city seems to already be taking.

When the city council met last Thursday, they asked the Mayor to attend and explain to the city what actions he was going to take under this new “emergency.” Neither the Mayor nor any senior members of his staff were available to take the question.

This is a pattern

Joe Curtatone has been Somerville’s Mayor for 20 years. We have plenty of examples of how he works. He knows what he’s doing here.

2019’s massive update to our city’s master plan, adorably named “SomerVision,” is not mentioned anywhere in the budget narrative for 2019. The 2020 budget proposal praises this un-budgeted boondoggle as accomplishments 1, 2, 3, and 4 for the planning department.

Last year, the city council tried to get rid of a particularly odious animal control officer who kept getting complaints for mistreatment of animals. On review, it turned out that this guy had been moved to animal control from parking enforcement after he punched a cyclist in the face while on the job.

The administration’s response to pressure to remove the guy was, in effect, “why are you hitting yourself?” Moves to reduce the animal control salary were specifically mocked for how they would lead to layoffs in unrelated job functions. My understanding is that the individual in question is still employed at city hall, though he was shuffled to a non-public-facing job.

The examples go on and on — the officer who was selling oxycodone on our streets. The officer who ought to be on the sex offender list for what he left on the school computer while pulling time and a half covering an elementary school sleepover. The woman in DPW whose supervisor’s response to a complaint was to move her office furniture into the restroom. The gay man who was driven out of the police force. The use of the reserve hiring list to guarantee jobs for relatives of the Mayor.

In every case, the city council has tried their best to work within the framework available to them — with limited success and sometimes at personal cost.

Blow it up

All of the above was an attempt to convince you that we’re dealing with a strongly entrenched administration who have massive structural advantage and experience in working this system. The city council can still seize the initiative here, but it will take bold action.

I think that we should defund the police.

In the business world we talk about “blowing up the negotiation.” When your counter-party is operating in bad faith, gaming the system, or just fucking with you — only a loser keeps trying to work from within that busted framework.

You get up and walk away. If you come back, and you don’t have to come back, you return to a different negotiation entirely.

If Somerville’s city council tries to treat the police budget with the nuance and introspection that it deserves, the Curtatone administration is going to run roughshod over them and take out any losses on the least powerful. This question of police and policing is an important conversation. We have desperately needed to have this talk for generations.

Curtatone is treating it as business as usual.

It was a big deal a couple of years back when we got -gloves- for the crossing guards. Some of our cops are making $300k per year from a cornucopia of overtime and “other” pay while city council has to log in to meetings from their phones.

We should, in the immortal words of Ripley, from the movie “Aliens”: Take off, and nuke it from orbit — it’s the only way to be sure. We should set the police budget to zero… or close enough to zero that the city would be forced to lay off officers and sell cruisers. That will force the Mayor back to the table with a one month budget and potentially an updated proposal that includes a bit of detail and starts the real negotiations.

Or else, you know, we would work out how to run the city without this heavily armed and basically unregulated $16M tax burden holding us hostage.

Anything else just costs us the crossing guards.

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This is the second in a series of posts about the mechanisms of government in Somerville, MA – originally posted to Medium. The first one is called “The other in Somerville’s budget.” These thoughts started off as a twitter thread. The stuff about the animal control officer is detailed in another thread, as well as in this FOIA request.

My mother used to tell stories about the 1967 race riots in Detroit. She was 17 years old, living with her parents at 7 mile and Woodward. She told me how the National Guard rolled tanks down the street while her grandfather hid in the attic cradling an old army rifle.

Twenty five years later, in 1992, Los Angeles exploded in fury – triggered by the Rodney King verdict. I was 17 at the time, safely in a suburb on the other side of the country. She told all the old stories – pointed out the patterns.

Now here we are – a generation later.

Decades from now, children will hear the lessons their parents learn this summer. Grandparents will nod and confirm. Perhaps a particularly lucid great grandparent will roll out a dusty story from that hot summer of 1967.

People don’t forget this stuff, nor should they.

Different stories get passed down over the generations in nonwhite families and in urban families. I know of at least one story we all have in common: It’s that nothing’s going to change.

America needs the kind of change that lasts for decades. We need new stories that can become as real and as trustworthy as the lessons our parents and grandparents taught us. We need new patterns. We are fighting hundreds of years of muscle memory.

The mostly-white, mostly-male, mostly-straight establishment needs to do way better than our parents and our grandparents did.

