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Understanding Dimension Reduction: PCA vs. t-SNE vs. UMAP with the Swiss Roll When dealing with high-dimensional data, it is often challenging to visualize and interpret patterns. Dimensionality reduction  helps us project complex datasets into fewer dimensions while preserving meaningful structure. In this post, we will explore two popular dimensionality reduction techniques—Principal Component Analysis (PCA) and t-Distributed Stochastic Neighbor Embedding (t-SNE)—using a classic example: the Swiss Roll dataset. The Swiss Roll Dataset The Swiss Roll is a synthetic dataset where points are arranged on a curved 3D surface, forming a spiral-like shape. The challenge in dimensionality reduction is to flatten this 3D spiral while preserving important relationships between points. In this figure, each point is color-coded based on its position along the spiral. Ideally, after dimensionality reduction, points with similar colors should remain close together. PCA: Preserving Global Structure Principal Component Analysis (PCA) is a linear  dimensionality reduction method. It works by identifying the directions (principal components) that capture the most variance in the data and projecting the dataset onto these components. When PCA is applied to the Swiss Roll, we obtain the following projection: Key Observations: ✅ PCA successfully collapses the Swiss Roll into two dimensions. ✅ It preserves the global structure, meaning the overall spiral shape is still visible. 🚨 However, PCA distorts local relationships—some points that were far apart in 3D may appear close in 2D. 📌 PCA is useful when the data follows a linear structure and we need a fast, interpretable projection. t-SNE: Preserving Local Structure t-Distributed Stochastic Neighbor Embedding (t-SNE) is a non-linear dimensionality reduction technique that focuses on preserving local relationships  in the data. Instead of a linear projection, t-SNE maps points into 2D space while trying to maintain the pairwise similarities between points. Applying t-SNE to the Swiss Roll results in: tSNE projection Key Observations: ✅ t-SNE successfully unrolls the Swiss Roll by grouping similar points together. ✅ It preserves local neighborhoods—points that were close in 3D remain close in 2D. 🚨 However, t-SNE does not preserve the global spiral shape; instead, it breaks the roll into clusters. 📌 t-SNE is great for discovering clusters in high-dimensional data but does not maintain global structure. Comparison: PCA vs. t-SNE Feature PCA (Linear) t-SNE (Non-Linear) Preserves Global Structure? ✅ Yes ❌ No Preserves Local Structure? ❌ No ✅ Yes Works Well for Curved Data? ❌ No ✅ Yes Good for Cluster Discovery? ❌ No ✅ Yes Computationally Efficient? ✅ Fast ❌ Slow If you need a quick, structured projection, PCA is a great choice. If you need to find clusters and preserve neighborhood relationships, t-SNE is better. Both PCA and t-SNE are powerful tools for reducing dimensionality, but they serve different purposes. PCA is best when global structure matters, while t-SNE is useful for local clustering. Understanding these differences is key when visualizing and interpreting high-dimensional datasets. I am still debating, if I understood the whole concept. But this is essentially it. :) What about UMAP? At this point, I questioned, don't we need an algorithm that can preserve the spiral shape better? The answer is UMAP. We can argue this is still not the perfect spiral shape but better than the tSNE's broken apart pieces. UMAP Prioritizes Local Structure UMAP is designed to preserve local distances  more than global distances. It maintained the order  of the Swiss Roll but didn’t force it into a perfectly smooth spiral. Why UMAP Might Be the Best Choice for You Feature PCA t-SNE UMAP Preserves Global Structure? ✅ Yes ❌ No ✅ Yes Preserves Local Structure? ❌ No ✅ Yes ✅ Yes Distributes Points Naturally? ❌ No (line) ❌ No (overclusters) ✅ Yes (balanced) Fast for Large Data? ✅ Yes ❌ No (slow) ✅ Yes (faster) Have you used any of these algorithms? How was your experience?

