What Does Ginkgo Bioworks Do?

Ginkgo Parnters with Agricen

"Ginkgo's unique approach to process development and optimization brought an efficiency for developing a custom fermentation process that we didn't see with other toll producers. This is work that we would typically do in-house, but we are always looking for ways to be more operationally efficient. We saw what Ginkgo's team offered and enlisted them to do what they are experts at – simplifying processes with challenging microbes. "

Ginkgo Parnters with Carnegie-Mellon University 

Combining recent advancements in synthetic biology with cutting-edge detection technology, the team expects to develop both a highly innovative orally administered pill containing specially engineered, tumor-targeting sensors and a user-friendly cancer screening device designed for at-home testing. As part of this team, Ginkgo plans to apply its cell and enzyme engineering expertise to support development of these new diagnostic tools.

Ginkgo Bioworks partners on Deep Origin-led team to develop new tools for predicting drug safety  

The collaboration, Pharmacological Research and Evaluation through Digital Integration and Clinical Trial Simulation (PREDICTS), aims to develop a revolutionary computational platform for drug safety.

As part of this team, Ginkgo will be leveraging its 'Datapoints' platform for perturbation response profiling to generate high-quality, high-throughput, structured data sets to support AI model training, including small molecule drug and genetic perturbations spanning multiple cell and tissue types. Readouts will include cell type-specific toxicity endpoints, DRUG-seq transcriptomics, and cell painting.

Ginkgo Bioworks Selected by PNNL to Deliver a Modular, High‑Throughput Phenotyping Platform for DOE's M2PC

Ginkgo Bioworks (NYSE: DNA) today announced it has been awarded by the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL) a four-year, up to $47M contract to co-design, build, and integrate a High‑Throughput Automated Phenotyping Platform (HTP‑APP) in support of the Microbial Molecular Phenotyping Capability (M2PC). The platform, selected through a competitive procurement process, is intended to enable the Department of Energy's (DOE) Office of Science, Biological and Environmental Research program to generate rich, reproducible microbial and microbiome data that ensure the U.S. remains at the forefront of the bioeconomy, safeguarding economic, societal, and national security benefits while maintaining global leadership in biotechnology innovation. Drawing on Ginkgo Automation's dynamic Catalyst scheduling software and modular Reconfigurable Automation Carts (RACs), the HTP‑APP is designed to automate end‑to‑end workflows—from media and cultivation to sample preparation and multimodal analytics—while supporting BSL‑2 operations, remote planning and execution, and laboratory integration. This modular approach is expected to help PNNL adapt the platform as scientific needs evolve, add new methods or instrumentation, and maintain high uptime in a user‑facility environment. 

Ginkgo Bioworks Awarded Project Agreement through BARDA's BioMaP-Consortium

BOSTON, Nov. 3, 2025 /PRNewswire/ -- Ginkgo Bioworks (NYSE: DNA) announced today that it has been awarded a contract through the Biomedical Advanced Research and Development Authority's (BARDA) Biopharmaceutical Manufacturing Preparedness Consortium (BioMaP-Consortium) to develop innovations that strengthen and reduce the costs of domestic biomanufacturing of monoclonal antibodies (mAbs) to protect against and treat infection by filoviruses such as Ebola (EBOV) and Sudan Viruses (SUDV). Ginkgo will lead a team composed of Advanced BioScience Laboratories (ABL), Inc., Isolere Bio by Donaldson, NeuImmune, Inc., and ProteoNic BV to develop and integrate innovative technologies that will span the entire process for producing mAb drugs.

To sum up these projects and figure out what Ginkgo does, let's look at the italicized highlights of Ginkgos roles?

Agricen: Ginkgo specialized in process development and optimization of a custom fermentation process. 

Carnegie-Mellon: Ginkgo specializes in cell and enzyme engineering.

Deep Origen:  Ginkgo specializes in generating data sets to support AI model training.

PNNL:  Ginkgo specializes in software that automates work flow in a manufacturing setting. 

BARDA:  Ginkgo specializes in Antibody production.

I worked for a company that had similar needs for help in manufacturing the antibody they were selling. The company began with two groups, Fermentation and Protein Sciences, their official designation. What they really needed was Upstream and Downstream production teams. The leadership simply did not know that such terms existed and were what they needed. Eventually Upstream and Downstream groups were hired and... they failed. The company had no choice but to pay the maximum required to get the work done properly by hiring one of the many manufacturing companies available in the biotechnology space. 

Long before Ginkgo came into existence, manufacturing companies had been working and advancing the science and technology of biopharmaceutical manufacturing. Ginkgo is one of the least experienced options in this space. 

Optimizing cell and enzyme engineering? Generating data sets for AI? Workflow software?

Perhaps Ginkgo has overextended it's "expertise" as a result of a CEO and board lacking in the proper background in industry. The leadership of Ginkgo suffers from what many in biotech cargo cults suffer. They moved straight from the University to industry, not learning what is already known from people who have learned from doing the work. Ginkgo specializes in stringing together a set of words that fool the cargo cult tribesmen into thinking work will be done to bring the big metal birds from the sky. They are competing in a field full of companies who have, for decades, been doing what they claim to do. 

It reminds one of the downfall of Theranos. Theranos claimed to have tests for 272 (?) tests done by your local hospital. Once they were up and running Theranos ended up using the technology of many of their competitors claiming the results were generated by their little toaster machine and the microblood draw device. The real experts were out there, asking tough question of Elizabeth Holmes at the conferences. These experts worked on the same problems. They had a very hard time solving problems that Theranos claimed to have solved, with no publications. 

In essence Theranos and Ginkgo are the industries version of the lab tech postdoc who becomes known as the Golden Child. The one guy in the lab who gets the results the PI wants, every time. He or she gets the big projects because the PI wants particular results, not the kind that come from honest work presented in an honest way. 

And so it behooves me to tell you what is missing...

Ginkgo has announced more partnerships than anyone can remember. What have the conclusions been? How many times have they accomplished the goal? How many press releases are about collaborations beginning rather than successful endings? If you were to ask Jason Kelly what has been Ginkgos biggest success story, what would he say? What about the top ten? What has been the cargo? How many airplanes have landed on their runway and what came out of the back of the big metal birds? 

