The Deposit Is Not the Description

The accession number arrived by courier at 8:42 on a Thursday, which is not a thing I would have noticed if the seal ring on the cap had not been the wrong color.

I am a depositary. That is the whole of it. Thirty-two years at the culture repository, first as a technician, then a supervisor, then a job title that reads depositary in the certificate header, in the parts of the federal register that nobody reads, and in the annual reports that go to the institute’s board. The repository holds living material for patent purposes. Material that a person or a company has claimed is theirs and novel, and that the United States Patent and Trademark Office will not consider unless it can be inspected, sampled, and revived by somebody who is not the applicant. That somebody is me, or one of the six people whose signatures are under my signature. I do not run assays. I never have. I log what comes in the door, and I certify what is physically in the tube on the day it comes in, in a form that says so in the specific words the law provides, and I do not ask what it is supposed to be.

That is the job.

VT-2291-07/RA. One accession number, one cryovial, and inside the cryovial seven replicons, which is not a thing you get to see, so I counted them afterward on my map and named them myself. The shipper was a foam box with a dry ice pack that had mostly sublimed. It had been at room temperature for about an hour. Condensation on the outside of the vial, a film of it, and the seal ring on the cap was not the color we issue. Ours are gray. That one was amber, or a pink that had gone pale, and I noted that, because I note things, and then I logged it.

A million and a tenth of a million base pairs across seven replicons. Three hundred and forty kilobases the first, then two hundred and ten, then a hundred and eighty, then a hundred and fifty, then a hundred and twenty, and fifty-five and forty-eight for the last two. Nothing on any of the seven for a flagellum. Nothing for a pilus. Nothing for the enzymes that build nucleotides from scratch, and nothing for twenty-one of the amino acids, which is why the medium has been carrying those twenty-one since the first generation and why you change nothing in that bottle, ever, or the culture stops. Nothing for the partitioning proteins, either, which is the omission that will cost them the most and which nobody at the company thought was worth a line in the paper. It imports what it is given, it copies the seven, and it divides. Five generations of that, and then the lab in the Twin Cities noticed what was in the plates, which was most of their lines carrying five or six of the seven, and the one line that still had all seven was the fattest and slowest of anything on the bench, and by the sixth week there was nothing left of it.

We hold a lot of things that cannot do what the paper says they can do. My problem is what is in the tube. I did not need to know what the seven replicons built. I needed to know that seven replicons were there, and that the thing was alive when it crossed my threshold, and that it stayed alive in the medium we keep it in, on the schedule we keep it on.

Both numbers go on the certificate. Not one. Two. Viability is a percent, a proportion of inoculated replicates that grow, and the regulation names a percentage below which I have to explain myself rather than just report the figure, and the form asks me for that number in a box with a line and a signature beside it. Completeness is a different measurement and the form has a box for it too, under the heading Remarks, where a depositary is permitted to write whatever the truth of the situation appears to require.

The paper said thirty percent.

I let that sit for eleven days while I did the ordinary work, because eleven days is not long, and because I have learned that a thing which seems wrong at the moment you first see it is frequently a thing you misread, and that a woman who cries wolf about a plasmid percentage will be crying wolf about plasmid percentages generally.

On the twelfth day I did a subculture from the primary into fresh medium, which is not the five-year re-test. The five-year re-test is in the freezer, in the log, three winters from now. What I did on the twelfth day was the thing I do anyway when a number in a paper sits wrong with me, which is to put a drop under the inverted scope and count, and I did it again the following week because the first count did not agree with anything I had read in that preprint and I wanted it to be my hands that were wrong.

Twenty-two percent complete. Then nineteen. Then, on a subculture taken from the twenty-two, complete at thirty-one percent, and the missing pieces different from the ones missing before, and in the plate from the thirty-one, five of the seven, and the two gone were not the two that had gone before. I photographed the five. The stain showed no contamination. I still have it.

Twenty-two. Nineteen. Thirty-one. The paper had one of those numbers. One. Which means it had one culture, on one day, and the thing has never once repeated itself since.

On the second Thursday I took the seven-sample tray up to Priya Raghunathan in QC, who is the best person in this building at reading a plate and the second best at ignoring what she reads.

She looked at the tray for a while.

“That is low,” she said.

“It is?”