Today I am trying to understand the logic behind dimension reduction (DR). I wanted to read and write about some simple examples to illustrate for myself and maybe help others learn as well. The initial example that comes to my mind is: taking a photograph. In a broad, physical sense , when you take a photograph, you’re mapping a three-dimensional scene onto a two-dimensional image. This is essentially a projection  from 3D to 2D, so in that way, it is  a form of dimensionality reduction: you’re reducing reality’s three spatial dimensions down to two. Other daily life examples (AI curated) that convey the core idea , taking something with many “dimensions” (or aspects) and representing it in fewer dimensions while preserving essential information are: Flattening a Globe into a Map What happens: A 3D Earth is “projected” onto a 2D map. Why it’s dimensionality reduction: We lose one dimension (from the globe), but we keep key relationships like continents’ relative positions. Caveat: Maps can distort distance or area (like Greenland appearing huge), which parallels how some DR methods distort global relationships while preserving local ones. Summarizing a Restaurant’s Quality into a Single Rating What happens: You might consider multiple dimensions of a restaurant’s quality—food taste, service, ambiance, cleanliness, price, etc.—but you often see a single star rating (like 4.5 out of 5). Why it’s dimensionality reduction: Many different criteria (dimensions) get “compressed” into one number. Caveat: You lose which specific aspect is strong or weak—just like DR methods sometimes lose nuance about individual features. Compressing an Image to a Smaller Size What happens: Suppose you have a photo with a resolution of 4000×3000 pixels (12 million dimensions if each pixel is one dimension!). If you resize it to 400×300, that’s only 120,000 pixels. Why it’s dimensionality reduction: You’ve drastically reduced the number of “features” while still preserving a recognizable version of the image. Caveat: You lose details and can’t zoom in without seeing pixelation. Using Principal Components to Summarize Test Scores What happens: Imagine a student has scores in 10 subjects (Math, English, History, etc.). You could run Principal Component Analysis (PCA) on those scores and reduce the 10 dimensions to just 2 or 3. Why it’s dimensionality reduction: You capture the main “patterns” (e.g., a “STEM aptitude” axis vs. a “Humanities aptitude” axis), letting you plot students in 2D. Caveat: You lose the specific breakdown per subject, but you gain a simpler, bird’s-eye view of performance. Buying a Laptop: Distilling Many Specs into One Decision What happens: When shopping for a laptop, you look at many specs—CPU speed, RAM, screen size, weight, battery life, price. Why it’s dimensionality reduction: Often, a reviewer or your own personal assessment might roll all of those into a single overall rating or “best value pick.” Caveat: You lose the nuance of each spec’s details, but gain an easy decision metric. Just like the restaurant rating or the laptop buying example, we compress multiple measures into fewer measures or a single score. The key is doing so in a way that preserves the most important relationships—whether that’s the overall “ quality ,” the essential structure of an image, or the local clustering of data points in a complex dataset. Any time you reduce the number of descriptors while trying to retain essential information , you’re performing a kind of dimensionality reduction . I hope this was helpful! I will write on popular dimension reduction techniques next.

Trying to beautify the place you are in, shows your joy of life.  Joy of life does not pour as rain. You have to cultivate it in yourself. Yes, that means effort. Today we worked on the backyard, added top soil, removed weeds, raked leaves and moss.  I am hoping to get some flower arrangements in some pots to decorate the deck.  It is easy to give up, stay down, and just let things go. It requires effort to stand up, fill buckets with soil, add plants or seeds. But the reward is bigger. Once: you feel healthier with more outside time, energy spent and increased productivity.  Second, the plants and flowers beautify your landscape and give you joy of life in return 🌷🌻🌺  Examine the blooming flowers in the super dry looking stems, how come they made it out? How come they are green? How come there is even a flower?  Third if you planted fruits and vegetables, you have fresh things to add to your table 😇 What are some ways that help you feel accomplished at home? Tidying up your desk? Laundry? Dishes?

