This is a short update to let you know that life has been a bit crazy in a great way! I’m combining both the training updates and the PhD updates into one newsletter. As you read through the next few bullet points, I am sure you will see why it has taken me a while to write an update.

Thanks for sticking with me.

Since January at work

• I finished a big chunk of my PhD work. I collected a large database of HCV sequences spanning all 8 genotypes and found some cool things in relation to genotype and viral load. I’ve submitted these findings to a conference. It was a lot of work, and I am really happy with this milestone.

• I finished the pilot of the viral forecasting group I was running.

• I am taking time off from my PhD to work at ARIA on the Sculpting Innate Immunity Opportunity Space. It’s cool to be able to work on something I care about at this scale, this early on in my career.

• I mentored a few people, and I hope they found it as helpful as I’ve found it rewarding.

  

Since January, in my training

• I completed my first Sprint Duathlon on February 1st.

• I completed the Cross Country Nationals on Feb 22nd (and suffered with shin splints after it).

• I completed my first Triathlon training camp in April.

• I completed my first Sprint Triathlon on May 10th.

• I competed in the British Sprint Triathlon Champs on June 8th.

• I competed in the BUCS Standard Distance Triathlon on June 21st.

• I am now nationally ranked in the UK, and you can see details here. To be listed in the same ranking as Beth Potter is quite wild.

• I am waiting to see if I have qualified for the EU Champs in 2026.

• I am focusing on Standard distance triathlons at the moment.

Naturally, all of this together has been both a bit overwhelming and extremely exciting. I unfortunately cannot say much publicly about my PhD or my ARIA work at the moment, so if I do post shortly, it will likely be about triathlon. For ARIA updates, you can fill out this form to hear more information.

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I apologise if this is not what you originally signed up for, and thank you for being a part of my journey!

Sofya

Top Learnings

• Learn from others' mistakes when possible. Especially from peers in your field.

• Consider taking an “intro” course for a fresh perspective on familiar topics.

• Schedule buffer time to absorb new intellectually intense material.

• Take a screenshot of your weekly plan and your post-week reality to help you find pitfalls.

• Attend an overview conference in your field every year or two to broaden your context.

A bit more about each of them

• Learn from others' mistakes when possible. Especially from peers in your field.

  • I interviewed eight current or recently graduated PhD bioinformatics/computational biology students about their workflow, paper writing coding and knowledge acquisition tips. I also asked them about how they got to where they are.

  • I learned a lot from the interviews and I think it’s helped me reflect and refine things I do in my work. Keep an eye out for the post on this!

• Consider taking an “intro” course for a fresh perspective on familiar topics.

  • I took a course on “How to Write an Academic Paper” which is offered by Oxford University. Unfortunately, the materials are not publicly accessible. I am working on writing up my notes from the course. I found it useful to streamline my writing and co-authorship delegation process.

  • The best test of this is putting into practice which will hopefully occur as I work towards the next few papers. Will keep you all updated.

• Schedule buffer time to absorb new intellectually intense material.

  • In January I identified topics I want to learn more about and grow in 2025. Most of them require intense mental capacity.

  • Overcommitment and time underestimation are still a weakness of mine that I am working on. I am a fan of the Planning Fallacy concept and focused on applying it more to myself this month.

  • For example for the “How to Write an Academic Paper” I scheduled four hours of prep time for the course, as we had required pre-reading and videos. I succeeded in my estimate — it took me exactly that amount. This made me a lot more prepared for the course itself and I was able to absorb the new material efficiently on the day itself. I plan to continue placing an estimate on various tasks and seeing how “off” I am to better calibrate myself.

    

  • This goes in line with being better at making accurate predictions. Here is a free app you can use to train yourself.

• Take a screenshot of your weekly plan and your post-week reality to help you find pitfalls.

  • I have started doing this, in conjunction with the energy calendar practice by Sahil Bloom which I’ve been doing for around a year already.

  • This is also helping me with better time calibration. The idea is simple, take a screenshot of your calendar on Monday and one on next Monday to see how you used your time. Think about where there were missed expectations etc.

  • I’ve found that even taking the first screenshot is effective as it makes me reconsider my planning as soon as I mentally know it will go on record.

• Attend an overview conference in your field every year or two to broaden your context.

  • I attended the Festival of Genomics and Biodata (aptly shorthanded to FOG) in London on January 29th and 30th.

  • Aside from the infectious atmosphere of the conference, I also found it extremely useful. I learned about the different types of omics:

  • My favourite panel was “Building Upon the Strength of the UK’s Healthcare Data - Pushing Research Towards the Next Frontier” with speakers:

    • Ellen Thomas: Chief Medical Officer, Genomics England

    • Kate Evans: Executive Director of Researcher Data and Product, Our Future Health

    • Naomi Allen: Chief Scientist, UK Biobank

    • Nathalie Kingston: Director, NIHR BioResource

  • They spoke about the future of how genomics data will be accessed, shared with researchers, and integrated into clinical care.

