Spoilers

So I've been trying to figure out what to do for my final learning diary presentation. The blog itself came out naturally, because ranting about 19th-century chemists is easier than pretending to be structured. But now the professor wants a synthesis. A clean, structured narrative. From me.
Which then made me realise that, if this course taught me anything, it’s that science is not clean and coherent. It is messy, political, and often disproportionately powered by people who refused to wash their hands.
So here I am, trying to brainstorm and reduce several hundred years of microbiology, plus my own lab trauma, into 8–10 neat slides.

Idea 1: Theory vs Observation
This whole course is just the same debate of Descartes vs Hume playing out across centuries in increasingly dramatic ways.
Bassi in the barn? Pure Humean pragmatism.
Semmelweis? Also Hume.
Liebig? Very Descartes.
Pasteur? Somewhere in the middle, but leaning towards Hume when the yeast started yelling at him.
This could be the backbone of the ppt. But also, am I overphilosophising? (Probably)

Idea 2: Crosslinks (My blog title is unmatched)
The best part of this course was noticing how many breakthroughs happened when people crossed boundaries:
a farmer (Bassi) doing microbiology
a Hungarian obstetrician (Semmelweis) paving the way for epidemiology 
a chemist (Pasteur) barging into biology

Science moves forward when people stop staying in their disciplinary lane. Ahmedabad University would be pleased.
A bit like how I myself connect my lab's cytoskeleton background from infectious disease to now evolutionary development, which is why I got into biology in the first place and what I hope to pursue.
It also fits my personality unfortunately well.

Idea 3: Messiness
Honestly, my favourite realisation was just how chaotic science has always been.
We love to pretend that:
experiment -> data --> theory--> Nobel Prize
When it’s more like:
ego --> confusion --> anger --> wine --> accidental discovery --> fighting in journals --> eventual acceptance.

An elaborate 5 stages of grief that anyone who’s worked in a lab can attest to. 

The tree of life? A mess.
Fermentation? A mess.
Understanding contagion? A long, complicated, tragic mess.
My experiments? Also a mess.
Maybe the ppt should celebrate this.

Idea 4: The Quote That Won’t Leave My Mind
Two years ago, my internship supervisor told me:
“Know the difference between being a scientist and a technician.”
Back then I understood the weight of her words but I don’t think I fully grasped the meaning behind it. 
Meanwhile, my dad (also a professor, God help me) had been giving a 45-minute expanded version of that same sentence at literally every lunch table for years.
But I only internalised it when an unrelated respected academic said it just once but crisply. 
Now, after Bassi, Semmelweis, Pasteur, it lands.

A technician follows instructions.
A scientist questions the framework.
A technician wants predictable outcomes.
A scientist expects the mess.
Suddenly all the stubborn historical men I wrote about make sense.
They weren’t technicians. They were scientists. Sometimes even a bit insufferable, but scientists.
This quote (but not my dad’s extended edition) could be my opening or ending for the ppt

Now what?

So, right now, we’ve got:
Science lives in the tension between theory and observation,
and the people who move it forward are always the ones willing to cross boundaries through the mess.
Every single blog entry fits under this umbrella.
Bassi’s observation over theory + pragmatism
Semmelweis’ data rejected because of ego
Pasteur vs Liebig’s disciplinary clash
And me trying to find a small place in this huge, messy and intimidating field of research. 
And all of that loops back to that quote from my internship supervisor and the extended release version of my dad’s. 
 History has a way of correcting and reinforcing. 

(Professor, if I do continue the blog even after the course ends, I hope you won’t mind me not properly introducing those I talk about anymore despite that being your biggest and very crucial earlier critiques) 

Descartes vs Hume (Science vs Pragmatism)

Agostino Bassi (1773–1856) is not a name that sparks the same level of recognition as Pasteur or Koch, but perhaps it should. He spent 25 years studying a mysterious disease killing silkworms called muscardine, and eventually proved it was caused by a fungus. Not miasma, not divine intervention or humoral imbalances, but a microorganism. He then actually told people what to do about it. Disinfect tools, isolate the infected, clean the damn workspace. All this, years before the Germ Theory was even established.

And he did this in a barn, not a lab or hospital.

Farmers, very sensibly, adopted his protocol almost immediately. They didn’t care about the metaphysical justification of germs.  All farmers cared for was:
Does it save my silkworms? Does it save my money? Then I’ll do it.

But medicine, the field we like to imagine as supremely logical and empirically driven, did not adopt these ideas for decades. Not because the evidence was weak, but because Bassi was telling people to disinfect before surgeons admitted (or accepted) that maybe their unwashed hands were killing patients.

And this is where I suddenly remembered why 20-year-old me used to get irrationally angry at 9:30 in the morning in class, heavily sleep-deprived, while arguing about Descartes vs Hume.

Descartes: Reason first. Concepts first. Logic your way to prove it.
Hume: No. Experience first. Observation first. World tells you what is true. 

We like to pretend science is purely Humean: observe --> test --> accept.
But historically? Science is often as stubborn as certain chemists I've ranted about before.

