Diary Page One#
Okay, I know you are very curious about who I am.
I am a descendant of the DH5α strain under the genus E. coli, which is somewhat equivalent to a family with a special mission among you humans. That's right, I am not a human; I am a tiny bacterium that you humans can only see through a microscope: just look at the smallest millimeter scale on your ruler, I am nearly a thousand times longer than that! But I don't think I am an ordinary bacterium—I mean intellectually, even though our family has indeed played an important role in your biological development—so I decided to document my life and introduce you to the world from the perspective of microorganisms.
I am an E. coli, and I won't disclose my height and weight, but no one has ever measured me specifically, and I don't have much of an idea myself. According to estimates by your human experts, my kind is usually a few micrometers long. Micrometers, you know? That's one-thousandth of a millimeter. Within our vast group of E. coli, there are various strains, such as the BL21 family, which is often used to express fluorescent proteins. Their special ability is that they can easily emit fluorescence when they have the fluorescent protein gene inside; whereas our family's special ability is to quickly replicate something called a plasmid inside. We have a love-hate relationship with plasmids: on one hand, when we have plasmids, we can gain superpowers to resist many harmful substances (like the antibiotics you humans take to treat bacterial diseases, which we absolutely despise), but the process of plasmids entering our bodies is quite painful for us. It is said that many of my ancestors died in laboratories because of this... sigh, let's not talk about that; there are also many strains like O157 that can make you sick with diarrhea. In short, we are everywhere, so you better wash your hands diligently to avoid accidentally ingesting our pathogenic relatives.
Speaking of my family, sigh, from the moment I opened my eyes, I knew I would probably be a poor little one without a father. I was cloned from my mother, who was cloned from her mother (my grandmother), so aside from age, we are all exactly the same, except for my great-great-great-grandmother—she is said to have mutated and was kept by humans as a rare treasure because she had unique characteristics. And because our matriarchal society reproduces through cloning, I have no father. But I have accepted this gladly; after all, I don't need a father to teach me how to live. Our pursuit is very simple: to keep producing offspring until we are too old or the environment is unsuitable for survival, at which point we stop asexual reproduction to prevent our group from going extinct. I initially accepted this setup, but over time I found it very boring. The most common topic of discussion among my family members is how to give birth to a perfect child like themselves and how to maintain their replicative enzymes (without replicative enzymes, our genetic material DNA cannot double, which would prevent us from having offspring). It is precisely because I am a unique and thoughtful bacterium that I plan to travel and see this vast world.
Here begins my travel diary.
Chapter One: The Food Heist#
As a heterotrophic bacterium, my mother, sister, grandmother, and great-grandmother expressed strong opposition to my desire to explore. After all, we cannot produce nutrients through photosynthesis like the blue bacteria of the green oxygen kingdom, and we have very little food stored. I understand their concern for me, but I still want to go out and see the world at all costs.
So, I shook my head resolutely, waving my flagella, and gradually drifted away...
Life on the road is full of challenges. For example, today, another vagabond and I both spotted a small piece of glucose by the roadside. She claimed she saw it first, but I didn't want to give up the food I had worked so hard to find.
"You are..." she sneered, "from the DH5α family?"
"How do you know?" I shot her a glare; right now, I didn't care about anything other than food.
She suddenly leaned closer and said, "I've seen your family of bacteria, you know? Haha, all your family’s bacteria are disabled! They accept plasmids from wherever, how pathetic."
"Shut up!" Although I admit our family has such characteristics, I don't think we are that pathetic. "We are sacrificing ourselves for the cause of science! We are helping humans produce and select the plasmids they create. What about you? What strain are you from?"
"Heh, not very old but quite temperamental," she laughed disdainfully. "What do I care who you are? Anyway, I’m claiming this piece of glucose!" With that, she waved her flagella and quickly ran toward the piece of food emitting an enticing aroma.