“It’s low. There’s a paper about it. Without the partitioning proteins there’s nothing holding the copies one apiece at division, so it’s a drift, and it’s a drift that runs one way, because a cell that dropped two of them has less DNA to copy and outgrows its neighbors every hour. Half your cultures will segregate down to a couple of replicons. It’s not a contamination question. It’s the design. Seven things that all have to arrive is seven chances to not arrive. Add a tiny bit of drift and you can get to twenty in five generations pretty easily. Ask them. They’ll tell you it’s expected, and it is, and they probably have the number in the second figure.” She handed the tray back. “You want me to write it up?”

“I want it in a sentence I can put on a form.”

“That is not what forms are for.”

I said that the form had a box for remarks, and she said “fine” and wrote me four words, Plasmid set incomplete, and signed it, and that is now the only thing on earth that means anything about what is in that vial, because the certificate is about the vial and the remarks are about the vial, and a lab notebook in the Twin Cities is about the lab.

The law did not ask her. It asked me.

The file came in that afternoon, thick, because companies send their file or they do not. Eleven inventors. A shelf space in a company I had never heard of, which is itself a fact about how little of this is being made by people who care about the making. A priority claim from 2019. A PCT. And forty-two pages of drawings, and the draftsman’s touch in figure 4, the arrows, all the little labels in that clean eight-point type.

The claims as filed, claim one: An isolated synthetic microorganism comprising a genome of approximately 1.1 million base pairs distributed across seven replicons, said microorganism being capable of growth by assimilation of exogenous nucleotides and amino acids and division by binary fission.

I am not a lawyer. I have read eleven years of claim sets because they come with the material, and you cannot look at a vial for six hours without wanting to know why anybody thought it was worth looking at. I am a depositary. But I know what a claim does, and I know the office is not generous.

I had read eleven years of claim sets and I had read Chakrabarty twice, and I knew the sentence the office was going to send, and I knew it before they did. In 1980 a bacterium was patented because it had been given plasmids that let it eat crude oil, and the Court held that it was not a natural phenomenon because no natural bacterium did it. Then there was a lawsuit about two genes, and there are two sentences out of it and only one of them is the holding. The holding is that the complementary cDNA, the version with no introns, is not a natural phenomenon and is eligible. The other sentence is the one the office prints, which is that isolated DNA is what exists in the cell and is a natural phenomenon and cannot be claimed. Same word twice. A cell that eats oil. A molecule without introns. Both were eligible because they were not the thing nature already made, and only one of those two sentences is what the law says, and it is not the one anybody quotes.

You cannot patent a cell for being a cell. If you can, then somebody in a laboratory in the nineteen thirties owns mitosis, and that person died in nineteen forty-four, and a plaintiff will walk into a courthouse with a flask and describe him.

That was the room, in June of the following year. I was the only one in it who could be harmed.

Counsel for the applicant, a woman named Aurelia Bhatt, forty-nine or fifty, glasses on a cord, she had read Chakrabarty and she had underlined something in it. Two junior associates whose names I got wrong in the email afterward. An inventor, Dr. Emmet Rask, sixty-one, gray, first-generation Minnesota, big hands, he did most of the talking for the first twenty minutes. A tech from the company, twenty-six, hired eleven weeks ago, named Daniel, who I think was there because somebody thought it would help. And me, because I bring the tube.

Bhatt had a table prepared. She had laid it out on the way up and she put her hand flat on it before she spoke, settling the paper down, and I have thought about that gesture for four months.

“So let’s establish where we are before anyone talks about solutions,” she said. “We have an organism, we have a deposit, we have a paper, and we have a section 101 problem. And I want to start there, because everything else is downstream of it.”

“I’d like to know what the 101 problem is,” said Rask.

“You can’t claim a cell for having a genome. Myriad. Isolated DNA, natural phenomenon, no patentable subject matter. And before anybody in this room says I know, I know what the holding was and I know what the dictum was, and I know that isolated DNA is ineligible is the dictum, and I know the holding went the other way and let the cDNA through. I also know that the examiner who reads your application reads the sentence the office prints, and the office still prints the dictum.”

“Then the ground moved,” said Rask.

“The ground moved. Two years ago the agency told examiners to stop reading Myriad and Mayo as a bar and start asking whether the claimed thing is markedly different from anything in nature, and after the Corvis en banc decision the office is granting method claims that would have been thrown out in 2016. On today’s guidance I think you can get this organism claimed. I do not want it. Every claim I file is a claim somebody walks around with for the next twenty years, and I would rather give up the object than the argument. But that is what the room should know before anyone decides this is unwinnable.”