  • They also outlined some of the current challenges: lack of standardisation between the different institutions, the legal burden of releasing medical records being on the GPs and the need for public dialogue to progress on to ensure more well-informed public participation.

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101 Guides I might write

• I have previously written Bioinformatics 101 and I also greatly admire the Codon Guide to Synthetic Biology and MIT’s How to Grow (almost) Anything course.

• I am considering writing the following guides:

  • Weekly Planning 101

  • How to write an academic paper 101

  • How to make a good visualisation 101

  • Should you do a PhD 101?

  • PhD Applications 101

  • Omics’ 101 (a BRIEF overview of the different ones)

  • Genomics 101

  • Wet Lab Work 101

• Let me know which ones you would want to write, or if there is one I have missed by replying to this email, leaving a comment, or sending me a DM on Substack.

Leave a comment

Papers

• Nature’s Index of Neglected Diseases (link)

• UKHSA launches new metagenomic surveillance for health security (link)

• Multi-Omics Playbook (link)

• Toward a Radically Simple Multi-Modal Nasal Spray for Preventing Respiratory Infections (link)

  • If you want the PDF DM me

• The BIOME study: a randomized controlled trial in healthy adults (link)

  • I signed up for updates from this pre-print

Links

• 30 probably isn’t the magic number (link)

  • How many vegetables you should eat per week

  • A nice read and explains where the science comes from

  • I signed up for updates from this pre-print (link)

  

• The case against morning yoga and routines (link)

• Simulation Clicker (link)

  • See how much time you waste on this.

  • I spent five minutes, but would could have also easily spent more than thirty.

• FixOurPics (link)

  • Hilarious and well-made.

  • Two guys trying to build their optimal dating profile by having people upvote. I think more should honestly do this before setting up their online thing if they have the time….

• Pastry World Championships (link)

  • Incredible that this exists

• Are "Dragon Babies" Bumping up China's Birth Rate? (link)

  

  • Lunar New Year (link)

  • Year of the Snake (link)

• Not yet gods (link)

  • Something I try to remind myself of from time to time.

Biotechnology

• Artificial Wombs: Revisiting the To Be Born in a Bag concept with a 2025 update on technological progress. (h/t Asimov Press)

• Menopause Research: Examining the current state of the science, key research gaps, and future opportunities. (h/t Erika Alden DeBenedictis and Foresight Institute)

• Point-of-Care Testing: Investigating their promise as a two-in-one solution for tackling pandemics and antimicrobial resistance. (h/t Akhil Bansal)

• Op-eds on any breakthrough/announcement eg Mirror Life

Meta

• Big Bets in Pandemic Preparedness: Highlighting the current transformative technologies and their potential impact on global health resilience. Review article.

• Pandemic Preparedness and Antimicrobial Resistance (AMR) Intersection: Investigating how these two critical issues overlap and influence each other. Policy focus.

• HIV/HCV/HBV Infection Prevention: Exploring whether infection prevention efforts have broader knock-on effects that improve pandemic preparedness.

• Sanitation as a Linchpin: Examining the role of sanitation as a foundational pillar for both global health development (GHD) and pandemic preparedness.

• Global Health vs. Pandemic Preparedness: Analysing trade-offs and shared challenges in these interconnected fields. Could some strategies “kill two birds with one stone”? Policy focus.

• Buddhism and Biochemistry: Reflecting on philosophical and scientific intersections between these seemingly unrelated domains. Ideally, this article would be written with three people: a Biochemist a Buddhist and me as moderator.

Athletics

• Immune Changes in Athletes: Investigating how high-intensity training and endurance sports impact the immune system. (A topic of personal curiosity!)

• Immune Changes in Extreme Environments: Exploring how polar or mountain expeditions affect our bodies, particularly in cold and high-altitude conditions.

• Physics in Sports: Exploring the science behind sports, such as what goes on in velodromes or swimming fins. A review article with a fun, engaging tone and diagrams.

• Biology of Female Elite Athletes: Interviewing an elite female athlete or sports performance researcher (e.g., Dr. Stacy Sims) to discuss the unique biology of female athletes.

• Open: Any topic combining science and athletics that fits within this broader theme.

  

If you’d like to co-write one of these ideas with me please reach out. If you are a reader and there is something you would like me to write about please let me know. I will continue to post my monthly PhD and Training updates for the foreseeable future, while I still feel that they are in line with my goals. This blog will not have any ads or a paid subscription feature in 2025.

• PhD Milestones can be fun (in the end…)

• I need to plan for conferences in advance

• Taking a week to prepare for next year has been very useful

• I was ready for a break

A bit more about each of them

• PhD Milestones can be fun (in the end…)

  • I passed my Transfer of status. My university has three exams: Transfer Viva, Confirmation of Status and the Final Viva. They are about a year and a half apart each. I am now a “PhD Candidate”.