I gritted my teeth and charged after her: "Why should I give it to you?" But it was too late; she had already picked up the prey and was admiring it closely. Hmph, if I can't provoke her, can I not avoid her? I turned to leave, but the bacterium that stole my lunch said leisurely, "Tsk~ I didn't say you couldn't eat. Since we are both E. coli, I'll share a bit with you." Although the capable should not receive food without effort, in the midst of wandering, life is still the priority. I quickly grabbed this hard-earned piece of sugar and ate it, but found it hard to swallow; it wasn't the taste of home... I suddenly began to miss the warm home: where it is always warm and humid, with endless glucose and beef extract peptone, and caring aunties. But I have already forgotten the way back home... Tears immediately welled up in my eyes; it was the first time I cried so freely and without restraint after leaving home for so long.
"What's wrong, crying so hard? Don't tell me your PTS system is malfunctioning," the rude vagabond was actually startled by my sadness. "I don't know... Wuwu, I don't know, I just... miss home... maybe it's wuwu, I feel... so bad... Wuwahwawuwu," I was already incoherent.
"Really." The vagabond seemed speechless and just waited for me to finish crying. "Hurry up and eat, or I'll eat it for you." I quickly activated my PTS transport system and absorbed the glucose into my body. "Really, you look like a kid who just ran away from home, so immature." The vagabond scoffed, "Kid, why not join me in the world? I feel sorry for you; I can still give you a meal later." She suddenly said somewhat sadly, "No wonder, why leave home to cause trouble? Now, you want to survive, you have to fend for yourself."
Actually, I didn't like her much, but as a bacterium with no support, it was better to find a companion. So I reluctantly agreed. "Hey, what's your name? You can't not tell me your name, right?" I asked.
"Then, you can call me Sister Bo from now on."
Chapter Two: I Got Infected!#
Thus, I began my wandering life following Sister Bo.
Actually, Sister Bo is not a bad person; she just speaks a bit harshly. Having been alone in society for so long, she knows things that I cannot reach, so I often ask her silly questions.
"Sister Bo, what exactly is our PTS system?" Actually, I only knew that we have such a system in our bodies; at home, everyone says, "Quickly activate your PTS system to receive today's nutrients!" So I vaguely understood that this is probably our system for absorbing food. However, those who see this shouldn't laugh at me; do you know what your digestive system consists of and how it works? So, study biology well, young one.
Sister Bo smiled: "Hey, it's rare to see you ask such a high-level question." She pointed to my mouth, "See that hole there? Hahaha, don't think we just put food in and forget about it; actually, there's a lot of knowledge inside."
"PTS stands for glucose transport system, which is an enzyme system specifically for transporting glucose into your body. Enzymes are made of proteins, and these proteins can act like catalysts, helping you quickly swallow glucose. Moreover, there's a strange thing: we eat glucose, but when it's transported into the body, it adds a phosphate group, turning into glucose-6-phosphate. However, I don't quite understand the mystery behind this; it seems humans care a lot about it. Generally, high school students learn about how substances cross cell membranes, including simple diffusion, facilitated diffusion, and active transport, but our PTS system's transport method is not included in any of these three, so if they study biology in college, they will learn about this transport method called 'group translocation,' but even they don't really understand it."
"Um... it feels complicated." I pondered for a moment, feeling that it was okay not to understand such advanced knowledge, so I didn't dwell on it.
During the days of wandering with her, we often bickered about food. Indeed, she could use her experience to know where food might exist; as long as it was near starch or cellulose, she would take me around, instead of just running to where there are many bacteria to compete for food like I did. However, during this time, we also passed through some very suitable places to live, but Sister Bo always said, "I don't want to stay in a greenhouse and lose my freedom, becoming a sacrifice under human control." And I, influenced by her, also didn't want to return to such a domesticated place. I left home precisely because I longed to explore the world, right? So usually, we would have a baby there and then leave, allowing my child to live comfortably, and I wouldn't feel guilty toward her.
On the journey, I gradually discovered that Sister Bo knows a lot, perhaps even too much for a bacterium. However, Sister Bo always kept her origins a mystery, and I didn't dare to ask further.