Ginkgo Bioworks Might Not Fail, Probably Will

On May 13, 2024 Ginkgo Bioworks Holdings Inc. announced that it received a notice on May 7 from the NYSE informing the company that is is not in compliance with Section 802.01C. The commons stock was under $1 per share over a consecutive 30 trading-day period. Ginkgo has 6 months to regain compliance.

The company has been in existence since 2008. It's IPO was in 2001. They entered the market through a merger with SPAC Soaring Eagle at a $17.5B valuation. They currently have a market cap of $0.94B. The CEO and co-founder, Jason Kelly has been the only CEO (16.3 years) at Ginkgo. He is asking for a raise.

The solution to the problems of the Biotechnology industry, as well as the recent debates of the Covid virus origination is the empowered laboratory work force. The people at the highest positions think they can bully underlings around like Steve Jobs at Apple. The problem is that Steve Jobs was bullying some very smart and useful people around. Biotech and the life sciences leaders have spent their time diminishing the significance of the work done by their subordinates. As a result they were all left with nothing but the narrative they started with. No scientific backing to prop up and/or propel the big ideas. We end up with pandemics they didn't see coming and $15B corporate failures. And it happens fast. 

If there were an empowered laboratory workforce, it might just work as Ginkgo claims their labs work. From a business perspective you want the projects to all work out. Need a protein? Here you go. Need a test? Here you go. The problem is spelled out in the Cargo Cult Science speech. It's not a question of how to arrange things differently, like the coconut headsets. There is a fundamental misunderstanding. 

Theoretically Ginkgo would be the empowered laboratory workforce. Someone with power applies skepticism to the claims of those in their group. They send the research out for testing. The testing is done in the empowered laboratory by skilled life long professionals. What Ginkgo does however is not at the skeptical level. They allow for the claims of magical molecules, develop the molecules and they hand them back to the people who thought them up. The original thinkers and Ginkgo have both avoided the empowered laboratory work force. No one has applied the scientific method described in the CCS to put the idea through the black box. Idea in, reality out. 

Half of the NIH $39B budget should go towards laboratories that test the work done by the grantees who receive the other half of the budget. 

Just as we saw with the e-mail between Collins and Fauci, forcing desired outcomes is how science is conducted at the highest levels. "This proposal from the three fringe epidemiologists who met with the Secretary seems to be getting a lot of attention-and even a signature from Nobel Prize winner Mike Leavitt at Stanford. There needs to be a quick and devastating published take down of its premises. I don't see anything like that on line yet. Is it on it underway?" - Francis Collins to Anthony Fauci

The empowered laboratory workforce would be interested in the database at the Wuhan lab. It would be easy to discover if they had anything to do with Sars-Cov2 if they had laboratory evidence. Collins and Fauci would not know how to find it. They wouldn't know what to look for. Instead they wield the kind of power that says, "write a paper and have it published in a major journal that disputes the ideas we can not abide". How does a scientist dispute ideas that may be true? Step one: Avoid the evidence!

Ginkgo has a similar scientific method. A company comes to them needing one of the many services. Let's say they want a protein made and manufactured to be sold as a drug delivery product. The company tells Ginkgo what the protein will do once it is made. Ginkgo makes the protein. They hand it back. The company now has to prove that the protein does what they said it will do. Sars Cov2 did not come from a lab in Wuhan and this new protein will deliver drugs to specific cells. If anyone says otherwise, take them down in the journals. 

What then is Ginkgos role in the success of their business partner? None. They take the money if the company succeeds at getting their desired outcome.

The desired outcome is not the actual outcome most of the time. The truth (reality) is tough. If you make widgets on an assembly line your job is well defined. If you make antibodies that bind to specific proteins you are making widgets. The complicated nature of the work is higher than that of the assembly line worker. The difference is akin to a person who makes cakes versus someone who makes rocket engines. If your job is to convince others that the widgets cure cancer, you are not making widgets. You work in advertising. You sell your companies product. You sell whatever they tell you to sell. The highest ranking officials tell you what the desired product will do. Everybody else lives and dies on whether or not the desired product does what it is supposed to do. 

Will Ginkgo Bioworks fail? It's not up to them. It depends on chance. Luck. Will their business model allow them to land that one product that will make them the kind of money they have structured into their payoff system? It's not up to them. They are on a fishing expedition. 

Truth in Science

https://youtu.be/LKiBlGDfRU8?si=ij36LqvMFEWwuLGT

Ginkgo Aquires Seattle Biotech Modulus

A big fish eats a small fish to sustain life. With that in mind let's look at the latest acquisition of Modulus Therapeutics by Ginkgo Bioworks.

A common standard among publicly traded companies is that they must maintain a stock price above one dollar per share. If they drop below one dollar per share for 30 days they receive deficiency notice. From there they have a certain period of time to get their finances back up to compliance. Atossa Therapeutics, another Seattle based biotech (Cargo Cult), recently went through what Ginkgo may soon be facing. On September 26, 2023, Atossa was notified by Nasdaq that it was not in compliance because they failed to maintain a minimum closing bid price of $1.00 per share for 30 consecutive trading days. They were required to go 10 consecutive trading days over the $1.00 per share price, which they accomplished on March 14, 2024, almost 6 months later.

Ginkgo Bioworks is currently at $1.08 per share. Year-to-date they are down over 36% in spite of their acquisitions and new contracts. They recently announced a new contract award of up to $6M from the Defense Advanced Research Projects Agency (DARPA) to develop materials that control the physical properties of ice crystals. They also announced the acquisition of a Seattle based company Modulus Therapeutics which specializes in cell therapies for autoimmunity. What value did they add to the company? More than an "up to" $6M addition?

Modulus lists funding at $3.5M seed money. They were founded in 2020. They have 2 to 10 employees with 11 associated members. Is there an office and a laboratory? Do they lease space? How much of the $3.5M is left and what did Ginkgo pay for the acquisition?

In value investing one has to piece together a picture of a company and it's future earnings. With biotech start ups it is virtually impossible to crunch the numbers because start ups don't make money. They spend it. In order to assess the value, as Ginkgo did, you have to understand the science. We will assume that Ginkgo leadership can at least justify the acquisition by touting the science and it's potential. What we cannot do is assess how much the company was worth monetarily and what Ginkgo paid for it. 