We tossed out our Ninja coffee maker because it was burning the coffee. I’d almost say my husband felt a wave of pleasure dumping it and going back to our old-fashioned coffee maker from Walmart. This ties into my previous post, "Why Are Some Things Expensive?" It’s frustrating to splurge on a high-end product with more features, only to end up with a worse outcome. Over the weekend, we got our car washed at an automated car wash station. As with most things in my life, this seemingly mundane experience triggered a cascade of questions. What are those black rotating brushes made of? If they can get dirty, does someone have to clean them? If they’re rubbery, maybe they just rinse off? How does the machine adjust to different cars? What if the rubbery things make scratches? Then, we pulled up to the vacuum station. Another round of questions. Where does all the dirt go? There’s a locked compartment—what’s inside? Oh, that’s where the coins go. How much does this car wash station make? How much does it cost to build one? Let’s assume it costs $200K. If each wash generates a $5 profit and 200 cars get washed per day, the station starts turning a profit after 200 days. Why am I using my precious ion gradients to think and calculate such things? You don’t just enter the lab as a Ph.D. scientist and turn off the questioning when you hang up your lab coat at the end of the day. The scientist’s mind is always on. And speaking of Ph.D.—Doctor of Philosophy. I’d argue I spent a good chunk of my middle school years practicing adolescent philosophy. But what does philosophy even mean? Why do we call certain people philosophers? I could question everything—outer space, the insides of atoms, patterns and connections between things, associations, and links. I could question cause and effect. I could even question questions themselves. Fortunately (or unfortunately?), this process never stops. As I climbed the hill from the parking lot, another thought hit me: movement, migration. What does it mean to migrate? What does it mean to be an immigrant? If humans move to Mars, what will we call them? Earthlings? 😂 Would plants grown in Martian soil nourish humans made from Earth’s soil? Who will be the first to test this? How will land be allocated on Mars? In the past, people built fences and—ta-da!—the land was theirs. Will we do the same on Mars? If I had $200K, I could have built a car wash station and made automated money. But I’m a Ph.D. scientist, so instead, I’ll keep asking questions. 😆

While shopping for a shirt for my husband, I noticed something strange—one shirt costs $20, while another (same fabric, same function) costs $150 just because it has a Ralph Lauren tag. What exactly are we paying for? I even saw a woman carrying a Michael Kors bag—clear plastic, no zipper. What’s the point? What are we really buying? Is it just about putting ourselves in a certain social class? Lately, my husband has been looking for a new car. I imagined him driving a Tesla, like many of our friends. Why did I want him to buy a Tesla? Was it about the car’s actual value? Was it about sustainability, charisma, or just keeping up with the crowd? He shut the idea down quickly—he doesn’t like Elon. But I kept questioning myself: what makes something worth it ? Last week, we got a new vacuum. We could have bought any brand, but we went with Dyson. Why do we trust certain brands more? In this case, we had firsthand experience—our old Dyson worked well. My father, a mechanic at heart, was amazed by Dyson’s clever engineering—how the vacuum’s suction powers the roller without extra parts. A brand wraps a product in confidence, and that confidence builds trust. The same logic applies to product reviews . When I buy books on Amazon, if a book has 300,000 positive reviews, I’m sold. But what if I’m overlooking high-quality books that never went viral? Is this just survival of the fittest  in the business world? And then there’s art . Some pieces sell for ridiculous amounts. Like the banana taped to a wall—that banana was one of the cheapest fruits you can buy, yet a collector paid who knows what for it. Then he just ate it. Scarcity and the Price of Treasures I used to tell my kids that humans, like children on Earth, dig things up and call them treasures. People want them, and suddenly, they become expensive. The harder it is to find something, the more valuable it becomes—like diamonds and pearls. That’s branding in its simplest form. But branding isn’t just about luxury goods—it’s everywhere, even in science. A research lab, just like a company, thrives on reputation and visibility. Branding in Science: The Prestige Factor For scientists, branding yourself or your lab depends on publications—the number, but more importantly, the impact . There are other metrics, like the h-index , but search committees often scan for elite journal names and prestigious university affiliations on a CV. Want to "brand up"? You need reviews —in the form of recommendation letters . And if your recommenders are famous, well-ranked, and highly impactful, then your letter shines even brighter. Selling your research is crucial for obtaining funding. Your idea must fill a significant knowledge gap, answering questions that bring science closer to real-world solutions. Even publishing a paper involves wrapping raw data into a compelling narrative—highlighting the "selling points" to make it stand out. Selling Yourself: A Tougher Game Branding yourself as a scientist is tricky. "I can solve your biomedical research problems"—too ambitious. "I run well-planned, controlled experiments, and if p < 0.05, I reject the null"—not exactly a TED Talk moment. But hey, in science, sometimes that’s all the branding you need. :)