Speaking of which, yesterday, after asking Sister Bo about the PTS system, we continued on, searching for food and resting places. Passing by a "refugee area" (actually a culture medium discarded by you humans), Sister Bo suddenly frowned: "Not good, this place is not suitable for long stays." "Why? It doesn't look much different from the refugee areas we usually see," I said. "No, take a closer look; their bodies are more swollen than ordinary bacteria." When Sister Bo said this, I realized it was true: those lazy bacteria leaning against the roadside or lying in the corners indeed seemed to have something inside them. Just as I was about to approach and ask them, Sister Bo suddenly pulled me back. Just as I was wondering why Sister Bo was so agitated, the bacterium lying on the street suddenly exploded! I saw it burst open, and then many holes appeared, with lots of small black things bursting out from inside. Even though Sister Bo and I reacted quickly, we still inevitably got splattered with some.
It was the first time I had seen such a thing, and I was almost going into shock. I hurriedly looked at Sister Bo, only to see her frantically shaking off the black dots on her body while shouting, "Get up! Shake off those black dots! They are bacteriophages! Oh my god! Shake them off, don't let them enter your body!" But I was already weak all over. When I looked down at my body, I found that the black dots were indeed slowly seeping into me. Everything went dark before my eyes, and I fainted.
Before falling into unconsciousness, the last sound I heard was Sister Bo's frantic shout: "Is there a doctor? Hurry, she has been infected!"
Chapter Three: Awakening#
When I woke up again, it was already a new day. However, our sense of time is not the same as yours; after all, in your eyes, we reproduce every 20 minutes, but we feel that this time is very long, equivalent to about half a year for us. The diary entry from yesterday was actually written today because I had been unconscious for a day.
When I woke up, I was lying in a strange place, surrounded by many other bacteria lying on the ground, their bodies very thin but their bellies swollen. I suddenly remembered Sister Bo's last words: "She has been infected!" So, am I going to die like them now?! "Sister Bo! Sister Bo!" I shouted; all I wanted to know now was whether I was really going to die. What if I wasn't infected? What if Sister Bo's judgment was wrong? What if, what if... she abandoned me? I smiled bitterly; yes, I am already an infected one, and she has no obligation to take care of a bacterium that is neither related nor familiar to her. If she continues to stay in this place, she might get infected herself. Thinking this way, I calmed down instead.
Today, due to feeling unwell, I cannot continue writing. Readers, please bless me; I do not want my life to end like this!
Chapter Four: The Old Hospital#
When I woke up again in a daze, I vaguely saw a piece of lactose beside me. No wonder, if there is glucose, who would eat lactose? After all, utilizing lactose requires us to activate a new gene to absorb and digest it. However, in such a crowded and messy place, having something to eat is already quite good, so I had to endure the poor taste of lactose and absorb it. After temporarily filling my stomach, I forced myself to walk around and take a look. How to describe it? Everywhere were sick bacteria with big bellies, but I didn't see any relatives or nurses. Unlike your human world, only a few healthy bacteria were quickly distributing food, their impatience and fear evident on their faces. On the walls were old reports like "Eight Regulations on the Prevention and Treatment of Bacteriophages Issued by the Central Government" and "A Certain Director of Our Hospital Developed a Vaccine Against a Certain Bacteriophage," revealing that this was an abandoned hospital. It seems that before being discarded by humans, this place once had a very healthy bacterial community system, but after losing human nutrient supplies and the sudden outbreak of bacteriophage infections, this beautiful proletarian society collapsed, and the previous welfare was lost due to the lack of supplies, leaving the bacteria poor and pitiful.
I think my life is going to end here, I thought. What terrified me was that this hospital was filled with a depressing atmosphere of death. No bacteria tried to save the patients, no bacteria cared about the emotions of the infected; we were like the social dregs abandoned by normal and healthy bacteria, waiting to die here. "Puff," a muffled sound behind me made me involuntarily turn around, but I quickly regretted this action: a soft bacterium, terrified to find many holes appearing on its body, didn't even have time to scream before it shattered, black things splattering out from inside, just like what I had seen before. I screamed and desperately ran forward, but in my fright, I found that the bacteria closer to her remained motionless, their eyes revealing despair and helplessness. They had become numb to this death! Other bacteria around even scoffed at my evasive behavior, one patient mockingly said, "You've already been infected; what are you afraid of? It's just a matter of dying sooner or later!"
