Is biology now in charge?

From the great Laura Deming:

One of my biggest personal fears is working in the wrong field to achieve the goal I care about. If you were around pre-1900s, and wanted to contribute to biology, you should have been a physicist (Robert Hooke, a physicist discovers the first cell, making a better microscope is a major driver of progress). In which field should you work to maximize progress in biology today?

…But something interesting happened around the 1950s. If you look at the most important techniques in biology, in the second half of the 1900s, they’re all driven by tools discovered in biology itself. Biologists aren’t just finding new things – they’re making their new tools from biological reagents. PCR (everything that drives PCR, apart from the heater/cooler which is 1600s thermodynamics, is either itself DNA or something made by DNA), DNA sequencing (sequencing by synthesis – we use cameras/electrical detection/CMOS chips as the output, but the hijacking the way the cell makes DNA proteins remains at the heart of the technique), cloning (we cut up DNA with proteins made from DNA, stick the DNA into bacteria so living organisms can make more copies of it for us), gene editing (CRISPR is obviously made from DNA and with RNA attached), ELISA (need the ability to detect fluorescence – optics – and process the signal, but antibodies lie at the heart of this principle), affinity chromatography (liquid chromatography arguably uses physical principles like steric hindrance, or charge, but those can be traced back to the 1800s – antibodies and cloning have revolutionized this technique), FACS uses the same charge principles that western blots do, but with the addition of antibodies…

Something special happens when a field becomes self-reinforcing. Previously, biology looked to physics and other disciplines for tools to break open new frontiers. But, empirically, since the 1950s, that has all changed.We don’t make mutant mice with x-rays and microscopes – we figure out the gene we want to go after, and we use high-precision biological tools to change it. Computer science has certainly played an important role in processing all of the information now streaming out of biological systems, but the major advances – the core things driving progress in biology forward – have come from biology itself. Biology is eating physics (and, some would jokingly suggest, based on the outperforming endurance of DNA compared to any modern hardware and plausibility of biological computation, possibly computation itself).

Naively, if we can expect n new discoveries / t tools we have, if the tools are static, maybe that’s a fixed number of discoveries per year. But if t tools increases, then we get more discoveries. What if it increases as a function of n?

This is important because it’s a self-reinforcing loop. The more things in biology we discover today, the faster we can discover things tomorrow. Biologists are the new engineers. But their tools look a lot different than any we’ve seen before. Sequencing is the microscope of tomorrow. And sequencing was built by biological tools.

The entire (short) essay is of interest.  Here is more on Laura Deming.

Comments

Apparently, biochemistry is not worth mentioning in her essay - literally.

Not only that, but CNTRL + F + "patents" gives no hits (I am guessing, not having read her article).

And this: "In which field should you work to maximize progress in biology today?" - easily answered: instrumentation. Did you know there's a Nobel caliber visualization technique of freezing a biological event at the near molecular level using "fluorescent" markers, and watching the chemical reaction? Imagine if they could perfect this so that you can see a cancerous cell and how/why it divides the way it does, why a cell dies (apoptosis), how a cell fights an infection (at the antibody level, not just macrophage level), and so on? You essentially solve all the big questions of biology. In other words: physics >> biology.

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you.

Yes, but kind of reverse. In the 1990s and 2000s a lot of departments renamed themselves from Chemistry to Chemistry and Chemical Biology to reflect the relationship between Chemistry and Biology. More Chemists were finding themselves doing mostly Biology. (I think).

Response to Clockwork.

"Biology is eating physics (and, some would jokingly suggest, based on the outperforming endurance of DNA compared to any modern hardware and the plausibility of biological computation, possibly computation itself). "

DNA for computation has never been anything but a gimmick. Do I need to take this person seriously?

You don't seem to appreciate that YOU are a "dna computer". Are you claiming that you are a gimmick? (as well as all of the math users of the world past, present, & future? not that computation is limited to systems which deal with abstract objects, an ant or an e. coli cell compute if "computation" is appropriately construed.

Wasn't the idea that the world was entering the Age of Biology the conclusion on the last page of Paul Johnson's "Modern Times" in 1983?

If that all impresses you, you should check out the advances in engineering that are coming from studying folded proteins that literally function as machines within the body.

It's a good sales pitch but a bit naive, perhaps egotistical. But, sales people is like that.