Confidence and Women: A Seedling That Grows This Women’s Day, I found myself reflecting on confidence—why do women, on average, have lower confidence levels than men? At a physiological level, one clear reason is vulnerability. Women face higher risks of sexual violence, and they bear the biological responsibility of childbirth. These factors alone could contribute significantly to the confidence gap. In some parts of the world, particularly in the Middle East, the concept of virginity further compounds the issue. A woman who loses her virginity unlawfully is often seen as "damaged" or "less valuable." You could watch a thousand episodes of Turkish dramas dissecting this theme. The message is clear: women are born into a world where they are often raised with these deep-seated misconceptions. It’s no wonder many struggle with confidence. But what about at the cellular level ? Could there be a biological factor at play? In one of my lectures, a student once asked, "Isn’t it unfair that women only have one active X chromosome while men have both an X and a Y?"  I laughed and said, "Yes, it does sound unfair."  But then I thought—perhaps it’s actually a mark of efficiency. Women get the same job done with just 45 active chromosomes. While ruminating on the unfairness of the inactive X chromosome, I came across something fascinating: about 30% of the genes on the inactive X remain active, and they may help protect women from cognitive decline as they age .  Hooray for the hidden advantages! Confidence, or the perception of it, plays a role in how women are treated, especially in professional settings. One striking example is the story of a Stanford professor who transitioned from female to male . After the transition, the same researcher presented the same work—but this time, a male colleague remarked, "His data is much stronger than his sister’s."  He failed to realize that they were the same person. Growing a Confidence Tree Recognizing the confidence gap is one thing, but how do we bridge it? I imagined a confidence tree —one that starts as a tiny seedling. Right now, I might be at the seed stage, but I can nurture it with intentional practice. To help my seedling grow, I need to: Learn to coexist with my imperfections Accept and encourage myself to be myself Stop assuming that everyone else in the world knows more than me The Confidence Code   suggests that formal education—college, master’s degrees, PhDs (possibly even postdocs)—doesn’t necessarily build confidence. If anything, diving deeper into research makes you more aware of how little you know. Constantly switching fields to find a job only amplifies this feeling. This realization of not knowing enough  is one of confidence’s biggest enemies. Still, under these non-ideal conditions, we can keep watering our confidence seedlings . I will keep showing up. I will keep adding knowledge, mastering skills, and growing new leaves. With time, this confidence tree will develop its own momentum. The more it grows, the more it feeds itself —like a bestselling author producing one hit after another, or a tenured professor winning awards and grants year after year. Women and Confidence: Progress and Role Models It’s astonishing to think that women weren’t even included in clinical trials until 1995. That they weren’t allowed to vote until 1920. Given this history, the fact that we now have female Nobel laureates and world leaders is proof of how far we’ve come. What does true confidence look like? I picture Liz Allison , my former department chair . When she led faculty meetings, it felt like a warm breeze—welcoming, open to ideas, and effortlessly in control. Nothing aggressive, nothing forceful. Just a natural and elegant  way of leading. I could choose to appear confident  while quietly battling self-doubt inside. I can also work to genuinely build confidence —not by reading minds, not by assuming what others think, but by focusing on my own growth. Most importantly, I need to embrace and love myself more . In an era of AI and endless streams of knowledge, I shouldn’t beat myself up for forgetting things. I am human, with vulnerabilities.  And that’s okay. Your Turn: What Are Your Confidence Tricks? Do you have strategies for looking, feeling, and behaving more confidently? What has worked for you?

