PALO ALTO, Calif. — “Success!” read the subject line of the email. The text, in imperfect English, began: “Good News! The women is pregnant, the genome editing success!”

The sender was He Jiankui, an ambitious, young Chinese scientist. The recipient was his former academic adviser, Stephen Quake, a star Stanford bioengineer and inventor.

“Wow, that’s quite an achievement!” Dr. Quake wrote back. “Hopefully she will carry to term…”

Months later, the world learned the outcome of that pregnancy: twins born from genetically engineered embryos, the first gene-altered babies. Reaction was fierce. Many scientists and ethicists condemned the experiment as unethical and unsafe, fearing that it could inspire rogue or frivolous attempts to create permanent genetic changes using unproven and unregulated methods.

A Chinese government investigation concluded in January that Dr. He had “seriously violated ethics, scientific research integrity and relevant state regulations.”

Questions about other American scientists’ knowledge of Dr. He’s plans and their failure to sound a loud alarm have been an issue since Dr. He revealed his work in November.

But now, Dr. Quake is facing a Stanford investigation into his interaction with Dr. He. That inquiry began after the president of Dr. He’s Chinese university wrote to Stanford’s president alleging that Dr. Quake had helped Dr. He.

“Prof. Stephen Quake provided instructions to the preparation and implementation of the experiment, the publication of papers, the promotion and news release, and the strategies to react after the news release,” he alleged in letters obtained by The New York Times. Dr. Quake’s actions, he asserted, “violated the internationally recognized academic ethics and codes of conduct, and must be condemned.”

Dr. Quake denied the allegations in a lengthy interview, saying his interaction with Dr. He, who was a postdoctoral student in his lab eight years ago, had been misinterpreted.

Image

Dr. He with a copy of “The Human Genome,” a book he edited, at his company Direct Genomics in 2016.CreditChina Stringer Network/Reuters

“I had nothing to do with this and I wasn’t involved,” Dr. Quake said. “I hold myself to high ethical standards.”

Dr. Quake showed The Times what he said were the last few years of his email communication with Dr. He. The correspondence provides a revealing window into the informal way researchers navigate a fast-moving, ethically controversial field.

The emails show that Dr. He, 35, informed Dr. Quake, 49, of milestones, including that the woman became pregnant and gave birth. They show that Dr. Quake advised Dr. He to obtain ethical approval from Chinese institutions and submit the results for vetting by peer-reviewed journals, and that he agreed to Dr. He’s requests to discuss issues like when to present his research publicly.

None of the notes suggest Dr. Quake was involved in the work himself. They do contain expressions of polite encouragement like “good luck!” Though Dr. Quake said he urged Dr. He not to pursue the project during an August 2016 meeting, the emails, mostly sent in 2017 and 2018, don’t tell him to stop.

As global institutions like the World Health Organization work to create a system to keep cowboy scientists from charging into the Wild West of embryo editing, Dr. Quake’s interactions with Dr. He reflect issues that leading scientific institutions are now grappling with.

When and where should scientists report controversial research ideas that colleagues share with them in confidence? Have scientists acted inappropriately if they provide conventional research advice to someone conducting an unorthodox experiment?

“A lot of people wish that those who knew or suspected would have made more noise,” said R. Alta Charo, a bioethicist at the University of Wisconsin-Madison who co-led a 2017 national committee on human embryo editing.

But she said scientists were not necessarily complicit if instead of trying to stop rogue experimenters, they advised them to follow ethical and research standards in hopes that institutions would intervene.

Rice University has been investigating Michael Deem, Dr. He’s Ph.D. adviser, because of allegations that he was actively involved in the project; he had said publicly that he had been present during parts of it. Dr. Deem’s lawyers issued a statement strongly denying the allegations.

Dr. He emailed Dr. Quake months before the gene-edited babies were born.

The correspondence Dr. Quake shared provides new details about Dr. He’s project, also called germline editing, including indications that the twin girls were quite premature and remained hospitalized for several weeks. They were born in October, contrary to previous reports.

