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Antibiotic resistance: this is what happens when you use antibiotics

Can you believe there was a time when tuberculosis was the number one killer disease in the world?

At only 43, Louis Braille, the French educator who invented the Braille system for the visually impaired, died of TB. And so did my favorite novelists Jane Austen and Emily Brönte, at only 42 and 30, respectively. If you are into music, you probably know Xian Xinghai, Carl Maria von Weber or Giovanni Battista Draghi. None of them reached 40.

Things changed with the discovery of antibiotics. No one freaks out when they get an infection. You can go to a local clinic and get an antibiotic. Antibiotics are so effective that most people think the doctor is not capable if they don’t prescribe them.

And that’s the problem.

If we’re not careful, by 2050, the world will return to that era where people died from simple wounds. Two weeks ago, my young brother complained about his ear. He visited a local clinic and was prescribed penicillin. A week later, nothing changed, except it was now more painful. He returned to the clinic and was given amoxicillin as a replacement antibiotic. Nothing changed.

I urged him to return to the clinic and he was finally referred to an otologist – ear doctor. The otologist asked him to take a different antibiotic, which is rarely prescribed. Today, he’s now a lot better. What happened?

My young brother’s ear was probably infected by a pathogen that was resistant to penicillin and amoxicillin. In 2015, antibiotic resistance was responsible for more than 700,000 deaths worldwide. That is almost twice the number of people killed by malaria, 438,000, in the same year. Compare that with a million killed by AIDS in the same year.

But it gets worse. It is possible that most of the people killed by malaria and AIDS it’s because of antibiotic resistance. It is not surprising then that if we don’t act now, antibiotic resistance will be responsible for the death of more than 50 million people in 2050.

In this article, I will talk about antibiotic resistance and what we can do about it.

Antibiotics in the environment

 

Image by Public Health Ontario

 

What happens when you take antibiotics? Up to 80 % of the antibiotics, you take go straight to the toilet. Your body only uses 20 %. But guess what? These antibiotics we flash in the toilet end up in the environment. Do you know why? Because most of our wastewater treatment plants were not designed to remove antibiotics. From there things get bad.

There are some bacteria in the environment and some of them are resistant to the antibiotics. When the antibiotics enter the environment, they kill the bacteria that are not resistant leaving behind the ones that are resistant. The resistant bacteria will now have less competition for food and they will multiply. So, when antibiotics enter the environment, they will result in an increase in antibiotic-resistant bacteria.

How to reduce antibiotic resistance

So then, what can you do? You remember I said when antibiotics enter the environment, the kill bacteria that are not resistant leaving behind the ones that are resistant. This means we need to reduce the amount of antibiotics that enter the environment. You and I need to reduce the amount of antibiotics we use.

Not every disease requires an antibiotic. When a doctor prescribes you an adequate, you should probably ask if it is possible to use a different medication. There numerous drugs that are an excellent replacement for antibiotics.

Let me repeat – not every disease requires an antibiotic. I know many people think if a doctor doesn’t prescribe them an antibiotic, then she is not a good doctor. Antibiotics are miracle medicine if not overused or misused. Otherwise, we will head back to the era that took away my favorite novelists.

This has nothing to do with antibiotics but I just have to say it – I have read everything, book or collection of letters, written by Jane Austen. I am her African superfan!

Image by Drew Hays

Early career research path: Walking in the jungle without a compass

I recently discovered that mapping a career path as a researcher is like walking through the jungle.

Some forests have beautiful roads adorned with scenic views, and even have a convenience store. But others, well, they are jungles – no roads just a plain old fashioned jungle.

A few weeks before my wedding, my brother and I walked through such a jungle. This is what happened.

My brother and I visited my aunt at her village. I was a teaching assistant and adjunct faculty at a college in Bulawayo, so I had to go back the following day. Unfortunately, my brother and I slept late and we missed the bus. And that meant we had to walk for about 30 miles to the nearest growth point.

At first, we followed the winding gravel road hoping to find a car heading to Karoi. We walked for more than ten miles and there was nothing. Exhausted, we decided to abandon the fancy road for the jungle. After all, we knew the direction we were had to take to reach the nearest growth point.

After walking for more than four hours, I was hungry and tired. Luckily, there were lots of mazhanje (brown berries) that season. So, after walking for an hour or so, we would eat mazhanje. But the problem with mazhanje is they make you thirsty.

Fortunately, we found a grocery store and asked for water. The shop attendant refused. The borehole was far and she couldn’t sacrifice her water for us. I understood. What else could I do.