Yesterday, I tossed two pieces of chicken bones with some meat on them into the backyard. Today, I saw a big hawk circling above. It landed cautiously, eyes scanning, body tense. It didn’t pounce immediately—it hesitated, as if suspecting a trap. I watched, curious. Why weren’t other animals interested? And how did the hawk even find the food from so far up? Unlike the hawk, I don’t need to hunt for food. Opportunities are sometimes placed right in front of me. But do I always take them? Today, I realized I missed two deadlines for my coursework. My professor granted me an extension, but I felt a sting of disappointment. I had failed my own expectations. One of my core strengths is responsibility—had I just let it slip? Guilt, Pleasure, and Balance Later, a friend told me she had just watched nine episodes of a Korean drama. I laughed, but I knew that feeling all too well. The pull of a story, the need to see it through—especially when conflict is unresolved. I get hooked, too. Maybe because my third strength is harmony. I crave resolution. And then comes the guilt. Guilty pleasure. But why guilt? Does all pleasure need to be guilt-free? Is it worth the guilt to indulge? It feels like a seesaw—if one side is up, the other is down. Too much indulgence and responsibilities suffer. Too much rigidity, and life becomes dull. Islam teaches about Siratal Mustaqim, the straight path—the path of balance. Winners are those who avoid extremes, staying in the middle. But how do I make sure I’m walking in the middle? The Many Faces of Depression Depression doesn’t always wear the same face. Sometimes it’s obvious—sunk in, withdrawn, avoiding the world. Other times, it wears a smile, enjoys life on the surface, but quietly ignores responsibilities. Time passes in distractions, in mindless scrolling, in waiting. The Siratal Mustaqim of depression is recognizing that sadness is okay. Disappointment is okay. Crying is okay. But we can’t stay down forever. We won’t always have someone else to pull us up. So we need to build the strength to stand up. And when we do, we need to show mercy to ourselves. “Poor me, you have been sad. It’s okay. Things will be okay.” Small Steps Toward Healing What helps shake off the weight of sadness?  • A small goal—saying one little prayer 100 times.  • Setting an alarm clock.  • Writing down feelings in a notepad.  • Calling a friend.  • Even chatting with ChatGPT. Sometimes, emotions need space. In Sufism, emotions are treated as guests. We welcome them, acknowledge them, but know they won’t stay forever. Imagine them like a flying carpet—hovering beside us, eventually fading into the background. But some emotions overstay their welcome. If we can’t process them alone, seeking another perspective helps. Not just any perspective—one that helps us realign with truth. Perspective and Humility One way to realign is to zoom out. I used to be a single cell—a fertilized zygote. Before that? Just atoms and molecules. All of me came from the soil, and one day, I will return to the soil. Thinking like soil brings humility. It reminds me that I am small. That my struggles are temporary. That even if I fail, even if I miss deadlines, even if I get lost for a while—life keeps moving. And I can, too. I didn’t plan to write about depression, but my words led me here. And maybe that’s something to respect. What About You? How do you deal with sadness? Are some methods better than other s?

Do you enjoy water sports like kayaking or rafting? My only experience with rafting was a mild one—Beaver’s Bend State Park in Oklahoma. It was peaceful, almost uneventful. The best part was watching the sky blend into the trees and river, listening to nature, and waiting for bites while fishing. Back when we lived in Dallas, we used to drive up there for fishing. The trout—especially in the “red zone”—were top-tier. If you had a cabin nearby, grilling fresh fish was the highlight of the trip. But back to pedaling… At Pocahontas State Park in Virginia, we tried something different: a water bike. You pedal just like a bicycle to move across the lake. We also kayaked there—this time with three kids in tow. Instead of peacefully admiring the water lilies, I was laser-focused on keeping everyone safe—making sure no one fell in or got too much sun. All I remember was pedaling as fast as I could. Lately, I’ve been thinking about pedaling in a different sense. What if I’m on the wrong boat? But even if I am, the only thing I can do is keep pedaling. It’s better than drifting aimlessly. It’s better than not being on a boat at all. I bought a book on confidence for women today. Amazon sent me a used one instead of new, which was frustrating—not because it was used, but because it wasn’t sold as such. I got the book thinking that learning to build confidence would help me develop leadership skills. But then, I came across a post that challenged that idea: I shouldn’t wait to be confident to take on leadership. Leadership isn’t about waiting until you feel ready—it’s about influencing action, taking responsibility, working through chaos, and being okay with uncertainty. Too often, I choose to let someone else take responsibility, just for my own peace of mind. And that’s what keeps me at the contributor level. The opening story in an Emotional Intelligence book stuck with me. A man is out surfing when he suddenly spots a great white shark. At first, fear and anxiety freeze him. But then, his mind shifts to survival mode, and he starts paddling for his life. He makes it to shore. Most of us aren’t facing sharks every day, but we are navigating uncertainty. Fear, doubt, and unknowns shouldn’t paralyze us. We just have to keep paddling. And if we inspire others along the way, that’s leadership in action. Every challenge, every unexpected turn, builds new skills—sometimes ones we don’t even have a name for yet. What skills are you working on? Have you found any shortcuts along the way?