"No! I am not like you!" I shouted angrily, "If you want to die, go ahead; I will absolutely not wait to die here! I must, I must find a way to save myself! Um... um!" Suddenly, my mouth was covered, and I turned around to slap someone. Not allowing bacteria to live and not allowing them to speak? However, the person behind easily dodged my strike, only for my palm wind to blow off her mask, revealing the face of the bacterium: that cynical gaze could only belong to Sister Bo!
Chapter Five: Escape from the Old Hospital#
"Shh," Sister Bo signaled me with her eyes. Having been with her for so long, how could I not understand her meaning? So I deliberately shouted, "What is this place? Huh? Bullying us patients like this? Come on, explain it to me!" "You are disturbing the order here and bothering other patients; what do you mean? Let's settle this privately, come on!" Half-pushing and half-pulling, Sister Bo and I quickly left the center of the patients and found a quiet place.
"Sister Bo, you..." "I came in to find you!" Sister Bo casually tossed aside her nurse's hat, "They wouldn't let bacteria just enter this place. Don't blame me for not coming to find you earlier; their selection of nurses is quite strict!" After talking with Sister Bo for a long time, I finally understood what happened a few days ago. It turned out that after I fainted, Sister Bo hurriedly found a few seemingly healthy bacteria and asked them where there was a hospital, but they all hurried away, afraid of being infected by me. With no choice, Sister Bo had to go to the guard's office for help. Who knew that the bacteria in the guard's office were all fake justices? They ignored the many infected bacteria on the street, and they regarded Sister Bo as a "reporter" who reported the existence of infected individuals. So, in front of Sister Bo, they swore, "Don't worry, we will strictly control her." Then, this group of government bacteria who only did superficial work threw me into this place. It was only after a while that Sister Bo felt something was wrong and disguised herself as a nurse to find an opportunity to approach me.
"Ah, no wonder this place is so decayed. Even if it hadn't been abandoned by humans, the bacteria would eventually perish due to corruption and the coldness of society," I couldn't help but sigh. "So the urgent task is to get you out of this corrupt tribe; we need to find a way to escape this old hospital first," Sister Bo said decisively. "Otherwise, if you don't get timely treatment, I might get infected too, and we both will die." So, after a bit of scheming between the two of us, we planned to disguise ourselves as nurses and sneak out the back door. Sister Bo quickly stole a few pieces of nurse equipment and brought me a large piece of lactose, saying, "Pretend you are distributing food; later, bribe the guard lady." Although it felt a bit unethical, we had to lower our moral standards to survive. Sister Bo had indeed been in society for a long time; we quietly slipped out the back door, and the guard lady happily said, "Oh, two little girls finishing work so early? Thank you!" Once we left the guard's range, we immediately started running. The infected bacteria we saw along the way, at the corners, on the bridges, and by the rivers, deeply imprinted in our memories. Is this what a collapsed society looks like? If the bacteria here could be more united, cooperative, and fair, perhaps the situation wouldn't be like this.
Suddenly, everything went dark before my eyes: perhaps the bacteriophages in my body were trying to invade my DNA again. I thought I was going to die, but Sister Bo shook me desperately: "No, you can't fall asleep! We have to escape this place!" While she desperately pulled me, she tried to take out food from her body, but we had already run out of supplies. Sister Bo gritted her teeth: "Get on my back!" I felt like I couldn't muster any strength, like a lump of mud stuck to Sister Bo. In a daze, I didn't know how long it had been when I felt something inside me tearing apart. I screamed and lost consciousness.
Extra Chapter 1: Thoughts on the Journey: About Opportunities#
Just like you humans, we also have an end to our lives, and one important reason for our aging and death is that our metabolism goes wrong: it could be due to natural slowing down, or external harm from ultraviolet rays, bacteriophages (which are viruses that can infect us bacteria), etc., that makes us sick and die. Moreover, we are much more fragile than you; even a little harm is enough to wipe us out. If you humans get a benign tumor, it can still be treated; after all, that is just a part of the trillions of cells in your body with DNA errors. You can simply remove the erroneous part through surgery; we cannot do that. We are a single cell, so if our DNA has any errors, it basically means game over for us. Therefore, mutations (sudden changes in DNA) are undoubtedly a death sentence for us, except for my great-great-great-grandmother—she benefited from her mutation, not only surviving but also being revered for acquiring a unique ability. Now, her descendants are spread across major microbiological laboratories.