The CEO of Modulus said this about the acquisition:

"I'm excited to announce that Modulus Therapeutics has completed a transaction with Ginkgo Bioworks, Inc. that will further strengthen Ginkgo's presence in the cell therapy engineering arena."

Jason Kelly of Ginko Bioworks said this about the acquisition: 

"Modulus Therapeutics has built an array of incredible cell therapy assets that we are excited to add into the significant cell therapy capabilities Ginkgo has developed to date."

Combined: Ginkgo and Modulus completed a transaction that added Modulus's cell therapy assets to Ginkgo's cell therapy assets. If you want to buy what Modulus used to sell, you have to pay Ginkgo. The question is, how well was Modulus doing? Was anybody buying and how will Ginkgo increase the value of the assets? 

Ginkgo is nearing the $1.00 per share cutoff. They must add value to their company to add value to their share price. While Ginkgo has been acquiring small fish into their system they have not become a bigger fish. The share value has continued to go down. The acquisitions have not led to significant projects or sales to bolster their value. With one block buster partnership they could easily fight off the delisting threat. But for now they must continue throwing spaghetti at the wall and hope it will stick. 

We can't write off scientific efforts. Somewhere within the walls of Atossa and Ginkgo lies science. Yet they do not make money. They will probably fail and no one will remember they we're here. How can it be with all of the PhDs/MDs and VCs? Something is missing. The science that exists is not being put to work properly. 

We call these companies Cargo Cults because they operate in that space. Atossa has long struggled to remain listed on the Nasdaq. They have had FDA warnings. They have yet to summon the big metal birds onto their runway. But they still go to work and do things, important things like dealing with the FDA, SEC and NASDAQ.  Ginkgo Bioworks do important and difficult things like acquiring companies and adding assets to their portfolio. They too have yet to demonstrate a cargo operation. When you spend more than you make, you are not in business for long. Unlike Atossa, Ginkgo may be too big to survive. In other words, they are unaware that they are in the Cargo Cult zone. Atossa seems to have a special skill in staying alive in spite of their dubious products and/or services. Ginkgo has spent too much on their CCS Airport.

Now it behooves me, of course to tell you what they're missing. But it would be just about as difficult to explain to the South Sea Islanders how they have to arrange things so that they get some wealth in their system.  It is not something simple like telling them how to improve the shapes of the earphones...

Third Millennium Thinking: A Conversation with Saul Perlmutter, John Cam...

Why are the authors of this book not crediting Richard Feynman?

From the speech: 

That is the idea that we all hope you have learned in studying science in school—we never explicitly say what this is, but just hope that you catch on by all the examples of scientific investigation.  It is interesting, therefore, to bring it out now and speak of it explicitly.  

But this long history of learning how to not fool ourselves—of having utter scientific integrity—is, I’m sorry to say, something that we haven’t specifically included in any particular course that I know of.  We just hope you’ve caught on by osmosis.

 

The first principle is that you must not fool yourself—and you are the easiest person to fool.  

Richard Feynman - Cargo Cult Science speech to the 1974 class of Cal Tech. 

They use the words explicitly and osmosis. They don't say Richard or Feynman.  

In my opinion people who pick up this book will cling to their biases as they read the book. They will be seeking evidence that they are correct and those who think differently are incorrect. Who wants to verify that they are wrong? Yet that is what Feynman tells us is part of the scientific method. We must explicitly attack our thinking and try to prove it wrong. 

The first red flag is simply the reliance on the authority of science. The authors are telling you that they know of the way and you need only follow them down the path. At the end of the path is certainty. Yet the Scottish Berkeley professor tells you that we have to let go of certainty. I would agree with that statement. What they don't mention, at least in this video, is that the certainty of scientists is no more accurate than the certainty of anyone else. Quite possibly scientists get it wrong more than bankers, judges, janitors and bakers. John Ioannidis published a paper claiming that 90% of published scientific medical research contains false information. What is the accuracy of truth in the National Inquirer? It is probably better than Cell/Nature/Science. 

Can you imagine a professional scientist claiming that The National Inquirer reports more accurate information than Cell/Nature/Science? It would be blasphemy! That is the religion of science. The scientific method would simply take the claim into consideration, define the terms and proceed too find the truth.  

Dr. Ionnidis was also embroiled in the scientific debates over the pandemic. The certainty of science was demonstrated very clearly during Covid. Scientists do not agree on what the rest of the world calls "science". They simply employ the concepts put forth and attempt to explain things that are useful to know. However, when the truth is not useful to those in power, the scientist must cave to the edicts of a Fauci-like leader or hold their tongue. To speak out with a scientific methodology will land you in the dog house with a damaged reputation. The profession of science is not a shining example of how to employ the scientific method. 

The second red flag is the timing of a book that claims now is the time for such a book. The scientific method has always been important. All times in our world have needed the scientific mind. The scientific mind will always be at odds with the rest of the world population. Would this book however delve into the Covid response? Did our professional scientists who went against the establishment receive proper attention or were they cancelled by other scientists? In other words, did our scientific establishment employ the scientific method during Covid?

Most people will read the book to validate that Trump is evil or that Covid was fake news. Whatever your political leanings, religious beliefs, rural vs urban viewpoint... this book may very well support your beliefs. People are going to believe what they prefer to believe. No book can fix that. 

Feynman's identifies the problem facing science when he spoke of the charge on an electron:

One example: Millikan measured the charge on an electron by an experiment with falling oil drops and got an answer which we now know not to be quite right.  It’s a little bit off, because he had the incorrect value for the viscosity of air.  It’s interesting to look at the history of measurements of the charge of the electron, after Millikan.  If you plot them as a function of time, you find that one is a little bigger than Millikan’s, and the next one’s a little bit bigger than that, and the next one’s a little bit bigger than that, until finally they settle down to a number which is higher.

 

Scientists get it wrong. That is part of the process. There is no authority who knows the proper way. Those who make the claim are gurus, shaman, preachers and snake oil salesmen. The scientific method is something that must be taken on by leadership. People will get it right and they will get it wrong. Who will be taken seriously is the issue. 