  • The exam consisted of me presenting my research to a panel of professors and submitting a report beforehand. I still experience anxiety presenting my work to people “higher than me” in academic status. Something to be aware of in the coming year.

  • Phew. Only two more vivas left. Still a long road ahead, but still.

• I need to plan for conferences in advance

  • 2025 is already filling up with conferences, plans etc.

  • Balancing attending academic training and meetings with my race calendar is challenging, but is also a fun problem at the same time.

  • Another problem that sometimes arises for me is “overplanning” so I am trying to find a good balance. The comic below summarises my thoughts exactly.

  

• Taking a week to prepare for next year has been very useful.

  • After my transfer, I took a week to catch up on papers and explore things more creatively.

  • I didn’t put pressure on myself to “produce” anything useful. This nicely aligned with the release of the Mirror Life paper and allowed me to respond. I also had a burst of creative energy and came up with another project idea for this year. If you like me, are interested in forecasting and biology, this might be of interest to you. Shoot me a DM.

• I was ready for a break

  • I am currently on holiday and I have been enjoying my time off and spending time with my family.

  • I’ve had lots of interesting reflections while being back in Russia about my personal life, academics, politics and mainly about the privilege I hold to be able to travel between these places during a time of geopolitical upheaval.

  • Thankfully I have recuperated, though the constant craving for a falafel wrap remains since August 2023.

  

Paper Corner

• Man arrested after high-value cheese theft - a truly British story (link)

• Graphs from The Anxious Generation (link)

• Counterarguments and then counter counter-arguments about social media and mental health (link)

• Why play is important to maintaining mental health. Relevant to both kids and adults IMO. (link)

• Even the Nordic Nations have a mental health epidemic (link)

• Alcohol and links to seven types of cancer. If you need yet another reason to cut down your alcohol consumption. (link)

Counter Update

You have two hands, both with the same design but mirror images of one another. This means they require different accommodations: for example, your right hand has a hard time using left-handed scissors.

This phenomenon exists in biology and chemistry and is called “chirality.” All molecules—such as DNA, RNA, or proteins—have evolved with one configuration, one chirality. But last week, scientists published a paper and a technical report showing it might be possible to engineer mirror versions of respective molecules.

This has good and bad potential. Mirror drugs could be harder for natural enzymes to break down, prolonging their effects (like a left-handed person trying to use right-handed scissors). On the other hand, it’s also possible that they could evade detection by our immune system, disrupt existing ecosystems, or introduce unforeseen molecular interactions.

In this article, we discuss the benefits and risks of mirror life and the challenges of a ban. We provide alternative recommendations for responsible approaches to the research. We also highlight the organisations currently working in the space, and propose practical steps, such as strengthening biosafety networks, implementing detection mechanisms for misuse, and introducing policy addendums to condition funding on meeting containment standards.

Mirror Life: Fire from Prometheus, or Pandora's Box?

Mirror organisms, isolated from natural life due to their opposite chirality, could offer containment advantages but also pose risks like immune evasion and ecosystem disruption. The recent paper in Science as well as the accompanying technical report outline the following pros and cons.

Possible Benefits:

• Possible applications in creating long-lasting, nonimmunogenic therapies

• Advancement of synthetic biology and molecular engineering techniques

• Potential scientific insights into fundamental biological processes and the development of a new understanding of molecular chirality

Possible Harms:

• Potential to cause lethal infections across multiple species

• Ability to evade immune systems in humans, animals, and plants

• Risk of uncontrollable environmental spread

• Resistance to natural predation and antibiotics

• Possibility of irreversible ecological damage

• Limited practical benefits compared to extreme potential risks

• Difficulty in developing effective countermeasures

• Potential for accidental or intentional misuse

Challenges with a Ban

A ban is not entirely feasible in the first place. For a ban to be impactful, all countries conducting this research must be in agreement. This is unlikely for two reasons:

• “Mirror life” is still hypothetical, so leaders may remain unconvinced of the need for a ban. Just like when scientists pursued the Manhattan Project despite believing for a brief time that the atomic bomb could set the world on fire, many countries may be willing to roll the dice on mirror bacteria.

• Countries have to trust that nobody will secretly continue research. The trust would require intrusive verifications. Such efforts in the Biological Weapons Convention have stalled for decades. It’s difficult to believe a ban on mirror bacterium will succeed where the UN has repeatedly failed.

• Even if feasible, a ban comes with inherent risks. Namely: scientists dedicated to their work might move to other countries with lax restrictions to continue their research, making oversight impossible. Walter Gilbert did this with his recombinant DNA research, dodging U.S. restrictions.

• Similarly, CRISPR technology has sparked ethical controversy over human germline editing. The U.S. and EU have enacted various bans on this kind of research (such as in the Dickey-Wicker Amendment, or under the Oviedo Convention). But CRISPR research continued elsewhere, such as in 2018 when Chinese scientist He Jiankui used the technology to allegedly create genetically edited babies resistant to HIV.