Today is the first day of Ramadan, and I’ve noticed something striking—time feels extended. Of course, in a practical sense, fasting removes the time spent on meals, but the effect is much greater than that. It feels as if the hours themselves stretch. This morning, I cleaned the first floor, and my husband managed to clean the second floor and the backyard. I prepared breakfast for the kids, baked a cake, made lunch, cleaned up, read 100 pages of my EQ book, and wrote this post. He raked leaves, did laundry, and we read books with our son. Then we made bracelets together—and somehow, it was still only 4 PM. This experience made me reflect: Is time really elastic? I’ve felt this before in different ways. When faced with a deadline, I often procrastinate, only to feel the intense pressure of time shrinking. Sometimes, I pull off a last-minute miracle. Other times, I ask for an extension. But what if I could create an internal extension of time—within its natural boundaries? In Turkish, we call this bereket—a kind of abundance. How can we cultivate more of it in our days? How can we use time more intentionally? A Simple Approach to Time Management With my kids, I suggest a structured schedule, especially on holidays. Before using technology, they map out their day to include a mix of learning, creativity, and play. A balanced day feels richer. I apply the same approach to myself. Summers, when I had a teaching job, used to feel endless if unstructured. But without direction, they can also feel unfulfilled. Filling time with purpose—learning, goals, social interactions—turns it into something meaningful. An 83-year-old friend of mine, Melanie Cottam, embodies this philosophy. She maintains a vibrant, structured life with water aerobics, meetings, courses, and planned social activities. She doesn’t just pass time—she fills it with purpose. Measuring a Day Well Spent Maybe the true “accounting” of a good day isn’t how much we did but how well we spent our time: ✔️ Did I learn something new? ✔️ Did I make someone happy? ✔️ Did I treat my body and soul with care? ✔️ Did I avoid wasting my time? The Brain’s Role in Time Perception My current reading, Emotional Intelligence 2.0, explores how we can build stronger neural connections between our emotional and reasoning brains. The more self-awareness we develop, the more intentional we become about how we live each day. And yet, despite everything I reflect on today, I know I still have so much to figure out. Will I feel the same expansion of time tomorrow? Or is this a moment of mindfulness, a slowing down, a sinking into time itself? I’m curious—have you ever felt time stretch or contract? How do you make the most of your day?

Did you receive a gorgeous orchid as a gift? 🤩 You admired its beauty 😍, took care of it… and then, one by one, the flowers fell off. The stalk dried up. 😔 Yeah, yeah… we’ve all been there. 😅 I wanted to master orchid reblooming all by myself. 🌱 And guess what? It’s possible! Here’s what worked for me. 👇 💧 The #1 Rule: Less Water, More Consistency! ✅ Orchids only need 1/4 cup of water per week. ✅ Stick to a strict schedule – pick a day and write it down. 📅 Example Watering Schedule (Tuesdays): ✔ 2/18/25 – 1/4 cup water ✔ 2/25/25 – 1/4 cup water ✔ 3/4/25 – 1/4 cup water ✔ 3/11/25 – 1/4 cup water + 1 drop fertilizer 🌱 🔄 Repeat the pattern! 📌 Pro Tip: Automate reminders on your phone 📲 or keep a physical note! 🚫 What NOT to Do! (Avoid These Orchid Mistakes!) ❌ Don’t wash the entire plant just because the leaves look dusty. ❌ Don’t submerge the whole pot in water—this can cause root rot. ❌ Don’t overwater! Even if the soil looks dry, stick to the schedule. ❌ Ignore viral hacks like garlic water, tying up a half apple 🍏, or other “root rescues.” If it’s dying, it’s probably too late. 😬 ☀️ Light & Placement: Where Should Orchids Go? 💡 Place near a window for natural light. 🌅 Mine faces northeast and sits on a homemade flower board in the kitchen. 📏 Keep it 3-6 inches from the window for ideal light exposure. 🌱 What’s Okay to Do? (Things That Help!) ✅ Repot when necessary – If roots are exploding out of the container, move to a bigger one! ✅ Trim bad roots and refresh the soil occasionally. ✅ Use the right planting mix ✅ Use breathable pots 🎯 Recap: The Secret to Reblooming Orchids! 💦 1/4 cup of water per week (no more, no less!) 📅 Stick to a watering schedule (every Tuesday works great!) ☀ Place near a bright window (but not direct sunlight!) ⚠ Avoid common mistakes! No weird internet hacks. 🌸 Let your orchids thrive & bloom again! 🌸 💬 Do you have any orchid tips that worked for you? Drop them in the comments! 👇😊