Dr. Quake is an entrepreneur whose inventions include blood tests to detect Down syndrome in pregnancy and to avoid organ transplant rejection. He is co-president of an institute funded by the Facebook founder Mark Zuckerberg and his wife, Dr. Priscilla Chan. He does not do gene editing and said he was surprised when Dr. He told him during a 2016 visit to Stanford that he wanted to be the first to create gene-edited babies.

“I said, ‘That’s a terrible idea. Why would you want to do that?’” Dr. Quake recalled. “He kind of pushed back and it was clear that he wasn’t listening to me.”

Dr. Quake changed tack. “I said, ‘All right, if you’re not going to be convinced that I think this is a bad idea and you want to go down this path, then you need to do it properly and with proper respect for the people who are involved, and the field.’”

That meant obtaining ethical approval from the equivalent of American institutional review boards (known as I.R.B.s), Dr. Quake advised, as well as getting informed consent from the couples participating and only editing genes to address a serious medical need.

“I didn’t think it was something he would seriously do,” said Dr. Quake, adding that he assumed if Dr. He sought ethical approval and was rebuffed, “presumably he’d stop.”

Soon afterward, Dr. He emailed: “I will take your suggestion that we will get a local ethic approve before we move on to the first genetic edited human baby. Please keep it in confidential.”

In June 2017, Dr. He, nicknamed JK, emailed a document saying a hospital ethics committee had approved his proposal, in which he boasted that his plan could be compared to Nobel-winning research.

“It was good to see that he had engaged with his I.R.B.-equivalent there and had approval to do his research, and I’m thinking it’s their responsibility to manage this,” Dr. Quake said in the interview. “If in my interactions with JK I had any hint of misconduct, I would have handled it completely differently. And I think I would have been very aggressive about telling people about that.”

Dr. He’s team working on an embryo in a sperm injection microscope in Shenzhen, China. Dr. He has said he was altering a gene mutation that allows people to become infected with H.I.V.CreditMark Schiefelbein/Associated Press

As a postdoctoral adviser to Dr. He and other students, Dr. Quake considered his role to be mentorship. Dr. He’s work in his lab did not involve gene editing; it concerned immune responses to the flu vaccine.

Dr. He was “bright and ambitious,” Dr. Quake said, but “he was, I felt, always in too much of a hurry and I, you know, worried that he was a sort that would cut corners a little bit.”

After leaving for the university job in China in 2012, Dr. He sought Dr. Quake’s help with starting a company based on a genome-sequencing technique Dr. Quake had invented. Dr. Quake, whose American firm selling that technique had gone bankrupt, made introductions that helped Dr. He license patents for his company, Direct Genomics. Dr. Quake visited in 2015 but eventually declined an offer to serve on the company’s scientific advisory board.

In Dr. He’s 2017 correspondence, he said he would be editing a gene called CCR5, altering a mutation that allows people to become infected with H.I.V. Many scientists have since argued it was medically unnecessary because babies of H.I.V.-positive parents can be protected other ways. Dr. Quake said he believed there was not scientific consensus about that.

In early April 2018, Dr. He’s “Success!” email said “the embryo with CCR5 gene edited was transplanted to the women 10 days ago, and today the pregnancy is confirmed!”

Dr. Quake did not reply immediately. Instead, he forwarded the email to someone he described as a senior gene-editing expert “who I felt could give me advice.” He redacted the name of the expert.

“FYI this is probably the first human germ line editing,” Dr. Quake wrote. “I strongly urged him to get IRB approval, and it is my understanding that he did. His goal is to help hiv positive parents conceive. It’s a bit early for him to celebrate but if she carries to term it’s going to be big news I suspect.”

The expert replied: “I was only telling someone last week that my assumption was that this had already happened. It will definitely be news …”

Dr. Quake considered that response “very blasé,” he said. “He’s not surprised at all. And he’s not saying, ‘Oh my god, you got to notify the mythical science police.’”

Dr. He visited Dr. Quake at Stanford to discuss the results of the experiment.