With that skeptical viewpoint I will read this book. It might be very good. The publicity however makes me wonder. Are the authors aware that the worst offenders against the scientific method are scientists themselves? Are they willing to point the finger at science? 

Appealing to the Authority of Man

At some point, if you are a Cargo Cult, you begin to realize that the Gods aren't going to step in. You are failing at getting the Cargo and the natives are getting restless. You must appeal to something more reasonable, something you can control. You find the highest ranking human in your group and begin to set up a new strategy. The big metal birds are not landing no matter how you reshape your runways. The headset made of coconuts and sticks cannot be made to summon the cargo planes. It has to be that the people are doing something wrong. They are not using the airport you have designed properly.

The first step is to set up a new agency. Then set up a few more.  Devote more resources towards the new groups. Let them define the issues and new terms to discuss said issues. Have meetings. Make claims that things are beginning to succeed, according to the new way of thinking...

BOSTON and LEXINGTON, Mass., Feb. 15, 2024 /PRNewswire/ -- The Defense Threat Reduction Agency's (DTRA) Joint Science and Technology Office (JSTO) for the Chemical and Biological Defense (CBD) Program has awarded, through the Medical CBRN [Chemical, Biological, Radiological, and Nuclear] Defense Consortium (MCDC) requirement 22-05, "Adjuvant Activity to Vaccines Prototype," a 5-year contract totaling up to $31 million including program options to the team of Ginkgo Bioworks, Inc. (NYSE: DNA) and SaponiQx, Inc. (a subsidiary of Agenus Inc., NASDAQ:AGEN) to discover and develop next-generation vaccine adjuvants. Partners in adjuvant discovery and development since 2021, Ginkgo, which is building the leading platform for cell programming and biosecurity, and SaponiQx, developing a visionary adjuvant development platform, will use a combination of high-throughput empirical and artificial intelligence/machine learning approaches, including Generative Molecular Design (GMD), to develop superior novel saponin-based adjuvants.

If you look at the SaponiQx website you see a rather sparse pipeline. QS-21 (available for supply) QS-7 and QS-X (R&D phase). At the inception of the company, which coincided with their partnership with Ginkgo, QS-21 was already "available for supply". Very little seems to have been done since 2021 in spite of the two powerhouses in the vaccine adjuvant space.

What has been accomplished is a $31M 5 year contract to develop what the two companies said they were going to develop using their combined expertise. The final piece of the puzzle was this agreement from DTRA, JSTO, CBD through the DBRN, MCDC requirement 22-25. 

If all goes according to plan there will be cargo by the year 2029. 

So Many Collaborations

I asked Gemini, "Who is The Cargo Cult Scientist?

"The term originated from a famous speech by physicist Richard Feynman called "Cargo Cult Science." He used the analogy of cargo cults in Pacific islands, who built elaborate mock runways and control towers in hopes of attracting cargo planes. Similarly, "cargo cult scientists" might go through the motions of research, collecting data and conducting experiments, but their work lacks the underlying foundation of scientific rigor and ultimately fails to produce meaningful results or contribute to genuine scientific understanding."

Okay then! Now let's look at a possible Cargo Cult Science project:

The Defense Threat Reduction Agency's (DTRA) Joint Science and Technology Office (JSTO) for the Chemical and Biological Defense (CBD) Program has awarded, through the Medical CBRN [Chemical, Biological, Radiological, and Nuclear] Defense Consortium (MCDC) requirement 22-05, "Adjuvant Activity to Vaccines Prototype," a 5-year contract totaling up to $31 million including program options to the team of Ginkgo Bioworks, Inc. (NYSE: DNA) and SaponiQx, Inc. (a subsidiary of Agenus Inc., NASDAQ:AGEN) to discover and develop next-generation vaccine adjuvants. Partners in adjuvant discovery and development since 2021, Ginkgo, which is building the leading platform for cell programming and biosecurity, and SaponiQx, developing a visionary adjuvant development platform, will use a combination of high-throughput empirical and artificial intelligence/machine learning approaches, including Generative Molecular Design (GMD), to develop superior novel saponin-based adjuvants. -BOSTON and LEXINGTON, Mass., Feb. 15, 2024 /PRNewswire/ --

They are going to research and develop variants of naturally occurring compounds known as Saponins.

This is an important concept because the current method for obtaining saponins is to extract the compound from tree bark. The process is not environmentally friendly.

Back in 2021 "Vaccines are one of the most powerful tools we have to fight pandemics, but ensuring widespread access to efficacious vaccines continues to be a major challenge worldwide," says Jason Kelly, CEO of Ginkgo Bioworks. "We're proud that our platform is being used by companies across the vaccine supply chain to develop and manufacture the materials necessary for life-saving vaccines."

Currently SaponiQx has one adjuvant available for supply (QS-21) and two in the R&D phase (QS-7 and QS-X. They have zero job openings. They have been working with Ginkgo since 2021.

The problem with Cargo Cult Scientists, according to Gemeni, "their work lacks the underlying foundation of scientific rigor and ultimately fails to produce meaningful results or contribute to genuine scientific understanding."

The collaboration touted in the recent press release by Ginkgo and SaponiQX has actually been ongoing since 2021. Where are the fruits of this labor? Meaningful results or advanced scientific understanding?

Instead we have a word salad. Who is now involved in making SaponinQX successful?

The Defense Threat Reduction Agency's (DTRA) Joint Science and Technology Office (JSTO) for the Chemical and Biological Defense (CBD) Program... through the Medical CBRN [Chemical, Biological, Radiological, and Nuclear] Defense Consortium (MCDC) requirement 22-05, "Adjuvant Activity to Vaccines Prototype," ...Ginkgo Bioworks, Inc. (NYSE: DNA) and SaponiQx, Inc.

The Cargo? A 5-year contract totaling up to $31 million.

Dying of Cancer

My mom died in 2023 from ovarian cancer. She was diagnosed in 2022, underwent surgery to remove a large tumor, underwent chemotherapy and died in July of 2023. There were no experimental drug trials offered as alternative therapies. There was no semblance of medical science advances. No antibodies against a specific protein on a cancer cell. No attempts to stop cancer cells from growing by targeting angiogenesis. No oncolytic viruses were injected into her body to take out cancer cells. No RNA anti-sense drugs, no RNA interference, no DNA gene therapy, no new anything. Just surgery, chemotherapy, death. 