It has been snowing for two days. My kids listen to a Turkish cartoon song (Kukuli): 📌 It is snowing, it is snowing, 📌 In thick, fluffy flakes... Later in the song, they sing: 📌 Autumn to summer, spring to winter, 📌 Days flowed like water... The word “flow” struck me. What flows? Why does it flow? What happens when things stop flowing? Rivers flow to oceans. Collected water in dams flows through turbines, generating electricity. Traffic flows, energy flows, investments attract more money. Inside our cells, ions rush through microscopic channels, opening for only milliseconds to prevent depletion. Chemical reactions in our bodies flow in cycles, in perfect feedback loops—just like the glymphatic system clearing plaques from the brain during sleep (NIH source) . Beyond Earth, our planet flows through the galaxy, carried in an unseen current of time and space. Emotions flow too, filling hearts and spilling into words—songs, poetry, speeches that strike a chord and ripple through generations. The poet Necip Fazıl once wrote: 📌 Human it is, like water, flows fold by fold... 📌 Water moves down slopes, step by step, 📌 Yet my fate is to be thirsty on the slopes. There is beauty in flow—when things move as they should. But when they don’t? Vessels clog , nerves tense, energy/idea/breakthrough generation halts. Funding cuts stall research. And I wonder, how hard is it to keep things flowing? Maybe the only answer is this: Let it flow. Let it flow, please.

When I was a kid I wrote a mini song: My rose bowed its head When it wept. Its petals fell away When we parted. Source I used to sing this around the house. Yesterday my daughter was adding lines and music to my broken glass poem. I asked her to pay me my fair share if she becomes famous and rich with her song 😂 Thinking of my rose song made me think more about roses. What was so special about them? Is it the snuggled layers of velvety soft petals, smell, thorns, or the aesthetic beauty overall?  Why so many layers ? Is it more beautiful if it has more layers? Then I thought about where else I see “layers” in my life. We got my daughter’s hair a pixie cut today along with “layers”. With the approaching cold front, I should wear “layers” to keep warm.   When I look up at the sky, I see that the atmosphere has seven layers. When I look down at the Earth, I find that it has seven layers too. The soil itself has layers of living things as history, geological events and sandwiched time in it.  What about a human life? The training and accumulation of knowledge happens as incremental layerings. A baby first crawls, then stands up, then walks and then can run. Competency increases with each layer and experience. If I want to learn Bioinformatics, I can take 101, then 102 and so on. There is a strategic layering system to learn everything. Scientific or historical layers of knowledge gives strength to an argument. A small business can incrementally reach financial success, layer by layer; sale by sale.  Let me talk like a molecular biologist for a paragraph. When we think about regulation of gene expression, we see many many layers as well. To enable gene expression, you would need to untangle the heterochromatin to euchromatin to make it accessible. Then, a whole gang of regulatory proteins along with RNA Pol 2 will transcribe a gene. The nascent mRNA undergoes a series of modifications: capping, splicing , poly A addition. It will travel to the cytosol to get translated -- only if it does not get degraded by RNAses or by an acting microRNA . Another gang of proteins work with the magnificent ribosome to make the new protein, which is further subjected to a whole gang of post translations modifications to regulate it further. Phew! This is a whole semester class if you are interested in learning :)) Are there cases where having layers is not helpful? I could think of unnecessary bureaucracy. Especially if the additional paperwork is not adding value or regulation. Sometimes having too many layers would unnecessarily complicate things. Sweeping unresolved fights under a rug, making a pile is not good. Processing fights requires scientific methods and is essential to a healthy relationship. So maybe not all layers are good.  Getting back to the pretty rose— in the religious corner— it symbolizes Prophet Muhammed. There is mention of him smelling like roses and people expect to smell roses if they happen to have a metaphorical visit. Many religious songs refer to him as rose and he is depicted as a rose since drawing faces of Prophets is prohibited in Islam.  I was surprised to find many layered things in our lives and appreciated the beauty of roses once more. If you happen to pass by a rose, bend down and smell it. Maybe if you are lucky it might have a couple pearly water drops on it too. So naive… Like a drop of water Resting on a rose petal. Do not bow your head, Do not let your pearls fall— Like a cherry branch Swaying in the gentle breeze.