I do know that rolling tanks down the streets didn’t work. Hiding in the attics clutching our guns didn’t work. Moving to the suburbs and isolating ourselves didn’t work. Militarizing the police didn’t work. Criminalizing poverty and blackness and addiction certainly didn’t work. Exploiting labor so hard that people can’t even afford to live in the cities where they work didn’t work.

We need disproportionate reactions of virtue, rather than violence. We need to commit to listening and compassion and partnership and rebuilding and generosity all out of proportion to every crime and abuse and horror. The 1967 riots were -triggered- by a raid on an unlicensed bar, but they weren’t -about- that bar. The LA riots were triggered by Rodney King’s death, but not fundamentally -about- him.

That’s why, even though arresting and prosecuting the man who killed George Floyd is an absolutely essential step – it’s mistaken, shortsighted, and frankly disingenuous to think that his arrest – a tiny shred of justice – addresses the real problem.

It’s about our karma as a nation – the stories that we tell – not any particular crime.

This is the work of generations. We should commit to starting today.

Please remember, as you decide how to act in the coming days and weeks: We are not re-opening because we beat the virus.

There is not adequate testing. There is no vaccine. There is no demonstrated treatment or cure. From a medical perspective, we are -exactly- were we were in March.

My dad used to say that if you don’t use modern medicine, the disease has no way to tell that it’s not the dark ages. It’s still very easy to die of an infected wound – just fail to clean and treat it. Skip the antibiotic cream and the bandaid the next time you cut yourself if you want to see.

Instead, we are re-opening because we no longer have the will to fight using the limited tools of business closure and stay-at-home orders. The pressure of profit, business, and political appearances are too great.This will be spun as a victory. We will be told that we never needed to close at all. These are damnable lies.

And so we re-open.As always, the burden and most of the danger will fall disproportionately on the disempowered and the vulnerable. Service workers will be made to expose themselves to bored and potentially infectious shoppers for the same low wages that they made in February. Employees will be punished for “absenteeism” if they fail to show up under these conditions.

This is how our system worked before, and it continues unchanged.

Please be kind, be compassionate, and be sensitive. If you’re in a position to make a difference for someone less powerful than you, please do so.

Individual actions matter.

Indeed, given the failure of our so-called leaders – they’re all we have.

I’ll be honest, I don’t want to go back to the “normal” we had in February.

I was killing myself with business travel. It was a slow sort of killing … but killing nonetheless. I was on a train most weeks and a plane most months. I was on track to hit lifetime platinum status with Marriott – more than 50 room nights a year for 10 years. A year and a half of my life in hotels.

For what?

Now I exercise almost every day, at least a little bit. I stock the fridge once a week, mostly with veggies and selected meats. Ordering delivery is a special treat.

My spouse and I have worked out patterns in our daily routines to let us be this close without killing each other. We’re going to keep many of those. We should have done that years ago.

I’ve re-connected with people and communities, and even made art. That was always available, I just didn’t make time for it.

Work meetings include space to check in with the other people in the room. We’re making accommodations for each other in ways that we never did before. Never ever. We know more about each other, and it’s okay.

Honestly, video hangout meals in the evenings with friends are -better- than physically getting together in many ways. Not least, the obligation to clean up the whole house, agree on food for everybody, and so on simply disappears. It’s all about showing up.

Seeing people in person is truly precious. We’ve gotten careful with each other’s space and vulnerability.

We all realize now, I hope, that the truly “essential” employees are the underpaid, ill treated, and all-too-frequently invisible laborers, drivers, cooks, and cleaners on whom we build our posh life. I hope we can go ahead and PAY them fairly rather than just blathering on about heroism.

I hope that as we re-open, for all the good reasons that we need to re-open, that we can keep some of what we’ve learned here.

I don’t want to go back to killing myself.

The thing that really frustrates me about the crises I’ve seen in my life is that, by and large, the financial devastation is 100% avoidable.

Absolutely, 100% avoidable.

Covid-19 has killed hundreds of thousands of people. That’s real and it’s not up for debate. I can’t language it away. You can’t un-dead the dead.

Money, finance, employment, bankruptcy, rent, and property ownership, by contrast, are human concepts. They are old, important concepts and I’m not suggesting that we do away with them generally … but with just a bit of flexibility during a crisis, we would have no need to fear economic ruin in addition to fearing disease and death.

With just a bit of a flex to money and property rules, the terror of economic devastation could be turned all the way down and we could let public health policy drive our response to a public health crisis.