“And your organism’s genius,” she went on, “the thing that made it worth building, is that it can exist at all. A million and a tenth of a million base pairs, and it cannot synthesize nucleotides from scratch, and it cannot make most of its own amino acids, and nature has never assembled anything like it and cannot. That cuts both ways. It’s your novelty and it’s your 101 exposure, and the more your paper says it doesn’t resemble anything, the more somebody in Wilmington finds a wild isolate with a lot of plasmids and a small genome and asks why you couldn’t have started with that.”

“And if we don’t say it doesn’t resemble anything?”

“Then you have no novelty, and Chakrabarty goes the other way.” She put a finger on the paper. “In Chakrabarty the corporation won because no natural bacterium ate crude oil. If you tell me your cell does not do anything a cell does not do, you have handed the examiner the entire case in three sentences. If you tell me it does do something no cell does, and it does not, then at some point somebody diffs a wild isolate against your genome and finds it. That diff is a motion to amend or a freedom to operate letter, and it will cost you the case, because the examiner can make it look deliberate.”

“So we’re liable either way,” said the junior associate, the older one.

“We’re exposed either way. Liability is a word for a different meeting.” She looked at me. “Ms. Halloran, I need you to tell me something about viability. Is the deposit alive?”

“Per the form, yes. Above the floor, comfortably. I’ll send the numbers today.”

“And is it the organism? Not a relative of it. Not the same cell line. The thing that arrived?”

“It arrived as seven replicons in a tube, and the thing in the tube is the thing they deposited.”

“Then my problem is not viability. My problem is that I cannot reproduce it from the deposit and I cannot reproduce it from the paper, and if either of those is going to fail I want to know it in August and not in the prosecution. There is a case from three years ago. Two people who were antibodies, and the Court said a patent must show possession, not a wish, and the way they put it is that you have to have a reasonable permanent solution in hand. A specification that describes a thing the inventor had never once possessed is not a weak patent. It is nothing. She turned back to the table. “And here’s the other half of it. Doctrine of equivalents. If I claim a cell with seven replicons and the organism loses one of the seven, an accused infringer points at the six. My answer is that the six do not produce a cell. Which is true. But if my cell is not substantially different, and the accused one achieves a substantially similar result, the court goes to function. To what the thing does. And what this does is live and divide. Which is not a function of the seven. That’s what I don’t like.”

The twenty-six-year-old said, “What if we don’t claim the organism at all?”

Everybody looked at him, and I want to say for him that he had gone straight to it without preparing anything, which in a room like that is either the worst mistake you can make or the best instinct you can have.

“Explain,” said Bhatt, and she did not sound unkind, which was worse.

“So claim one becomes a method. You claim making the organism. You claim the seven-replicon construct, the method of assembling it, you claim the medium, you claim the process, and the organism itself is a product of the process.”

“That part’s right,” said Bhatt. “Product by process is eligible. Aerojet was a microorganism and a good process and the Federal Circuit still held 101, because a product claim reads on the product no matter how many steps of manufacture you write down above it. But you’re a half a step behind yourself and you should hear the half step out loud, because it’s the half step that’s going to cost you the claim. Product by process reads on the product. Your infringement analysis is on the cell, not on the bench. Somebody builds the seven by hand, or buys them, or conjures them, and makes the same cell, and they are infringing, and how they got there is a fact about the case that helps them and not you.”

“So the format is free,” said Rask, “and the scope isn’t.”

“The format is free,” said Bhatt. “Go on.”

“You claim the method, you claim the medium, and the organism is an embodiment that goes in the specification and stays out of the claims. And then the interesting step is the one where the seven come together in a cell and get out of the container.” He put his hands flat, one over the other, and I saw where it came from. “A method claim on a thing that isn’t stable. You claim making it. My answer is that after generation four you cannot make it, and you cannot make it by your own method, and if you cannot make it your method has a fatal, permanent, structural defect which is the definition of obviousness failure and enablement failure at once. You’d be patenting a procedure you cannot repeat. And the man who came up with it is twenty-six.”

The twenty-six-year-old said, “It segregated. That’s not the same as nobody knowing how.”

“It’s the same to a section 101 examiner who has to read your specification and believe the sentence that says the construct is retained,” said Rask.

“Which brings us to the deposit,” said Bhatt.

“Which brings us to the deposit,” Rask agreed.

She turned to me and asked me to go and get the tube.

I went and got the tube.

It is in a foam container in a pass-through that requires a badge, and my badge is a paper card now with a photograph on it that is eight years old, and I signed for it and carried it up two floors in a cardboard tray lined with a thermal bag that had a hole in one corner from 2019.