Alternate Recommendations

Current biosafety and bioethics frameworks may already mitigate risks from Mirror Life, thus a more viable alternative to a ban alternative would be either strengthening current frameworks or creating a specific mirror life oversight body.

• Strengthening FSAP or DURC in the US: The U.S. Federal Select Agent Program (FSAP) or the Dual Use Research of Concern (DURC) regulatory programs are examples of legislation that require certain biosafety levels of particular kinds of research (usually BSL-3 and 4). Novel legislation could make federal funding for mirror life conditional upon meeting heightened biosafety standards, or could even outright demand it irrespective of funding. This way, safety, containment, and oversight are promoted without pushing research underground.

• Create funding incentives to limit research to only safer organisms: Adjusting funding to incentivize companies to pursue mirror-life research in organisms with low generation times or that have difficulty replicating in natural environments (such as extremophiles, halophiles, spore-forming bacterium, etc.) could promote normal research progress while mitigating public health risks in the event of containment breach. For example, some scientists conduct research solely on “auxotrophs” that cannot survive outside of the lab to prevent containment breaches.

• Create a specific monitoring body for Mirror Life research: The Mirror Biology Dialogues Fund supports global conversations on the risks and governance of mirror life by organising events such as workshops, seminars, and symposia. Its goal is to foster collaboration among researchers, policymakers, and stakeholders to address challenges and develop practical frameworks for the responsible oversight of mirror biology. This fund is a first step. A specific monitoring body with expanded capabilities could also be set up.

• Create a mirror life safety and awareness conference: There are biosafety conferences that promote brainstorming and networking, such as the ABSA conference. White the MBDF is hosting side events at conferences but is not funding standalone events on mirror life. Hosting a conference aimed at biosafety and responsibility for mirror life that invites regulators and innovators specifically could promote international consensus, making a ban more likely in the future, while also spreading good ideas about containment and responsible research practices. There also could be downsides to such a public event as this, thus the benefits versus the risks of such an event should be further considered.

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Conclusion

While the realization of mirror life certainly possesses inherent risks, trying to unilaterally ban research would be ineffective if not self-defeating. This is due to the high unlikelihood of achieving needed consensus, as well as the risk of backfiring by sending research underground and away from oversight, as demonstrated by past instances with the Biological Weapons Convention. Therefore, we should get creative (and fast) on how to shepherd this research into more controlled pastures that guarantee safety moving forward.

We believe that the Mirror Biology Dialogues Fund (MBDF) is leading the way in creating spaces to further the dialogue around mirror life. The International Biosecurity and Biosafety Initiative for Science (IBBIS) and the Global Biological Standards Institute (GBSI) also seem well-placed to act further in this area.

Instead of focusing on proliferating a ban, we recommend:

• Strengthening existing biosafety networks and warning systems

• Identifying detection mechanisms for mirror life misuse and ensuring that the relevant stakeholders are implementing them in their networks.

• Writing white papers for addendums to FSAP and DURC where they limit, revoke, or make the funding of this research conditional upon meeting certain containment standards.

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Top Learnings

1. Storing and organising your papers is challenging (very much a work in progress)

2. How to budget enough time for submitting data in academic settings

3. Reading papers twice helps me retain content better

4. Using an app blocker on my phone helps me focus

5. Visualising data well is an art

A bit more about each of them

1. Storing and organising your papers is challenging (very much a work in progress)

   1. I am working towards my first milestone exam (coming up in December) of my PhD. Oxford has three checkpoints: Transfer of Status, Confirmation of Status and the final Viva. For this, I’ve had to get my papers a bit more organised.

   2. Currently, I have a folder in Zotero (desktop app) for each chapter in my thesis and sub-folders of themes within it. I also use Research Rabbit to find related papers and authors.

      

   3. When writing a paper, I create a new subsection with the respective title. Currently, I have been writing in Google Docs with the Zotero plug-in, but I am likely to switch to Overleaf next year. Thanks, Laura and Qijing for the suggestion.

      

   4. What programs do you use for your papers and for writing? Please reply to this post in a comment or through DM. I’d love to know.

2. How to budget enough time for submitting data in academic settings

   1. This one I am still not well-calibrated on this. I think that’s normal and takes academics a while (I think!!) Getting author permissions is tricky and budgeting enough time for revisions and reviews.

3. Reading papers twice helps me retain content better

   1. I read it first with a quick glace and take some notes and then I come back to it a few weeks or months later and read it again in a chunk with the other papers of that topic. Eg I am currently re-reading all the codon usage papers (see the screenshot above) and seeing if I can form any new connections.

   2. Maybe once I have enough context knowledge this re-read won’t be necessary, but for now it has proved instrumental. The second re-read makes me only choose the relevant papers, which also helps me cut down on the volume.

4. Using an app blocker on my phone helps me focus.

   1. I use Opal. I block my phone 10:30pm to 7:00am and block Whatsapp from 7:00am to 9:30am. I also do 2hr or 1.5hr focus blocks during the day and they really help me. I think I can I try to be more consistent with them too.