Why, exactly, is the stock market still open while the economy is closed? That’s absolutely, on the face of it, going to lead to massive losses (on paper) while nobody can do anything about it.

Why, exactly, are we still insisting on super-strict rules of bankruptcy … so that the businesses who miss out on support by days or weeks wind up gone forever?

Why, exactly, do we have to unroll our financial problems in real-time, from home, while disease stalks the land? Why do we use the same merciless rules that govern our economy the rest of the time in times of crisis?

All the rules about money are choices, collectively made by humans.

We could make different choices, and it would be a lot better for everybody.

Getting serious for a moment:

It’s time to stop pretending that, if we can only hold out long enough, everything is going to go back to exactly how it was before this pandemic.

It is not.

Please ignore what our so-called leaders are saying about miracle cures, quick fixes, and “just another couple weeks.” These are harmful lies, peddled by scared people who quite simply don’t know what to do.

I don’t know what to do either. Not exactly. It’s not drinking bleach, I’ll tell you that much.

Great leaders, coaches, and strategists acknowledge hard truths. They acknowledge a difficult or a changed situation and then make new plans.

This pandemic has wrought lasting changes on the world. We are only beginning to see the outlines of how it will be in these “after-times.”

Some things are gone forever, including far, far too many people. So we grieve, and then we heal, and eventually we thrive again.

Buddhists say that “attachment leads to suffering.” This is not a moral judgement – but a simple acknowledgement of a rather obvious truth.

Recovery programs say: “Let go or be dragged.” Same deal.

It’s time to start building for the new future, even while we grieve the lost past, and also before we know how everything is going to turn out.

I know this is hard. We’re going to figure it out – together.

The epidemic has really put a dent in my blogging.

I’m amazed at the people who have been able to maintain their usual steady, productive output. For my part, I feel like I’m running on about half my usual emotional / mental capacity. I make lists and set priorities early in the day, acknowledging that at some point in the afternoon I am likely to be left with all the motive power and creativity of a potato.

In terms of input, I’ve been following Emily Dresner for slice-of-life diaries and well-informed snark, Elizabeth Bear for sensible advice, context, and practical tips to make food go further, Amal El Motar because hearing a poet’s voice in a dark time is a godsend, and Gareth Powell for his tenacious commitment to helping creative people get through this together.

The only news outlet that I trust to not nuke my state of mind is Stat News. They focus on the biotech industry, and are subscription based, which keeps the screaming-terror alerts to a dull roar. Eric Topol aggregates high quality information on his twitter feed, including the sensible metrics on the spread and human toll of COVID-19. Beyond that, honestly, I treat the internet with caution.

Thomas Pueyo put a post on Medium back on March 10 that is, for my money, still the best entry-level explanation of the challenges in measuring and reporting on the spread and impact of the disease. If you only have mental energy for one mid-length article, read that one. It’ll inoculate you against the major sorts of misunderstanding and disinformation that we’re being peddled these days.

Speaking of which, I’ve muted the president and his cronies on social media, and I won’t read so much as a summary of his news conferences. The office of the president, shamefully enough, is nothing more than a fountain of disinformation, grandstanding, ego, and bullying. That was painful and damaging before the epidemic hit – and now it’s going to get tens to hundreds of thousands of us killed.

Through it all, there are bright spots:

I attended the very first virtual meeting of my city council, and even thought there were rough spots with the technology – it gave me hope. If you work with local politics at any level, you quickly become aware of the challenges in providing access to, and soliciting input from, the entire community. There are so many barriers, and they all point in the same direction. Political access is inequitably allocated to able bodied people who speak english fluently, have the time and energy to attend meetings, are in “good standing” with the law, and so on. In this virtual meeting, I saw the glimmerings of a possible future where things could be substantially more accessible, open, and fair.

Along the same lines, I think that we can all see that internet connectivity is at least as much of a life-essential utility as a twisted-pair phone line … and perhaps even on the order of gas, electricity, and water. The outpouring of offers of aid on my various neighborhood groups and lists has been incredibly heartening. My various social groups, after taking a bit of a pause, have self-organized around virtual coffees and happy hours.

I’m also super glad to see some shred of dawning recognition that the (traditionally) low-prestige jobs like driving trucks, preparing and delivering food, keeping spaces clean, and so on are actually incredibly critical to keeping our society running.

I hope we get to keep that.

Stay safe and well out there, everybody.