And it was not a very good existence. My mom became weak to the point we were ready to put her into a nursing facility. She lost her appetite often and simply had to force herself to eat something for energy. In the end we found her lying on the couch unable to get up. We called 911. She went to the hospital. The nurse told us that our mom would be released later that day. Nope, was our response. Two days later my mom passed away at the age of 77.

I suppose this is how we go. At 77 you are in danger of succumbing to a number of things. Our cells have kept us going for over 28,000 days. We wake up with renewed energy. We go to bed with the energy spent. We wake up recharged. Along the way we may do bad things regarding diet and exercise. We may breath in air pollution. We may challenge our systems with drugs, alcohol, and/or tobacco. When we feel something is wrong we go to the doctor and they diagnose the symptoms. 

As each day comes and goes we are one day closer to the end. As we approach the age of 77 we are getting close. We don't know how long we have but that is for the best. A positive attitude can go a long way. 

Sleep is biochemistry inside the brain. Our bodies need to sleep so our cells can be replenished. There is a cleansing process that occurs during stage 4 sleep. There is a pleasant dream phase called REM. If we drink too much the biochemistry shuts down the day in a sudden sleep. We call that passing out. We awake before the normal amount of sleep feeling poisoned. Food can also affect the sleep process. Too much Western society fast food or processed food will also cause trouble. A day of eating mostly vegetables and natural food with a fair amount of exercise that ends at the same hour (no drugs/alcohol/cigarettes) will lead to a pleasant nights sleep with an awakening with restored energy. 

In the end my mom was not pleased with how she slept. She awoke with little energy. She made her way to the recliner where she would spend the day. Good Morning America was followed by Gunsmoke, Leave It to Beaver, Happy Days, The View... The last show made her an angry old person. The old time shows made her happy as if in a state of REM sleep. No mental challenges. The future was filled with chemotherapy and ultimately death. I don't mean to be depressing but for her it had become real. She did not have the energy to fight back. 

So that is all. Cancer is wrapped up in the complexity of our DNA. It makes itself known when we can no longer stop the force it has on the overall system. We have little to show for our research. Just money spent and careers of the successful scientists. 

Ginkgo Announces New Advisory Board!

 January 8, 2024

Today we’re thrilled to announce the formation of our new Biopharma Advisory Board!

This council of experts from across the biopharmaceutical industry will provide critical insight into the development of Ginkgo’s core platform service offerings across target discovery, drug discovery, optimization, and manufacturing. The group, which will conduct regular meetings at Ginkgo and with its partners, includes (in alphabetical order) —

How many of these CEO's have signed deals with Ginkgo Bioworks to provide Ginkgo with revenue rather than Ginkgo providing the CEO's with income? 

“We try never to forget that medicine is for the people. It is not for the profits.”

– George Merck

I would like to focus on one of the members of the new committee. Previously I have talked about one of the new members of Ginkgos Advisory Board.

• John Maraganore, PhD, served as the founding Chief Executive Officer and a Director of Alnylam from 2002 to 2021. Under his leadership, Alnylam helped lead the interventional RNA revolution by launching the first RNAi therapeutic medicine, ONPATTRO®, in 2018, followed by four more RNAi therapeutics through mid-2022. Dr. Maraganore was the chair of the Biotechnology Innovation Organization (BIO) from 2017 to 2019 and is an active mentor to leaders across the biotechnology industry. John is the principal of JMM Innovation, and also serves as a Venture Partner for Arch Ventures and Atlas Ventures, an executive partner for RTW Investments, a senior advisor for Blackstone Life Sciences, and as an advisor for M28.

A quick search of ONPATTRO: 

Wikipedia

Onpattro is a medication used for the treatment of polyneuropathy in peop[le with hereditary transthyretin-mediated amyloidosis, a fatal rare disease that is estimated to affect 50,000 people worldwide.

The per-patient cost is between US $451,430 and $677,145, depending on the number of vials needed. As of 2020, there were 1050 people globally receiving parisian, generating $65.5M in net revenues. 

The FDA

Alnylams Pharmaceuticals push for parisian to be expanded to a much larger pool of patients...

In a briefing document released ahead of the Sept. 13 meeting of the FDA's Cardiovascular and Renal Drugs Advisory Committee, the agency called into question the efficacy of the drug in treating that pool of patients.

Remember, medicine is for the people, not the profits. 

Patisiran was already approved by the FDA in 2018 for the treatment of hereditary ATTR amyloidosis polyneuropathy, which made it the first-ever RNA interference therapeutic approved by the regulator.

Nevertheless, vutrisan - sold under the brand name Amvuttra - still represents the company's most lucrative product. In its second-quarter 2023 financial update, net revenues for the drug were $132 million, versus $91 million for Onpattro. In the fourth quarter Onprattro sales were down to $79M.

For the full-year 2023 net product revenues of $1.24B were reported. The revenues come from sales of its four marketed products Onpattro, Amvuttra, Givlaari and Oxlumo.

Onpattro: $355M

Ambuttra: $558M

4060 patients worldwide were receiving commercial Onpattro and Amvuttra as of year-end 2023.

Givlaari: $219M

Oxlumo: $110M

650 patients were receiving Givlaari as of year-end 2023

430 patients were receiving Oxlumo as of year-end 2023

So roughly 5140 patients are generating $1.24B. 

Yahoo Finance

In October 2023, Alnylam experienced a massive setback after the FDA issued a Complete Response Letter (CRL) in response to the company's supplemental new drug application (sNDA) for the label expansion of Onpattro to treat the cardiomyopathy of transtheyretin-mediated (ATTR) amyloidosis. 

However, following this development, the company shifted its focus to the phase III HELIOS-B label-expanding study of Amvuttra in the treatment of cardiomyopathy of ATTR amyloidosis. 

CCS

John Maraganore has long struggled to get dubious RNAi drug products on the market. From the perspective of the market, he has succeeded. But then again, so did the Covid vaccine. Safety and efficacy can be dealt with best under emergency conditions. John Maraganore has succeeded. He is a hard working man. Long listed here as a Cargo Cult Scientist he has created over $25B in market capitalization. 