Let me tell you about the glory of my great-great-great-grandmother.
It is said that at that time, our ancestors were still living in human laboratories, and scientists would check on our reproduction status every day. Sometimes we would see scientists deliberately applying survival pressures like low temperatures, ultraviolet rays, and sugar deprivation to the bacteria they raised, allowing the fittest to survive—selecting individuals that could resist such pressures, while those that couldn't would leave this world helplessly. Sister Bo was right; we laboratory bacteria have always lived according to human whims; the useless ones are ruthlessly eliminated. Our family survived because we proved our value early on (amplifying plasmids), which was fortunate. When my great-great-great-grandmother was born, she looked just like the other DH5α bacteria in the family, but after a while, one summer, she and some bacteria from her family were taken out of the culture medium by a graduate student. After being transferred to solid culture medium, they were inadvertently placed on a windowsill. Although the graduate student quickly returned the petri dish to the 37-degree incubator after realizing the mistake, the nearly 50°C high temperature baked most of the bacteria to death. A day later, the graduate student was pleasantly surprised to find that my great-great-great-grandmother not only survived but also gave birth to many bacterial babies. Later analysis revealed that it was due to a mutation in her DNA that allowed her to produce a protein not found in other bacteria. This protein was very optimistic and proactive, so it could mobilize the other proteins that were negatively working under high temperatures, allowing my great-great-great-grandmother's body to function even under high temperatures. Later, this gene attracted a lot of attention, and my great-great-great-grandmother even made it to the cover of a magazine!
However, my great-great-great-grandmother was a lucky one, as she happened to be placed in harsh conditions where she could survive. Many bacteria, placed in the wrong conditions, not only did not achieve glorious lives but also lost their lives: for example, my aunt, who used to eat with me often, proudly showed me her mutation: the ability to produce a protective protein against penicillin. However, she was later placed in a culture medium containing erythromycin and ultimately died at the hands of erythromycin. Her last words were: "I don't blame myself for not having the ability to resist erythromycin; I only blame that graduate student for not placing me in the right conditions." It seems that you humans often have similar situations in life, such as a talent scout recognizing a fast-running horse and liberating it from carrying goods to achieve great feats on the battlefield. So, having a discerning talent scout is indeed a very fortunate thing. However, you humans are happier than us because you can choose your profession and specialty based on your interests and talents, unlike us, whose fates are controlled by researchers. Therefore, you must use this advantage to live in the right position and lead a happy life!
Extra Chapter 2: Things Learned at Home: About DNA Replication and Having Babies (1)#
Speaking of which, bacteria are destined to die, so what we care about most is the social value we create—the ability to produce offspring through asexual reproduction. When having babies, what we bacteria need most is to pass on the DNA that sustains our existence to our offspring. If we encounter problems while replicating DNA, it is like when you copy homework questions; if the copier malfunctions and prints "1+7" as "1-7," your answers will certainly differ from the standard answers. Moreover, if you continue to use a good copier to copy "1-7," it will also not produce "1+7." This error will make her children and their children live very uncomfortably. Therefore, we pursue completeness and correctness when replicating DNA.
DNA is our genetic material, as well as the genetic material of viruses and advanced life forms like you. It can control us to perform a series of physiological activities. For example, when the temperature is very high, my great-great-great-grandmother can produce a protein that adapts to high temperatures, and this protein is produced through a series of manufacturing processes from DNA. With the help and encouragement of this protein, other parts of her body can also be mobilized to allow her body to carry out metabolism under high temperatures. However, most E. coli, lacking DNA that can produce positive proteins, will feel "Ah, it's so hot, I don't want to live," and thus give up having babies, leading to their demise. In short, DNA is equivalent to the core of our life; without DNA, no living organism except prions can survive.
Speaking of prions, they are a freak; they cause chaos everywhere, and mad cow disease is caused by them. This freak has no DNA, only proteins, yet it can proliferate. Its method of proliferation is to incite originally diligent proteins to join its cult, ultimately becoming the assimilated, reactionary proteins. The seduced reactionaries will then drag their colleagues and classmates into the cult, leading to a rebellion of proteins in the animal's brain! Consequently, the animal will suffer from mental illness and die pitifully. No wonder in our world, it is often referred to as a terrorist that "made a deal with the devil." Therefore, you humans must never join cults; otherwise, your world and beautiful society might be destroyed by yourselves!