   2. You can try it for 30 days free.

   3. I also use OneSec they have a free version and this is for social media specifically.

5. Visualising data well is an art

   1. I went to a workshop with Charlie from OWID and got some really useful tips on making effective visualisations. If I get permission I will write up a public version of the notes that I took during the session. They were super useful.

   2. I am a HUGE fan of OWID and their mission: Research and data to make progress against the world’s largest problems.

      

   3. Look at the use of the descriptive title, colour, white space and annotations! Read the article here.

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Paper Corner

1. Probabilistic weather forecasting with machine learning (link)

   1. GDM released a new model for better weather prediction

   2. I was just thinking about how possibly we haven’t progressed in that area as much recently and then BAM!

2. The Effect of Yoga Practice on Labor Pain: A Systematic Review and Meta-Analysis (link)

   1. 660 pregnant women (average ages of 25–35).

   2. 7 RCTs, 1 non-randomised CT and 1 observational study

   3. Pain intensity was measured using a visual analogue scale.

   4. There seems to have been a reduction in labour pain, but the variation in methodology in the studies is quite high.

3. Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage (link)

   1. A paper by one of the people assessing my Transfer of Status.

   2. RNA viruses have distinct nucleotide signatures.

   3. The bias was particularly enriched in unpaired, single-stranded regions of the RNA genome. This could be due to:

      1. RNA stability - eg A and U destabilise the paring, leading to more loops

      2. Immune evasion: maybe the nt composition in those regions helps the virus evade detection by pattern recognition receptors (PRRs)

   4. This is relevant to my research as the virus that I am studying also might have some similar trends.

As always if you have issues with accessing a paper DM me or send me an email.

Counter Update

Papers are up! Coding is going steady. No complaints this month.

Thank you for reading!

Sofya

Top 5 Learnings

1. Creating stricter criteria to narrow grant and opportunity selection is vital.

2. My lack of immunological context is the limiting factor again, not my coding ability.

3. I am finally not burnt out.

4. Nice over-ear headphones are worth it.

5. Takes more than two hours to solve on a “fresh brain”? Ask for help.

A bit more about each of the 5

1. Creating stricter criteria to narrow grant and opportunity selection is vital.

   1. I’m fortunate to be at Oxford, surrounded by a network of supportive colleagues who share many grants and opportunities with me. But with so much coming my way, it’s a challenge to narrow down which opportunities align best with my goals.

   2. Warren Buffet said it well: “The difference between successful people and really successful people is that really successful people say ‘no’ to almost everything.”

   3. I am working on figuring out exactly what kind of things I want to say yes to.

2. My lack of immunological context is the limiting factor again, not my coding ability.

   1. From January 2024 to April 2024 one of the reasons that I struggled with a project because I didn’t have sufficient background knowledge in immunology. I wasn’t able to develop that knowledge quickly enough to not hinder the research process. I have now reached a knowledge gap once more, where I have technical results, but I am unable to fully independently develop a plan for the next steps, due to a lack of surrounding context in immunology.

   2. The plan is to read roughly ~1 paper per day for the next month to build up more contextual knowledge about innate immunity and the pharmacokinetic interactions that happen in HCV drugs. I will provide an update next month on how it went.

3. I am finally not burnt out

   1. The current research pace seems sustainable.

   2. I used to take trips to “escape” work which was a clear sign of things being out of balance.

   3. I am still overcommitting, however I think this is slowly improving. It’s not linear and sometimes I feel that it’s one step forward two steps back with my mental health.

4. Nice over-ear headphones are worth it.

   1. I got some for my birthday. I am wearing them right now and jamming out to Alive by Sia. They help to reduce stimulation. Other things that I have entered into my Spotify this month are “Energetic Classical” and “Electro Classical”.

5. Takes more than two hours to solve on a “fresh brain”? Ask for help.

   1. I was encountering an error when making my forest plot diagrams - see the image above for a reference of what it is. Yes, it’s light green just like the matcha!

   2. Turns out I needed to add a bunch of spaces in one of the lines to fix it, which my lab mate told me about after about ~5 seconds of looking at my code. Could I have avoided this and asked them sooner? Yes. Yes I could have.

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Paper Corner

1. Breakthroughs in hepatitis C research:

   from discovery to cure (link)

2. Health Benefits and Chemical Composition of Matcha Green Tea: A Review (link)

   1. Had to keep with the light green theme for this newsletter! I just like matcha …

3. Introduction to forestploter (link)

   1. The page that helped me with forest plots. Not a paper.

Counter Update

Mistakes weren’t as useful anymore, as I have significantly decreased my “error” rate, which didn’t change much from month to month. That's a good sign, I guess. Adding a metric for papers now.

Thank you for reading!