Alas, only 5,140 patients are receiving treatment. Those patients are already very sick people. They get results only a professional statistician working in the Cargo Cults can detect. We have to wonder what it is like for the patients receiving the RNAi drug product. Do they feel a difference? Are they less sick?

In the Cargo Cults the natives still look to the skies. They believe what they are doing will one day provide results. Ginkgo Bioworks has said that John Maraganore has produced results and he will now advise them on how they too can see the massive returns on their investments. Although the expertise of John Maraganore was in RNAi drugs, he seems to have now moved on to biotechnology capital. He is an investment strategist. He advises on money. Ginkgo does not do RNAi drugs. Nonetheless, they have found an ally. A man who knows that medicine can make great profits even if the people don't need them. 

Book List

 1.  Betyrayers of the Truth - William Broad and Nicholas Wade

The lures of careerism and big money, the pressures of huge research factories, the repeated failure of supposedly fail-safe mechanisms of scientific inquiry to detect and correct fraud - Betrayers of the Truth is about how science really works and why scientists are tempted to cheat. 

2.  On Bullshit - Harry G Frankfurt

Most people are rather confident of their ability to recognize bullshit and to avoid being taken in by it. So the phenomenon has not aroused much deliberate concern. We have no clear understanding of what bullshit is, why there is so much of it, or what functions it serves. And we lack a conscientiously developed appreciation of what it means to us. In other words, as Harry Frankfurt writes, "we have no theory."

3.  Innumeracy - John Allen Paulos

Mathematical Illiteracy and It's Consequences. Innumeracy - the mathematical counterpart of illiteracy- is a disease that has ravaged our technological society.

4.  A Drunkards Walk - Leonard Mlodinow

How Randomness Rules Our Lives. 

5. Predictably Irrational - Dan Ariely

Challenging assumptions about making decisions based on rational thought. No amount of education can reliably prevent us from making mistakes. We can be, because of our biases, the easiest person for us to fool. 

A healthy dose of skepticism is necessary when looking at information. Be it the modern day media to science to technology, we all must have the ability to separate the truth from everything else. Our bias is our biggest enemy. We will prefer certain truths over others. 

Wax On Wax Off

It is assumed, in science, that a true genius comes along once and a while. All of the people in between are just stewards of the collective knowledge given to us by the geniuses. They teach the new generation about the work. As Richard Feynman pointed out in Cargo Cult Science. "That is the idea that we all hope you have learned in studying science in school—we never explicitly say what this is, but just hope that you catch on by all the examples of scientific investigation." In the process of learning the thing that was discovered long ago we hope to learn how to think as well. 

What is "what this is"? It is not the fruits of the labor that matter most in science. It is the scientific method that we learn, teach and practice (as scientists) that matters. The journals Cell, Science and Nature all insist that the fruits of the labor defines the level of genius of the scientist. They do not seem to value the labor of thought, experimental design, execution and proper conclusions as much. This leads to the individual scientists focusing on their narrative more than their methodology. 

The Cargo Cult Scientist believes that the method is what matters. The scientific politician focuses on the fruit. Think of it like Ginkgo Bioworks laboratory produced meat. Technologists can produce meat-like substances. They cannot produce the biologically produced meat that evolved over billions of years. Would you prefer cutting into a steak or scooping up the pooding produced by a biotech company?

Think of that disgusting meat the same as the miracle molecules we put into peoples bodies. We find individual proteins the are part of a complex system. We manufacture them because that is within the complicated paradigm of our understanding. Then we take the final product and use it in our simple understanding.

Indeed Ginkgo Bioworks seeks to replace your companies research team. BIOLOGY BY DESIGN! I suppose, unlike nature, Ginkgo will design biology to do what you want it to do. The problem is in the understanding of the scientific method. We don't design biology. We seek to understand it. 

As always, we return to the problem of Simple-Complicated-Complex. Ginkgo Bioworks programs cells to "make everything from food to materials to therapeutics". Programming a cell is complicated. So the biotech or biopharma company hires Ginkgo rather than hiring a research staff. They get the cell line they want. They have the product that comes from a bio-engineered cell. Now what? 

I ran into this problem at every biotech company. One example was producing a library of peptides that could be screened to find that one magical peptide that would deliver RNA to specific cell targets. RNA interference won two scientists the Nobel Prize in 2006. It was all the rage in knocking out gene products in biotechnology. But it didn't work in most situations. Why? It was assumed that the laboratory staff were doing something wrong. When this square peg couldn't be hammered through the round hole people began looking for a peptide or protein to deliver the RNA to the cell target. The narrative was in place. The project failed. We were all let go. The project was turned over to a prestigious professor at a European University. He too produced nothing to support the narrative. The narrative was simply changed. The science was working! Occasional reports were put out via company press releases that the scientist was making progress.

The project was most likely doomed from the start. Yet if, in an alternative universe, we had been allowed to fail we could have learned. Had we been given years of exhaustive research we may have made some valuable discoveries in our failures. We would have advanced our knowledge in the process/methodology. Instead we all went on to the next attempt to maintain employment in biotechnology. Most of us failed to do so. 

The future of Ginkgo Bioworks is no different. They are pursuing the idea that understanding complicated biotechnologies will lead to the kind of discoveries that make science work. There is a disconnect there. Like Mr. Myagi in the Karate Kid taught, wax on, wax off. Why? It was a Hollywood creation based in dubious reality but the concept is real. In science, the method is the thing. Learn how to conduct research and the results will teach you new things. Unfortunately, in business, there is not enough time to wax on and wax off until the time comes to apply the knowledge. People in offices who mostly attend meetings need data. They need charts and claims of near future riches. Ginkgo promises you they can help. In time you will end up with a few fish but no understanding of how to fish. 

When You Have to Succeed

 Ginkgo Bioworks will help you succeed. They have a stake in your success. So much so that you will have to pay them in perpetuity if you get a drug approved. Not so much if you hire a staff of scientists to be your R&D.

I was somewhat to surprised to see a drug that came from a biotechnology company I worked for, being advertised during a streaming sports event. I did not know what they named the drug but I could tell they were selling the narrative my former employers had developed from day one. I looked it up and there it was. The one and only drug ever approved from an employer of mine in my 13 years in biotechnology.