Sigh, every time I talk about this freak, I get angry; it has harmed too many lives! Forget it, forget it; I won't talk about it anymore. Oh, one last thing: the best way to prevent this freak from entering your body is to ensure that when eating beef and lamb, it is thoroughly cooked. Even the most upscale restaurant's steak should be well done, as this devil's heat resistance is simply intolerable.
Okay, let's stop here. In short, DNA is the most important part of our bodies, and to ensure that our offspring can live well, we must guarantee that every replication during reproduction is flawless. Therefore, its health has always been a hot topic among women of all species. Bacteria do not need to find boyfriends or girlfriends, so we are usually quite carefree, but when it comes to DNA replication, we never dare to be careless because the most important thing in our lives is our children. If our bodies are not well and we give birth to disabled children, we will be laughed at by everyone—although we only care about giving birth and not raising them, bacteria have known since childhood how to absorb nutrients and reproduce themselves; it's a kind of instinct. We place great importance on our DNA replication system, just like you young girls always think about how to take care of your faces. We also think about how to maintain our replication system so that we can keep reproducing until we are old. Generally, our DNA is replicated first, divided into two parts, and then we stretch our bodies as much as possible. When breaking apart, our bodies can flow quickly like the surface of a soap bubble to fill the gap, so they won't break.
Extra Chapter 3: Things Learned at Home: About DNA Replication and Having Babies (2)#
Now the question arises: we are very cautious about DNA, and it takes 40 minutes to replicate once, which is about the length of your class, but our bodies are filled with a desire to reproduce, splitting every 20 minutes. What should we do? Haha, actually, we are quite clever: we increase the number of DNA replication systems! DNA is long, and for those small DNA polymerases, it is like a long one-sided zipper. They and their buddies run along it, building a new side that can fit perfectly with the original one-sided zipper; while a group of polymerases is replicating and running far away, we will place two batches of polymerases at the two starting points to let them run and repair the DNA zipper. Then, when the first batch of polymerases completes this "zipper marathon," my body starts to split, and then one of the batches of polymerases that made the zipper will follow into my daughter's body. My daughter can quickly start a new round of replication marathons by producing new polymerases through inherited DNA.
This way, we can ensure that even with a 40-minute replication speed, we can complete the task of splitting every 20 minutes. The repaired zippers will temporarily join together, and when the next replication is needed, the zippers will be opened by helicases, and the two single strands will replicate separately, with one remaining in the mother and the other passed to the daughter.
However, there is another very important question: what if our DNA is accidentally damaged? Our ancestors have suffered this pain, so many ancestors without self-correcting DNA have unfortunately gone extinct. The ones still alive are descendants of bacteria with self-repair mechanisms. This confirms Darwin's saying, "Survival of the fittest."
Our DNA has four self-repair mechanisms. The first one has a very nice name called "photoreactivation," which can directly repair the abnormal structures formed by ultraviolet light on DNA under natural light. However, this is something only we bacteria can do; you humans cannot repair DNA by sunbathing. However, it is good for your children and the elderly to get some sun, as it can synthesize vitamin D and help your bodies absorb calcium. The second one is what you humans call "excision repair," and the third is called "recombination repair." Uh, since I didn't understand the complex principles explained by Sister Bo, I can only barely distinguish that excision repair involves cutting out the erroneous part and then completing it again, while recombination repair involves cutting out the entire erroneous segment and then repairing that section of DNA. The last one is interesting; it's called SOS repair. After an error occurs, our enzymes become flustered and, in order to complete the workload, randomly find a part to patch up and continue working. As a result, the originally correct fitting places bulge out or sink in, forming a strange pairing, and the offspring's DNA may mutate. The newly born bacteria might be disabled or even die because other enzymes related to DNA cannot run on it. However, a few bacteria may benefit from misfortune, but the probability is really small. Therefore, we do not seek to have abilities beyond ordinary bacteria; we only wish to be a good ordinary bacterium!
This is also why we are so cautious about DNA replication.