Sofya

1. I didn’t prioritize my mental well-being over results and took too long to quit a project I wasn’t in love with.

2. I didn’t ask for help from my supervisors soon enough after a personal or work-related problem arose.

3. I didn’t start doing the “hard thing” every day sooner, such as reading a paper I was avoiding, or writing a few lines of code to get started.

4. I avoided presenting my research and asking for feedback from others early on. This led to me getting stuck in idea silos and having longer feedback loops.

5. I didn’t start marking the 1:3:5:10 priorities of my days and sticking to them until March 2024.

6. I put too many things on my plate. I still do. I am still working on this one.

7. I didn’t realize how much of a positive effect team sports would have on my mental health vs individual training.

8. I avoided fixing a small problem in my work and mentally outsized it to be much bigger than it is, wasting 2-5 days. I am now trying to decrease this feedback loop.

9. I didn’t back up my data often enough. Oops.

Of course, these are still a work in progress. Just today I had to force myself to write out my 1:3:5:10 and sometimes I still avoid reading “that” paper, even though once I do it starts making much more sense.

What is 1:3:5:10? It’s a prioritisation technique I use where I write out the one most important thing I have to do today. Then I write out the one most important thing again and add two secondary goals under it. Thus I write out the one most important thing four times, reinforcing it in my brain. Then I work down the list starting with the one thing. It works well. FYI exercise usually comes in my top three for the day as it helps “unlock” my ability to do other things efficiently.

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I welcome questions, thoughts, and discussions about these.

Sofya

Top 5 Learnings

1. I now know #that-feeling-when-you-have-a-new-finding even if the finding is very small.

2. A new virus, Saruyama virus (SAYAV), was detected in Japanese ticks using next-generation sequencing (NGS).

3. Meditation is working I think.

4. If you present enough it gets easier (even in academia) and your anxiety almost goes away.

5. DAGs are my friends and I need to be less scared of them.

A bit more about each of the 5

1. I now know #that-feeling-when-you-have-a-new-finding even if the finding is very small.

   1. I think I might have gotten some results, and my supervisor hasn’t disagreed with me yet. It’s been a few weeks too. It was very rewarding to finally get the graph to work on a technical level. It seems to (hopefully) work on a scientific level, but I’ll let my thesis committee decide that.

2. A new virus, Saruyama virus (SAYAV), was detected in Japanese ticks using next-generation sequencing (NGS).

   1. I got to attend HCV-Flavi-2024. It was my first academic conference on Hepatitis C. It was really interesting to meet people for who this research is their life’s work focus.

   2. I went to a talk with Ryosuke Suzuki who helped to identify a new virus SAYAV using NGS. You can read their paper here. If you have issues with accessing it please DM me.

3. Meditation is working I think.

   1. I noticed this as I no longer need to put my practice at the start of my day. Sometimes I find myself being naturally mindful during the day. I am also able to identify feelings of overarousal and I now don’t immediately label them as negative. Eg instead of immediately defaulting to “I am anxious” I am sometimes able to investigate the feeling and it ends up being “I am excited” or “I am excessively hungry”.

4. If you present enough it gets easier (even in academia) and your anxiety almost goes away.

   1. In September I presented my work twice. It’s still nerve-wracking, however, I am slowly developing a better understanding of what I am doing and why I am doing it. This makes me a little less hesitant to stand up in front of a room of academics. Who knew that practice helps? I am proud of myself for putting myself out there and slowly rewiring my brain from the fear response around this topic.

5. DAGs are my friends and I need to be less scared of them.

   1. A directed acyclic graph (DAG) helps to provide a visual representation of the causal relationships between a set of variables. I’ve been using DAGitty to make mine. I procrastinated a LOT in making my first one and this slowed my analysis. The reason? Maybe I labelled them as “too complex” for me. Any real good reason? Not that I can think of.

   2. Lots of great resources on them here.

      

Paper Corner

1. WHO HCV 2024 report, is pretty accessible to non-scientists and you can skip to the graphs only (link).

2. New SAYAV virus discovered in ticks (link).

3. Scientists successfully transplanted lab-grown insulin-producing cells into a patient, restoring normal blood sugar control without external insulin. This approach met safety standards and showed promising results one year later (link).

Counter Update

Haven’t coded nearly enough in September, lots of days away, conferences and report writing. Hoping to change this in October. I have finally surpassed the # of mistakes with the # of days coded. Interesting that this was the same month that I got results.

Thank you for reading!

Sofya

Top 5 Learnings

1. It’s hard to estimate how long things will take

2. Scheduling time to step back and think about the bigger picture is crucial

3. Prioritization is one of my main challenges currently

4. Un-learning gender stereotypes

5. I needed to brush up on my maths

A bit more about each of the 5

1. It’s hard to estimate how long things will take

   1. I have attempted to make a plan for the next six months.

   2. I am using the Todoist free version, though it is a bit glitchy sometimes on the Mac Desktop app.

   3. It’s hard to predict whether the research milestones that I have planned for myself are going to take one week or three months, as my ability to solve things varies highly.