I set it on the table and said, “It is labeled 07/RA, it is five of the seven slots on my map, and it is at nineteen percent complete as of yesterday’s subculture, and it is alive, and I certified the arrival, and I will certify whatever is in it on whatever day you ask me to.”

“Then give me the number at certification,” said Bhatt. “Because if the certificate says nineteen percent complete, the office gets a deposit that does not do what the claims say, and their answer is not to narrow anything. Their answer is that the specification is not met, because the claimed invention was not possessed. It is not a best-efforts problem. It is a ‘was the thing ever made’ problem.”

“Then what do you want me to certify,” I said, and I said it more sharply than I meant to.

“I want you to certify what is true,” she said. “Which is what you certify. And then I will write around it.”

The room did not laugh at her, because she had not said anything funny. The certificate is true on the day I sign it. The applicant wants it to keep meaning that on every day after.

They talked for four hours. I stayed for three of them because I had the tube and no one told me to go, and because in three hours I learned more about what my certificate is for than in thirty-two years of certifying them.

Emmet Rask went to the certification set early, with a date in it: August 14. The Budapest term runs thirty years from the filing of the application that leans on it, and not from my log, and not from a paper, which is the last comfort in that sentence and not much of one. He had thirty years and, as of that June, no second round of money. Everything he was still waiting for would have to be in the tube before the money ran out, or he would have to start over with a second deposit, and the second deposit would be worse, because the first one is on the public record and a stranger can compare the two and see.

I went back to the freezer that evening and I did what I do with the difficult deposits, which is nothing for a while. I read. I took a second subculture to the nineteen-percent plate and nothing came up at all, which is a thing that can happen and is not, on its own, a fact.

I want to be accurate about what I did and why, because I have thought about it more than about anything else, and there is no version of it where I was gathering evidence. I was doing the calendar. Deposits are re-tested on a schedule; the schedule is the institution’s, and it is written down, and when I put the next re-test in a log the log asks for the date I expect the tube to be what it was on arrival. There was a field for that. There is still a field for that. I filled it in and I put the date eleven weeks out and I wrote, in the expected-condition column, as received, because that is what the field means, and it is the only thing it means, and I have never in my life written anything truer or less useful than I wrote in that box that day.

The eleven weeks ran. At the fourth re-test I did a full inventory, not because anyone asked, but because the replicon boxes are in a rack in numerical order and my job is to know what is in the rack.

It was on five.

Not a subtle loss. Five of seven, and the missing two were the same two. I want to be exact about this, because it would be easy to make it sound like the large pieces went first, and it would make a better story, and it would not be true. The two that were missing were the two smallest, fifty-five and forty-eight kilobases, the two at the end of my map. On them was every base pair the paper had never assigned a function to. A hundred and three kilobases of material nobody could say what it was for, no ortholog in any database the company had run. Nothing for a flagellum was ever on any of the seven, and nothing for the twenty-one amino acids the supplement carries, and that part of the paper holds.

What went is what the paper had nothing to say about. And what stayed is what the paper named. Over seven months in a stainless steel box, the cell kept everything it had been described as, and threw away the part nobody had described.

I sat down on a stool in a cold room with a paper map in my hand and worked out the base pairs I was looking at.

A hundred and three thousand. The final set is a million, give or take four thousand. The claim says approximately 1.1 million.

Approximately, in a claim, is doing an enormous amount of work. It is not a number I can put a range on. Nobody has ever defined it, which is why it survives, and if I can hold approximately 1.1 million against a million I have not got a technicality, I have got a description.

That was the ninth of December, 2027. The June meeting over, the claim set as filed, the certificate not sent.

Here is what I said at that meeting in June that I have not put in writing anywhere except in this, which is a document you do not have and which is not a deposition.

I said: the certificate is a statement about a day. It is true on the day I sign it. The organism is not. The form has room for both, and the room is exactly the width of the gap, and they are asking me to keep standing in it.

Nobody argued with me. Rask said, “That’s what the deposit is for. You document it at the times the schedule says.” And Bhatt said, “And I’d like the certificate to say the deposit was viable on receipt, and to describe the current state as a change observed over storage, which is true and which keeps possession in play.”

And I said, “If you say ‘at the time of deposit,’ then the examiner’s examiner has a deposit that was what you described when you made the deposit, and eleven months of nothing in between, and the disclosure you owe under 112(a) is a description of the thing as it is on the day I sign.”

“Right,” she said.

That is the whole of what I said. I did not decide anything.