Six months later, in mid-October, Dr. He emailed again: “Great news! the baby is born (please keep it in confidential).”

Dr. He asked to meet on a planned visit to San Francisco, saying, “I want get help from you on how to announce the result, PR and ethics.”

Dr. Quake replied, “Let’s definitely meet up.”

In that meeting, Dr. Quake recalled, Dr. He walked him through what he had done. “And I pressed him on the ethical approval, and I said this is going to get an enormous amount of attention, it’s going to be very closely scrutinized. Are you sure you’ve done everything correctly?”

Dr. He’s response unsettled him, he said. “The little corner-cutting thing came up again: ‘Well, there were actually two hospitals involved and you know, we had approval from one and we did work at both hospitals.’ And I said, ‘Well you better make sure you have that straightened out.’”

Back in China, Dr. He wrote: “Good news, the hospital which conducted the clinical trial approved the ethic letter,” adding, “They signed to acknowledge the ethic letters from another hospital.”

Dr. Quake replied, “Great news, thanks for the update.”

In late October, Dr. Quake texted someone he called an “extremely prominent scientist in the field,” writing: “First genome edited human baby — done! (in China, where else?)”

“Interesting. Source?” the scientist responded.

“Someone I know well who walked me through all the data,” Dr. Quake wrote. “Should go public soon.”

He added, “Mums the word for a few more weeks but I thought you would like to know.”

At the scientist’s suggestion, they spoke on the phone.

Asked about the scientist’s reaction, Dr. Quake said, “Also not terribly surprised, not an oh-my-god thing, like it’s inevitable, like the inevitable has happened.”

Dr. He explaining the experiment at a summit on human genome editing in Hong Kong on Nov. 28. Dr. Quake had asked him to “please remove my name” from the slide acknowledging people who helped with his research.CreditAnthony Wallace/Agence France-Presse — Getty Images

The scientist suggested that Dr. He share his work at a genome-editing conference in Hong Kong.

About a week later, Dr. He’s publicist, Ryan Ferrell, contacted Dr. Quake, worried that Dr. He presenting the project publicly so soon could cause “severe and permanent harms to his reputation and the field.” And, “the twins are still in the hospital, so no positive imagery.”

Dr. Quake, in Hong Kong for other commitments, met Dr. He and Mr. Ferrell, telling them, “you’re going to be held to a very high standard,” he said. “‘People’s first response is going to be you’re faking it.’”

He advised Dr. He to submit the research to a peer-reviewed journal, and Dr. He did so.

Then, because journal review takes time, Dr. Quake said he advised Dr. He not to go public in Hong Kong, but to speak privately with key experts there so they can “get socialized to what’s coming and will be more likely to comment favorably on your work.”

But Dr. He was not persuaded. “I do not want to wait for 6 months or longer to announce the results, otherwise, people will say ‘a Chinese scientist secretly hide the baby for 6 months.’”

Dr. Quake pushed back: “It is prudent to let the peer review process follow its course.”

But Dr. He went forward with his Hong Kong talk. Two days before it, after news of the twins broke, Dr. Quake emailed, “Good luck with your upcoming presentation!” But he added, “please remove my name” from the slide acknowledging people who had helped.

“He was spinning up this huge press thing around it,” Dr. Quake explained in the interview. “It was going to go well or poorly, I didn’t really know. But it wasn’t something I was involved in and I didn’t want my name on it.”

Dr. Quake is not sure what consequences he thinks Dr. He should face.

But he believes that the shock and horror some scientists now express belies the unruffled response of the experts he consulted.

Asked if he should have handled things differently, Dr. Quake said: “Well, hindsight is 20-20. I mean, you could say yes I should have done many other things.”

“But,” he continued, “as these things unfold, you’re in the moment, and you know, he’s doing legitimate scientific research — many people would define it that way. He’s got I.R.B. approval and his institution is regulating the human subject stuff and you sort of believe all that.”

He added: “To the extent that it wasn’t obvious misconduct, what does a person in my position do? Encourage him to do it right, his research, right? I mean, that’s what I believed I was doing.”