The technology was standard stuff. Make an antibody against a target protein. Sort through the B-cells and make a list. Test the antibodies on the list, pick one, viola.

After our first project failed to get past a milestone with a big pharma partner we were in trouble. We had to move on to the next drug in the pipeline fast. We revived an abandoned project... long story short... I saw the drug on a commercial while watching UFC fights.

What happened to the guy who cloned the antibodies and sorted through them? He has been out of the business for many years. I haven't talked to him but I see from LinkedIn a curious lack of progress in his career. 

What would the difference have been had Ginkgo Bioworks done the work of finding the antibody that became the drug? Firstly there would be a considerable ongoing cost. My co-worker has long since cost anyone in biopharma a dime. Secondly, Ginkgo would have had to learn a new skill. The system of cloning and manufacturing came from a specialized yeast system. So specialized was this system, it had not been done before. The standard CHO cell system was, in the narrative of the company, subpar. They had a better system. Yeast! They had the same expression and yield results. The truth was that they expressed about 1/10th the antibodies of the standard CHO cell system and the yeast extract needed created a nightmare for downstream process development. 

The problems that came with using yeast cells were not insurmountable. They had to be handled however by far superior minds at contract manufacturing organizations (CMO's). The antibody selection was simple. The laboratory work was complicated. The manufacturing issues became simple to complicated thanks to the experience of the CMO options. 

Ginkgo Bioworks did not exist at the time my former employer could have considered them as a partner. We went with a company that had many decades of experience developing manufacturing methods that resulted in drugs that could be sold. 

Ginkgo is attempting to be your laboratory professionals. Sit in your cubicle/office and make decisions based on your needs for success. Like Donald Trump, who worked as a biotech CEO in developing the Covid vaccine, you lay out the plan. Vaccine, now, go! But the people who work in the labs have to actually produce something. It could be Ginkgo or it could be the people you hire and dress in white lab coats. Either way, you tell them your narrative and they provide you with the data you need or they go away. Even when they have succeeded, they go away. 

The difference with Ginkgo Bioworks? You have to keep paying them as long as the drug makes money. My ex co-worker and all of the people who developed the drug advertised on the UFC stream... gone. 

Ginkgo Bioworks

 

Ginkgo Bioworks, Biology by Design

We begin with the very first statement on the Ginkgo Bioworks website. THEY design biology. Something goes wrong in a biological system? They, like auto mechanics, fix what went wrong. 

Once again, The Cynefin method of thinking leads us to the fundamental flaw. 

Simple, Complicated and Complex.

Biology is complex. Biotechnology is complicated. Some laboratory techniques are kind of simple.

Biology is the most advanced manufacturing technology on the planet. We program cells to make everything from food to materials to therapeutics.

There it is. Biology is not a manufacturing technology. It is a branch of science. We must return to our basic understanding of how we perceive the world. 

Science is a system of knowledge. It is concerned with the physical world and its phenomena. It entails unbiased observations and systematic experimentation. In general, a science involves a pursuit of knowledge covering general truths or the operations of fundamental laws.

Science can be divided into different branches. The physical sciences study the inorganic world and comprise the fields of astronomy, physics, chemistry, and the Earth sciences. The biological sciences such as biology and medicine study the organic world of life and its processes. Social sciences like anthropology and economics study the social and cultural aspects of human behavior.

Science is a system of knowledge. We have to apply our version of The Scientific Method in order to advance our knowledge. We used to think the Four Humors regulated our health. We have changed our minds on that one. We have added more and more understanding to the point where we know what we are made of and to a small degree, how it happens. DNA codes for chains of amino acids that form proteins. The proteins do the work.

What then makes Ginkgo Bioworks different among the herd of biotechnologies? They offer a variety of services and technologies. Each is there to help the customer speed through their research without the need to establish their own laboratories. Let's look at one offering.

Whether you’re looking to discover and synthesize a novel functional protein, optimize your protein production, or enhance processes to scale up your protein manufacturing, Ginkgo’s best-in-class capabilities empower your protein R&D.

Is Ginkgo a manufacturing organization? Do they have decades of experience successfully developing and executing upstream and downstream manufacturing processes? 

No matter what you want to do, Ginkgo claims they can do it all. Fermentation, strain optimization, scale up your manufacturing processes... they got you covered.

How does this compare to the CCS concept of The Empowered Laboratory? Ginkgo will help you develop the shape of your molecules. They will help you make them and manufacture them. The Empowered Laboratory work force will challenge your assumptions. They will test your theory. They will employ unbiased observations and systematic experimentation.

To be fair and honest, Ginkgo is real. It exists and has put its money where its mouth is. They make their claims and they invite you to use their services. On the downside, they are in business to make money. They do not care if your drug stands a chance. They are taking your money to do what you want done. While your success is their success, they have also taken the low road of shielding themselves from the standard biotechnology pitfalls of research. Some things just don't pan out. Ginkgo will take that journey with you but it is you who ultimately stands alone at the end of the wrong path. Ginkgo simply cashes your checks and goes back to their business.

George F. Merck famously said: "We try to remember that medicine is for the patient. We try never to forget that medicine is for the people. It is not for the profits. The profits follow, and if we have remembered that, they have never failed to appear. The better we have remembered it, the larger they have been."

I don't make the claim that Ginkgo Bioworks doesn't care about the medicine or the patient. I will admit that they are indeed about the technology. They are certainly better at many aspects of biotechnology than most new companies. A new company, or a new group within an established company, has to develop. Ginkgo will put you ahead of the curve in getting started. Ginkgo is there to help you advance your technology, not your science. 

If you think of science as the unbiased observations and systematic experimentation employed in the pursuit of knowledge covering general truths or the operations of fundamental laws... Ginkgo Bioworks is not concerned. Science would be up to the customer of Ginkgo. Once you, the customer, has got your science right the profits will come. Ginkgo will assist you in maximizing your profits by helping you design the physical biological products you seek. 

What is missing? Science. We do not design biology, we study biology. With our current understanding we can attempt to make interventions that disrupt the path our biology has put us on. If we have cancer, we can attempt to stop the cells from dividing out of control. If we have protein imbalances that cause disease, we can make antibodies to fight excessive protein concentrations. But what we are fighting is not well understood. By employing the scientific method, we can get to a greater understanding. We can see how our behaviors involving diet and exercise effect our health. 