I want to tell you about the donor. There is a form, in the third file, tab eleven, and it is two sides, and the first side is the ordinary side: name, address, date of collection, and then the paragraphs, eleven numbered, in eight-point type, which is what consent language does to itself. It says, in item eleven, that the material may be used “for the development and commercialization of products and processes, without limitation.” It says, in item four, that the donor receives no compensation and no share. It says, in item six, that the donor may withdraw consent at any time, and that on withdrawal the material already in an archive may be destroyed, if it is technically feasible to destroy it.

Section six is the sentence that has stayed with me. If it is technically feasible.

A deposit has to be available to the public. Anybody who wants it, anybody at all, for as long as the patent lives, without restriction and without asking the applicant first. That is the condition the whole thing stands on, and it is in the regulations and in the treaty and in the statute’s own insistence on an adequate written description, and it is why a certificate carries the weight it carries and why my signature is worth what it is worth.

Item six puts a condition on it. What is public is what a thirty-one-year-old woman in another state has not thought about since the day she signed eight-point type. And the second half is worse, because the repository cannot assess feasibility without her. Feasibility is assessed against a request from somebody who wants the material. Destroy the material and you destroy the requester’s right along with it. So the only answer the archive ever has to that question is the one she gives, and there is nobody above her in the system to ask.

I read it in the December meeting room, at the table, out of the third file, tab eleven, on a photocopy I had made myself because nobody at the company had asked for one.

Her name was Renata Okonkwo, she was thirty-one, she had a puncture on the rear fender of a bicycle that had nothing to do with anything, and I wrote Okonkwo on the map in pencil because you pencil in a map.

The section 101 problem did not go away. It was still there in August and it will be there in 2029. It stopped being the story in December, when I found out who signs the consent form.

The amended claims went in on the third of January and the application was allowed without an office action, because that is what happens when you take the entire section 101 issue out of a claim instead of winning it. Claim one is now a method. The organism is a product of the process, not the claim, and it is in the specification as an embodiment and it is not in the patent. The method does not require that the seven replicons all be retained after generation four, and the reason it does not is not generosity. The reason is that they are not.

The scope I lost in the exchange: any cell containing the 1.1-million-base-pair construct. Which was nothing, because nothing living made it, except the one in the tube, and the one in the tube is at a million and falling.

The scope I have: making a synthetic cell with seven replicons carrying exogenous-material dependence. Which is less than nothing, because anyone who runs a seven-replicon system with a maintained selection has been doing it for thirty years.

It is a real claim. Somebody who has read it will understand a class of work they did not have before, and there is no obviousness problem they can pick at, because the method does produce a cell, a cell that has been produced, that still exists, that is four lines up from mine in a box in a room that is colder than this one. And the method genuinely cannot be performed without taking my seven apart and putting them back together in an order, and that is an act with a date on it, and the date is the part that counts.

Then I signed the certificate, which is a different document from the patent, at the top of the tube’s file, above the vial, where it will be found.

It is one page. It has a number at the top which is not my accession number but contains it. It says the material was received on the fourteenth day of the month, from a courier whose name was not on the manifest. It says it was viable at receipt and at the time of deposit, with two measured figures that are not the same figure, both true, one of them under the viability line and one of them in the remarks. It says the material is a synthetic cell comprising a genome distributed across seven replicons. It says approximately 1.1 million base pairs, because that is the name the deposit has, and a repository does not rename things.

And the last line of the remarks box, which is the only line anybody will read in fifteen years, is this: Characterization at time of deposit as set forth in the disclosure of the deposit agreement, as further observed 12.09.2027 and maintained thereafter. See continuation log.

And then my name, which is on every certificate in this building and has been since 1995, and then a number for the person I can reach, which is my number, because they are both me now.

I did not put Okonkwo anywhere on it. She is not relevant to the certification of this material, and tab eleven is in the file, and the file is closed, and I did not close it.

I will say one thing about Daniel, because he came back in January, alone, from another state, with no tube and no file, to tell me that the applicant had taken new counsel and he was not sure they had the money for her, and that she had not read Chakrabarty, and that he was sorry, and that he had thought about it in a truck for six hours, and that he did not get the impression that I had said anything wrong.

He wanted to say that and he stood in my doorway for it. I told him the deposit file was closed and that I could not discuss it with anybody, including the person who told me about it. The certificate is the only instrument I have, and the only standing I have is the standing of a woman who is hard to get anything out of, and I would not spend it on somebody who feels bad.

The next re-test is due in eleven weeks. I put the date in the log. There is a line above the date for the condition I expect the tube to be in, and it says as received, because that is what the field means, and there is a space next to it where a number goes, and I did not put a number.