The funny thing is that you assist to any bio-***** congress, researchers are acknowledges in a sincere way the contributions from and collaborations with other fields of science.

Beyond the sales banality, the US is the powerhouse in genetics because private and public funding has been there to develop new ideas.

Along with the fact that so many Americans have no particular cultural reason to reject the sort of dedication to genetics which so marked a previous German government.

Of course genetics is not eugenics, except somehow, it just seems to ever so coincidentally end up that way in the eyes of many proponents of making the human race a much better race, one small step (or a few million - whatever) at a time.

Every grandparent out there has practiced eugenics.

You mean they killed and/or sterilized one or more of their children?

Do tell us more about your undoubtedly fascinating family history.

They practiced eugenics versus dysgenics. That is, they mated with individuals likely to pass on their genes successfully. That's why men like women with hourglass figures and women like men with broad shoulders. You might say reality itself is eugenic.

Are you a Creationist?

No, it's biotechnology applied to agriculture and medicine.

Germany has a complicated past with genetics. Russia has a ridicule one: Lysenko. And the rest of western Europe, I really don't know why they're allergic to modified organisms in agriculture.

'Germany has a complicated past with genetics'

Sadly, Germany has an extremely uncomplicated past regarding genetics - humans were placed into different groups, and those that did not meet the proper standards were killed. Just the same way you would do with animals, which is why Germany tends to have a problem in current times with that whole 'well, if we do that with animals, why not with humans?' framing.

"If you were around pre-1900s, and wanted to contribute to biology, you should have been a physicist": wot, like Darwin and Mendel?

"Biology is eating physics": what does she mean? If she means that scientific prestige is moving from physics to biology, that's right but it's been obvious for many decades. I dare say that even some physicists will admit to it. Surely physicists can't be as arrogant as they were when I was a fresher, a million years ago? ("Oh yes they can" shouts the cynic.)

Anyway, to the point: will economists' physics envy be replaced by bio envy?

Re: "Anyway, to the point: will economists' physics envy be replaced by bio envy?"

+1

"If she means that scientific prestige is moving from physics to biology, that's right but it's been obvious for many decades."

Very true. E.g. Caltech made a biologist its president for the first time in 1997, MIT in 2004. Deming however is trying to make a bigger claim than just prestige, but about the nature of scientific advances. I think she has somewhat of a point, but as the comments here have noted she is overclaiming.

Biology is eating Physics?

Hah! The smart money is worried about Biology eating Politics.

Biology will eat Ideology.

Unfortunately we cannot say the same about economics.

This essay is ripe for fisking but it's Friday morning and I have a conference to go to, so let's take a non-random sample.

"If you were around pre-1900s, and wanted to contribute to biology, you should have been a physicist (Robert Hooke, a physicist discovers the first cell, making a better microscope is a major driver of progress)."
Robert Hooke wasn't a physicist. There was no physics back in the 17th century except for the one we retroactively labeled as such. He was (like Newton) a "natural philosopher", which was an easy thing to be pre-silloization of science. The entire essay could in fact be read as glorification of silloization: biology is so far apart from other fields now that the only meaningful discoveries come from within: unlinke Newton and Hook, few are now able to interpret what's going on in other disciplines and apply it to their own. This is not a good thing.

"PCR (everything that drives PCR, apart from the heater/cooler which is 1600s thermodynamics, is either itself DNA or something made by DNA)"
No chemistry here, no Siree. Also: yes, this applies to crude qualtative PCR in a simple thermal block. Upgrading that to something like real-time PCR or even more sofisticated methods like nano-PCR has nothing to do with biology.

"/a list of methods including PCR, DNA sequencing, gene editing, ELISA, and FACS/"
Nothing but biology there, except for everything that Deming herself listed. NB: any advances in these methods (and the 32-color FACS of today, or the 90+ color CyTOF are a huge upgrade to what was there in let's say the 90s) have little to do with biology. This doesn't even consider improvements in computation enabling more sophisticated analysis of the raw data.

"Sequencing has become the new microscope."
Maybe. And sequencing as a concept is biology. But until there is a biological apparatus capable of human-readable sequencing, sequencing as a tool is entirely dependent on non-biological methods.