2. Scheduling time to step back and think about the bigger picture is crucial

   1. I spent a while focusing on fixing bugs and technical issues, forgetting the bigger picture of what I was doing. Recently I had a useful meeting with one of the postdocs in my group where they helped me think about my study design and why I am doing what I am doing.

   2. I don’t think I have a great grasp of this yet, but I am working towards it.

   

3. Prioritization is one of my main challenges currently

   1. I struggle with getting the “right” things done in a day.

   2. This has been a consistent challenge for me. I’ve tried the Eisenhower Matrix, and I’ve tried the One Thing method. I’ve adopted the 1:3:5:10 method (my version which I will explain only if it it reliably works).

   3. For example, I am writing this newsletter as it was an open tab on my computer from the previous day when I opened my computer to do something else self-awareness-am-I-right? If anyone has suggestions regarding this please reach out!

   4. While writing this I found this blog with other ideas, maybe I should try them as well.

4. Un-learning gender stereotypes

   1. I read two books in August - The Gendered Brain and Not Just For The Boys

   2. I had a lot of negative stereotypes about my academic and sporting abilities that were ingrained in my brain. I am currently trying to actively notice sexism and unnecessary gendering in my life. I am unsure where it will lead in the long run. Currently, it has helped me gain more confidence in my scientific ability.

5. I needed to brush up on my maths

   1. I am learning about linear algebra and game theory. Some of this will end up being useful for my research.

   2. The main update from learning #3 is that I am no longer self-limiting or self-selecting against reading the more “challenging” articles or papers.

Paper Corner

1. Cocoa consumption can improve markers of cardiometabolic risk (link)

   1. n = 1986

   2. No effect on body weight, BMI, waist circumference, triglycerides, HDL-c and HbA1c.

   3. Some reduction in total cholesterol, LDL-c, fasting blood glucose, SBP and DBP.

   4. So there might be protective effects on cardiometabolic risk markers.

   5. I love this study as it validates my unreasonable love for cocoa

2. Effect of Saffron Versus Selective Serotonin Reuptake Inhibitors (SSRIs) in Treatment of Depression and Anxiety: A Meta-analysis of Randomized Controlled Trials (link)

   1. What is saffron?

   2. n = 416 for depression analysis and n = 240 for anxiety analysis

   3. The paper concludes that there isn’t much of a difference between saffron and SSRI effectiveness, with saffron having fewer adverse side effects.

   4. How much should one take? Most of these studies had the dosage at 30mg per day. Yes, you can buy this in your local supermarket.

3. Effects of intensive lifestyle changes on the progression of mild cognitive impairment or early dementia due to Alzheimer’s disease: a randomized, controlled clinical trial (link)

   1. n = 51 and n = 49 that finished the study

   2. You can see the supplements, the exercise guidelines and the type of diet that they followed in the methods section

   3. There has been a statistically significant microbiome shift in the test group, which is cool

4. Timing matters? The effects of two different timing of high protein diets on body composition, muscular performance, and biochemical markers in resistance-trained males (link)

   1. Love a study only on men (sigh)

   2. n = 40 but only n = 31 finished

Counter Update

I am trying to uphold the following main principles in all areas of my life: 1% small improvements add up over time. The original article by James Clear is here.

Thank you for reading!

Sofya

Top 5 Learnings

1. Reviewing my friend’s papers is way too fun

2. Hepatitis A spread in Gaza

3. The ComplexHeatmap package is great

4. How to run logistic regressions (in progress)

5. How to balance many different research threads (in progress)

A bit more about each of the 5

1. Reviewing my friend’s papers is way too fun

   1. I’ve had the pleasure of helping one of my friends edit their thesis recently.

   2. Below is a joyful expression of my love for pretty figures, *aesthetics*

      

2. Hepatitis A spread in Gaza

   1. I learned about the widespread outbreak of Hepatitis A in Gaza

   2. What is Hepatitis A?

   3. News articles about it here and here. Numbers are pretty poorly documented which is very understandable.

   4. After about ~30 minutes of looking into coordination efforts, I couldn’t find a responsible organisation. The closest I found were the IMC and OCHA. If anyone has any leads, please let me know via DM or the comments.

3. The ComplexHeatmap package is great

   1. ComplexHeatmap is fabulous for … you guessed it … making heatmaps

   2. For more packages see my Bioinformatics 101 post

      

4. How to run logistic regressions (in progress)

   1. I am learning how to run logistic regressions and how to account for the different confounding variables. It’s tough work (for me!). I will post an update about this hopefully next month.

   2. I’m learning about principal component analysis and how to interpret the outputs.

5. How to balance many different research threads (in progress)

   1. I have some general graphs about my dataset that I am making, logistic regressions that I am running (not particularly successfully atm) and a theoretical research thread that I can also pull on to unravel the explanation for the data analysis.