As the pharmaceutical industry strays further and further away from science and focuses more and more on single protein interventions (biopharmaceuticals) we can expect little value to come from them. 

So they've arranged to imitate things like runways, to put fires along the sides of the runways, to make a wooden hut for a man to sit in, with two wooden pieces on his head like headphones and bars of bamboo sticking out like antennas—he's the controller—and they wait for the airplanes to land. They're doing everything right. The form is perfect. It looks exactly the way it looked before. But it doesn't work. No airplanes land. So I call these things cargo cult science, because they follow all the apparent precepts and forms of scientific investigation, but they're missing something essential, because the planes don't land.

Is Ginkgo Bioworks a Cargo Cult Biotech?

Biology By Design. Biology is the most advanced technology platform on the planet. We program cells to make everything from food to materials to therapeutics.  - Ginkgo Bioworks

The CEO of Ginkgo Bioworks, Jason Kelly, has a very clever introduction to biotechnology. He presents a slide with a picture of an Apple computer, an iPhone, a camera, and a metal watch on a gray desk decorated with a potted plant back lit with a lamp. "What's the most complicated device on this table?" he asks. His answer is the plant. He is incorrect. 

Here at the Cargo Cult Scientist, we have covered this logical error.

https://www.mindtools.com/atddimk/the-cynefin-framework

The Cynefin method of thinking describes simple, complicated and complex systems. The process of creating a slide presentation is simple. The iPhone is complicated. The plant is complex. 

The technology products are complicated. The plant is not a complicated device. It is a complex living organism. 

In this article from MIT Technology Review by Anthony Regelado, the author points out a an inconvenient truth. "Given Kelly’s spiel, it is surprising that 13 years after it was founded, Ginkgo can’t name a single significant product that is manufactured and sold using its organisms."

It is the Cargo Cult looking to the skies for that magical cargo. It has not yet arrived.

The ceremonial practices of the biotech cargo cults are studied here at the CCS. We must look at the science and then back at the ceremonies of the biotech executives. There are plenty of real science and technology concepts employed at Ginkgo. As is true with all bullshit, the truth is a valuable tool. The difference between real science and cargo cult science however is in how the truth is employed. Is the truth employed in generating new scientific avenues and technologies? Is the truth used to convince people of things that aren't so? 

In my next post I will tackle just one claim from Ginkgo Bioworks. I will pick it randomly and discuss the issues from the perspective of the empowered laboratory workforce. I am not Bill Gates or Cathy Wood sitting in an office receiving a sales pitch. I am a guy who knows how to do the work. 

Desperate Things

 

“The mass of men lead lives of quiet desperation. What is called resignation is confirmed desperation. From the desperate city you go into the desperate country, and have to console yourself with the bravery of minks and muskrats. A stereotyped but unconscious despair is concealed even under what are called the games and amusements of mankind. There is no play in them, for this comes after work. But it is a characteristic of wisdom not to do desperate things..” - Henry David Thoreau

Is the modern day life science professional wise? Does s/he go to work each day with a purpose to discover new things or have they found employment that they desperately need? In my 13 year career in Biotechnology I was merely employed. During that time I learned many important things but they were learned on the periphery of my official work. 

Biotechnology is a wonderful thing. What most biotech employees do is not. They can employ the technology but does it result in scientific advancement? They turn on the machines, fill out the paperwork and go home as early as they can. Many of these employees are fully aware that their work is not science. 

Take, for example, an employee at Theranos. At the high point there were nearly 700 people working at Theranos. 2 (CEO and President) went to jail, 2 (laboratory technicians) were whistle blowers. In between were a whole lot of people engaged in "desperate things". 

Thought experiment: You have been working at Theranos for a few months. You are driving to work. The sun is coming up and it is going to be a beautiful day. But you are worried. You have to give a presentation soon and the results you need are just not coming in. You know what needs to go up on that PowerPoint slide. You have a meeting with your technicians. Will they have the data you need to please your superiors? 

The desired outcome IS the only instruction. Those above you have given you instructions on what they need from you. You have then given instructions to your group. They must now go into the laboratory and achieve the desired outcome. The problem is that they are using a machine designed by other people. The machine cannot achieve the desired outcome. They turn on the machine, inject the sample, and await the results. They show up to the meeting with the results. 

As you drive to work you imagine a genius has arrived at Theranos. He knows that the samples are not properly biochemically presented to the machine. He makes the adjustments that only a true biochemist can make.  The results come in easily. Eureka! The machine works! Anyone can now prepare the samples, inject them into the machine and get accurate results. With great pride and joy you will stroll into your presentation with results sure to please all in attendence. You acknowledge and thank your staff. You finish the presentation by laying the ground work for full bonuses and future promotions. 

But you are not the genius who can make everything work. Even worse, you are just smart enough to know that the project was doomed from the start. Why? Bad science. The finger prick sampling of blood introduces factors that destroy accurate testing. You know this. You know your technicians can't overcome this reality. You need the job however. You have kids, a mortgage, a new car. Everyone thinks you are a success. As you drive to work on a beautiful day, you are living a life of quiet desperation. You must throw your technicians under the bus. 

If you read Bad Blood you will remember the story of George Shultzs' grandson. He was a technician at Theranos who was not getting the desired results. His superiors were threatening him to get those results or else. He became a whistle blower by talking to a reporter at  the Wall Street Journal. His superiors, those who drove to work on beautiful days with worried minds, began to suspect the technician would spill the beans. He went to visit his grandfather only to find two Theranos attorneys awaiting his arrival in a room on the second floor. It was an ambush. He needed to sign the nondisclosure contract or face dire consequences. He bravely became a whistle blower rather then live a life of quiet desperation. 

This is of course the extreme. But most scientists face unpleasant consequences when the desired results are not forthcoming. True science will overcome this dilemma eventually. True science works and will provide the path to making things work. True science will only allow for it's proper application. This is known as technology. You can keep trying but only proper application produces useful predictable technology. You must use the scientific method. If not you must live a life of quiet desperation.