"These tools don’t just find new biology, they’re also being used to change it. Look to the market, where biology-driven therapeutics are coming out in droves."
This sounds like something a venture capitalist heavily invested in biotech would say, no? Only, as someone already mentioned, if you want your biologic drug to be made you don't need a biologist you need a biochemist. Then you need a clinician to give it to patients. Then a biologist comes in to explain why it did or didn't work. (I hope I don't have to explain that last sentence was a joke).

"Biologists are the new engineers."
Life sciences have engineering envy. I should know, I'm a physician-scientist in a pretty big laboratory/research hospital. I love what I do and have great respect for molecular biologists, immunologists, geneticists, etc. that I work with. But let's not get carried away here.

I had high hopes for this kind of biological engineering 20 or 30 years ago. It has been slow to arrive. Don't get me wrong, it will be neat when it does, but in the meantime Amazon is not promising mutant pelicans for product delivery.

Off topic, you can build something 5x faster than a Cray C90 to fit in a shoebox.

https://climbers.net/sbc/nanopi-fire3-arm-supercomputer/

Somewhat more mature.

Maybe it has arrived, but as the old joke goes it isn't evenly distributed. Monsanto can make a custom organism, but eBay is not yet full of bizarre small shop innovation.

Ridley Scott wanted Han Chinese doing genetic engineering in sidewalk bazaaes. He got Mexicans in taco trucks.

But with 280 characters.

“Han Chinese”. Are there any other kind?

Minor quibble - true, that "sequencing" has changed everything - but it is "engineering" that has made "sequencing" possible - Indeed, if one reads David Lee's book "Xrays to DNA" you realize that so much of what we take for granted (ideas, concepts) all came about BECAUSE of the "tools" that were developed by "engineers" ...!

What caused the cost curve of sequencing to fall by over 6 orders of magnitude? Was it biology? Or was it computation? Mostly computation.

Like everything else: it’s the computation, stupid.

I'd be interested about how this plays out across subdisciplines. The number of different fields within biology is so large now that borrowing within "biology" can still mean borrowing from wholly new literatures and ways of looking at things.

Question for any technical people here who know their stuff. The author states that "Computer science has certainly played an important role in processing all of the information now streaming out of biological systems, but the major advances – the core things driving progress in biology forward – have come from biology itself."

Informatics, machine learning/AI, modeling, big data, etc., is all the rage nowadays. Pharma, biotech, and medical device companies are implementing it too. Are these life science companies innovating in this area on their own or are they collaborating with computer scientists and IT people? Then who is a bio-information or bio-statistician?

There have been firms specializing in genetic computation since the 1990s. I had a friend who moved to one in New Haven, Connecticut around that time. By now I'm sure there are old and established firms and university departments.

Discipline boundaries are somewhat arbitrary. Bioinformatics certainly can be considered part of CS, and DNA sequencing would not be able to work without advances in processing power.

"One of my biggest personal fears is working in the wrong field to achieve the goal I care about. "

Sad commentary on the modern university; you can't work in an area unless you have a degree in it? What happened to teaching students to learn??

That said, I tend to agree that there hasn't been a major breakthrough in physics or "technology" for a long time.

You mean like a gravity wave detector or a new particle? Or perhaps you mean an interstellar asteroid or a blue LED or atomic tweezers or ... OTOH, if by "major breakthrough" you mean something that forces us to revise the Laws of Physics, then well, while the Standard Models (both Cosmological and of Fundamental Forces) haven't had "major" tweaks in a long time, there has been progress in defining (limiting) them. (or possibly more accurately: in confining the parameter space for them (or their progeny).

I believe she is talking about technology. If she and other nitwits understood technology they wouldn't waste their time on electric cars and such.

NSF funding by agency from the 40s until recently confirms Deming's main point. Funding for the physical sciences dominated the life sciences beginning with the Manhattan Project during WWII until the late 50s or early 60s. Since then funding for the life sciences has taken off.

But funding dominance isn't the same as intellectual or philosophical dominance. My opinion is that physics still retains its foundational importance over biology as one of the core sciences.

Source: National Science Foundation, National Center for Science and Engineering Statistics, Survey of Federal Funds for Research and Development. DHT07_v66 TABLE 7. Federal obligations for research and development, by agency: FYs 1967–2017. Funding information for earlier years requires accessing the NSFs online archives.

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