Farmers without philosophical allegiance simply asked:

Did cleaning work?

Yes?

Okay, we clean.

No debate. No 100-page justification.
Just results matter.

But science has to balance the two:

- Too much rationalism: you reject reality because it’s inconvenient.

- Too much empiricism: you collect facts with no framework to connect them.

Theory must guide observation, but observation should be allowed to correct theory.

Bassi had a pragmatic mentality toward infectious diseases. Science advances when someone is willing to say, “Okay, let’s look again, without wishing it were true.” And that was what many doctors at the time were lacking. Pragmatism has no ego.

(Professor, had this class existed before I took that philosophy course 2 years ago, I would've been unbeatable)

Stubborn Chemists Part II

 After thinking about Semmelweis and Liebig, I couldn’t stop myself from falling down the Pasteur rabbit hole. Pasteur hasn’t even been discussed in class yet, but since I’m presenting on him soon, I got curious and, naturally, got distracted by historical drama.

Louis Pasteur (1822–1895), a French chemist and microbiologist, was in a long-running feud with none other than Justus von Liebig (1803–1873). Remember Liebig? The same organic chemistry giant who also had a feud with Semmelweis because he treated infection as nothing more than decomposing organic matter? He also had very strong opinions about fermentation. He claimed sugar breaks down on its own into alcohol, with no living organisms involved. A kind of decomposition, but for organic matter.

Pasteur, on the other hand, insisted that fermentation was a biological process driven by yeast and not spontaneous chemical decomposition.

Their rivalry stemmed from a difference in perspective.  As we saw earlier, Liebig prioritised theory first, followed by observation. It seemed like he was only looking for observations that fit his theoretical framework, which inherently made him biased. Pasteur, meanwhile, was a chemist who blurred the lines between chemistry and biology. That willingness to cross boundaries and seriousness in considering the little globules under the microscope as alive is what made his discoveries revolutionary. Just like Semmelweis and his observation on handwashing, observing carefully and trusting the evidence, even when it contradicts established theory, can save lives  or, in Pasteur’s case, save wine (and also humans from germs).

What I like about Pasteur is that he worked in the messy overlap between chemistry and biology. Fermentation was neither fully chemical nor fully biological, so no one wanted to take a chance with it. And he was fierce. But he wasn’t exactly a people-person. He was considered, to put it mildly, difficult-  extremely competitive, stubborn, and a bit dismissive of critics, but I guess if you casually come up with the vaccine to anthrax and rabies, discover fermentation, pasteurisation and a bit of stereochemistry, then I think it's okay to be a bit mean sometimes.

And not to mention, he was very nationalistic. Pasteur often framed his work as a triumph of French science over German science, which added another layer to his rivalry with Liebig. I mean, saving France from spoiled wine is probably peak French nationalism, so it makes sense.

(Professor, yes, I like historic feuds.)

Stubborn Chemists

In yesterday's class, we read a context paper by. H O Lancaster (surprisingly, a mathematician in the 90s writing about a physician) on about Ignaz Semmelweis, and honestly, it was a bit frustrating. In the mid-1800s, Semmelweis, a Hungarian doctor, observing maternity clinics, noticed that mortality among women attended by physicians was much higher than among those attended by midwives. He figured that cadaverous particles from autopsies left over in the physicians' hands were the culprit. 

His solution? Wash your hands with chlorine and lime after touching a corpse before delivering a baby. Revolutionary.

What I found interesting, though, is that the chemistry community of the time, including someone like Justus von Liebig (a giant in organic chemistry), had a simple theory about organic matter and disease. Contagion was not a thing, and all infection was just chemical degradation. No biological mechanisms, just chemical explanations with neat formulas and reasoning. Semmelweis actually accepted Liebig’s view that infection was caused by decomposing organic matter. Disinfecting with chlorine worked because it destroyed those “Liebigian particles.” So he stood in the middle ground of not fully miasma, and not yet contagion. However, despite the evidence, his peers resisted. Not because his logic was flawed, but because admitting he was right meant doctors themselves were killing patients.

This reminded me (although in hindsight I admit it's kind of a tangent and not exactly analogous) of some modern chemistry debates. James Tour, a well-respected synthetic organic chemist, denies abiogenesis, that biomolecules emerged from non-living matter. From a certain perspective, it makes sense. He’s looking at the chemical framework he knows and trusts. He sees the complexity of organic molecules and the difficulty and just statistical improbability (something I logically very, very, very, very strongly disagree with, but maybe another time) of assembling them in a lab and concludes that it is not possible. Just like Liebig, the focus is on theory and known chemical rules.

Semmelweis’s story reminds me that observation can, and often does, outweigh theory. He didn’t need to fully understand the chemistry behind “cadaverous particles.” He saw the correlation, tested a solution, and saved lives. Whether he relied solely on correlation and not causation is another topic for debate. Tour, on the other hand, is trapped in the reverse. Theory comes first, and observation is secondary. Maybe one day experiments in prebiotic chemistry and synthetic biology will one day do for today's theories what handwashing did for Semmelweis.