   2. I spend around 25% on the general graphs, 50% on the logistic regressions and 20% on the theory. Around 5% is reserved for general anguish and not knowing what to do, which is quite lower than in my previous projects so I take this as a win.

   3. I think balancing these will become harder as the PhD progresses and (if?) I add more projects to my repertoire. Any suggestions on this would be appreciated.

What I’m reading

1. Paired Ends has started writing again. If you enjoy my posts, you will likely find what they write interesting.

   

2. Clinical and biological insights from viral genome sequencing (one of the famed *banger papers* as seen in the screenshot above)

3. Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes

4. Base-stacking and base-pairing contributions to thermal stability of the DNA double helix

5. I recently finished Insight by Dr Tasha Eurich, I recommend this book (4/5).

Counter Update

More coding! Less mistakes related to poor anxiety management or not sharing when I have a problem with my supervisors. I am trying to be careful to lean into noting which areas I have a lot to improve in.

I will end with a fun graphic from Mounika Studio. I enjoy her work and I think this is a great visualization of how it can sometimes feel like we are going in circles, when in fact we are progressing. This is me talking to myself of course as I edit the same graph for the nth time ….

As I sit, slightly delirious from an accidental lack of sleep I am swiftly finishing this post after realising that we are in fact in July already. Welcome to my ramblings and takeaways from June.

Top 5 Learnings

1. My current project is 70% thinking 30% coding

2. Caffeine is not my friend

3. Summer and time outdoors are incredible

4. Stay in your (chronotype) lane

5. Ask for help sooner (force yourself if you have to)

A bit more about each of the 5

1. My current project is 70% thinking 30% coding

   1. As a heuristic: last week I spent ~4 days actively and passively thinking about how to do the next step of my project and only ~2 hours coding the next step.

   2. I think this is currently due to my lack of conceptual understanding of the methodology, I am curious to see if this time gap will change as the months go by.

2. Caffeine is not my friend

   1. I uh, accidentally (or without thinking really) had a full espresso shot and quite little food. I can confirm that I was wired and anxious for about 4-5 hours afterwards. I will not be repeating this same procedure. For all my coffee lovers out there able to tolerate more than 1 espresso shot I will watch you in awe from my hiding hole.

3. Summer and time outdoors are incredible

   1. Running, climbing, dancing and walking outside, have done wonders for my mental health. I am hoping to keep at least a lunchtime walk and stretch as late throughout the year as I can.

   2. I have also spent less time on social media since my creativity void is being filled by this blog

4. Stay in your (chronotype) lane

   1. Staying up until 3 am does not work for me, Oxford balls, late flights or pure vinted scrolling are all on the list of “bad” excuses.

   2. I find it quite hard to get my sleep schedule back to normal afterwards.

5. Ask for help sooner (force yourself if you have to)

   1. Scheduling meetings with my supervisor and asking the nice postdocs in the group for help has been extremely useful.

   2. This is a public reminder to myself to do this more.

Random fun highlights:

• talking to my friend about his master’s thesis

• bonding with my lab mate over (possibly) breaking the coffee machine. At least I now know where the decaf grounds go (maybe maybe maybe)

• another one of my friends made a presentation to describe their ML research with a cake analogy

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Paper Corner

• An overview of hepatitis C virus genotypes and its control

  • Shaving accounts for 14.5% of HCV transmission. What?

• Not a paper but the talk by David Robinson from the Bill and Melinda Gates Foundation was interesting

Counter Update

• I will post the counters (made with Indie) so that there is a reference for the number of mistakes vs days that I’ve coded etc.

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I am currently finding my voice online, as well as trying to stay afloat during my PhD.

Top 5 things I learned

1. Switching projects - easier than I thought

2. Two weeks of a proper break can make a huge difference

3. Reading a paper ≠ reading a paper

4. If you think you might not be in a flow state = you’re probably right

5. Having an indie counter in my notion for some reason is really motivating

A bit more about each of the points above.

1. Switching projects - easier than I thought

   1. I switched from a wet lab to a fully computational project. I am now working with Azim Ansari on Hepatitis C clinical data analysis.

   2. A lot of the immunology fundamentals I learned in my previous project are still very useful and have made the transition smoother.

2. Two weeks of a proper break can make a huge difference

   1. I love having time to read, run, sleep and see friends.

   2. Will have another trip like this in the calendar soon.

3. Reading a paper ≠ reading a paper

   1. I am slowly developing my system of reading and processing papers

   2. Once I have it a bit more figured out and streamlined I will share it

4. If you think you might not be in a flow state = you’re probably right

   1. I knew it, all the signs were there, and yet I took about ~2 months to switch

   2. I guess I have this tendency in other areas in my life

5. Having an indie counter in my notion for some reason is really motivating

   1. I made these using Indify

   2. I have two counters: the number of days I’ve been coding and the number of mistakes I’ve made in my PhD

   3. I am sure at least one of these counters will get high!

   4. If you have ideas for other counters I should have - let me know

Thank you for reading!

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