We take the “obvious” for granted, I think. Washing hands now feels like the most basic thing ever, yet it was revolutionary. Denying life from non-living matter might feel rational from one lens (to a minority, but a very vocal and adamant minority), but maybe we will look back and think, “How did anyone actually doubt this?” History has a funny way of humbling us.

 It also makes me think about how I approach my own experiments. Am I looking for results, or am I too caught up in what should happen?

Or maybe that's just a coping mechanism for all my failed experiments.

(Professor, I realised after writing this that the whole James Tour thing isn't a great analogy. I think I just needed to rant because his views on this topic are (I'll be nice)... rather misplaced.)

The Flying Dutchman

 First off, let me acknowledge Leeuwenhoek. He opened up a whole new world with his lenses and, more importantly, rose up the ranks despite his social standing (a pov that I had never heard about and that should be focused more on instead of just giving him the one-dimensional title of the "father of microbiology"). His story shows remarkable perseverance, resourcefulness, and a rawness that makes you empathise with him. 

That being said, from here on, I will not fix any typos in his name because Dutch is a ridiculous language, and I'm done with this.

What really grabbed me, though, wasn’t Leeuwonhoek's letters but Nick Lane’s reflection on how we eventually tried to organise all those “little animals.” The passage about Stanier and van Niel seeing bacteria as indivisible functional units, and then Woese coming in with ribosomal RNA to redraw the entire tree of life, only for us to later realise the “tree” was kind of a misleading reductionist fantasy, for some reason, blew my mind.

It’s so interesting that microbiology swung from “we’ll never figure out phylogeny” to “here’s a definitive tree” to “actually, it’s a tangled mess cuz of lateral gene transfer and endosymbiosis.” The "unity of biochemistry" both explains and makes the tree of life more complicated. The fact that eukaryotes are literally genomic chimaeras, stitched together from archaeal and bacterial lineages, makes the whole idea of a neat branching diagram feel a bit old-fashioned. Evolution is messy and opportunistic, not a neat little diagram, which is probably why I've always loved it.

(Professor, I promise I do actually have more reasons to go to the Netherlands and not just to meet my boyfriend. Great country)

Fracastoro's pilot germ theory

 Long before microscopes or an idea of tiny microbes, Fracastoro in the 1500s suggested that diseases might spread through invisible “seeds of contagion.” In a world still blaming bad air, divine punishment, or planetary alignment, which was an idea that cut sharply against the grain.

What strikes me is how bold it was. Fracastoro had only logic and observation to lean on, but no real way to prove it, yet he was willing to stake his reputation on a theory most people probably found absurd and borderline sacrilegious. It seems obvious now, even conceptually, but at the time, it was a radical shift. The seed of germ theory was planted centuries before the word “germ” even existed.

As brilliant and surprising as it was, it was also premature. Without experimental proof, his theory was left to gather dust until Pasteur and Koch brought the evidence to light centuries later. It's pretty mind-boggling how early these ideas took root, and the fact that they're even remembered, and we get to study them. Like Mendel and Leeuwenhoek, ideas gather dust but are then rediscovered, which is pretty hopeful.

Pretty interesting reading, although I think I got way too carried away when I went down a rabbit hole on miasma and ended up learning about Aristotle, Plato, and Galen's ideas, not necessarily even related to disease. I've taken 6 bio courses this semester with no philosophy/history course on the side for the first time, so I guess I got too excited when these names came up.

(Professor, I hope you’ll consider my philosophical detour as extra credit instead of academic procrastination.)

Better late than never

  Aaaand I’m already late with this blog. PhD applications ate up my time, and honestly, I wasn’t really sure how to even start writing something like this. Diaries, essays, awful poetry, sure, but this is intellectual diary-writing without any swearing, so a bit tricky. But maybe that’s already a crosslink to this class- science is never neat, and neither is the process of putting your thoughts on paper. Leeuwenhoek’s letters weren’t polished journal articles either. They were more like messy updates he hoped someone would take seriously. I think we would've been friends.

What I like about this course is that we get to read science in its raw form. No glossy figures or endless methods sections. Just a person trying to describe what they saw and why it matters. That feels close to what I do in the lab every day- try something, scribble it down, try to convince myself (and my PI) that it’s real. Plus, I really wanted to take a good history of science course like I have been for the past 2 semesters and this was perfect.

Also, “Crosslinks.” The name comes from cytoskeleton proteins (my master's thesis work), but also from the connections I want to make between old discoveries and my own work. Like Leeuwenhoek peering at “animalcules,” and me staring at glowing cytoskeletal filaments. Different centuries, same feeling of euphoria.

If this diary works, it’ll be part science reflection, part personal rant (probably 60%), part history lesson. Basically, a messy weave of ideas like actin filaments tied together.

Takeaway: Being late doesn’t matter as much as showing up honestly, which is also how most of these discoveries were made.

(This is just a plea to my professor to not penalise me for being late. Think of it as me staying authentic to the spirit of 17th-century scientific correspondence.🙏)