We walked for another mile and found a homestead where folks were there. It was the farming season, most people had gone to their fields. My brother asked for water and they gladly gave us. But they forgot to clean the cup or cover the water container. There were floating dead cockroaches inside the cup. I drank the water.

As I look at my career prospects today, that tragic trip with my brother comes into my mind. Unfortunately, on this trip I have a wife and two kids who never never volunteered for a crazy trip.

Sometimes, I am filled with envy as I watch my peers getting better opportunities. Their graduate supervisor helped them find a postdoc or faculty position, appointed them an associate editor or board member at a high impact factor journal, and even recognized their effort in most of the research groups publications through co-authorship. They are walking through the jungle on a paved road lined up with convenient stores.

My case is different. I have to create my own opportunities. This is why I have sent probably 2,000 job application letters. This is why I wrote book chapters thinking that they were considered for tenure. I have even written book reviews. I am just trying to dig up a road through a dense forest.

Once or twice a week, I commit myself to writing a peer review report. I’m really serious about peer review. Because I heard when you’re a good peer review, the editors might consider you for associate editor or editorial board membership appointments. I don’t know but I will keep on trying everything and see what works.

I have met people who are worse than the shop attendant in this jungle. On numerous occasions, I rewrote manuscripts for peers. They would go on to submit the manuscripts, and they got published. But my name would not be on the authors list, or even the acknowledgement – an unwitting ghost author. It’s a jungle out there.

I have realized that no one is going to come to me and tell me what I should do if I want a career in academia. I know there are numerous books and blogs about securing tenure after PhD. But none of them are for an African researcher working in a foreign land. It’s a jungle out there.

Image by Kiwihug

My wife sacrificed her career for me: early career researcher confession

My wife sacrificed her career for me to become an early career researcher. And I’m not sure if it was worth it. I am currently a postdoc in South East Asia. But my story begins in January 2011.

Shortly after our honeymoon, I received a call from the US consulate public affairs office. “Congratulations, you are a 2011 recipient of the Fulbright Fellowship.” I always wanted to study in America. And I always wanted to be a professor. My dream was fast becoming a reality.

What about my wife? I had been married to Surprise for less than a month and I was about to tell her that I was leaving for America. In our perfect dream, America was a land of opportunities; I will go there, save money for her air ticket, and she would join me shortly after.

As someone who grew up in extreme poverty, saving from my $1200 Fulbright stipend wasn’t hard. In three months, I had enough money to buy the ticket and my bank statement had enough balance to act as proof of financial support. So Surprise went for the US visa interview, excited that she was finally going to be with me.

My wife’s visa application was rejected. I was dejected. The consular made me chase a white rabbit. And I lost more than $2,000 in the process. He knew I was a Fulbright Fellow earning peanuts while leaving in the most expensive state. There are some sadistic people out there.

On first visit, the consular said he could only give Surprise a visa if she had a proof of insurance cover. I bought the J2 health insurance from Seven Corners. And I lost $1,000 in the process.

The consular changed his mind, he demanded a letter from a doctor who would attend to Surprise in the US. She was pregnant. I found the doctor, but he said he can only make that recommendation if he did a physical examination of Surprise. I gave up. My wife gave up.

Surprise finally joined me seven months later. My wife had a teaching qualification from Zimbabwe but didn’t have a bachelor’s degree. For several months, we searched for cheap colleges but couldn’t find any.

Reality finally struck, we were too poor to afford college. My Fulbright stipend wasn’t enough for one person, but we were a family of three. And soon enough, we were four. At that moment, my wife shelved her dream and took up a jobs in retail; Kmart, Ross, and even at an Amazon Fulfillment Center.

Our family life became non-existent. Surprise kept two jobs for us to survive. She left the house at 5 am, drove an hour to Amazon, break her back packing or retrieving orders. Around 5pm5 pm, she would drive for an hour to Kmart. Most of the times, she would stagger home at almost midnight.

My wife was exhausted all the time, but I felt terrible. Our dream had become a nightmare. But I had hope. We had hope. After I receiving my PhD, I was going to get a good job. Surprise would go back to college and get her bachelor’s degree in education or psychology.

I got my PhD but didn’t get a job. One thousand three hundred applications, five months, and one job interview later, I got a job at a university in Zimbabwe. The salary was modest, but the country’s economy was showing signs of fatigue.

After working for two semesters, my family left Zimbabwe for China. I took up a job as a postdoc hoping to publish enough articles so that I could easily get a faculty position. Again, my wife applied for undergrad at universities in China. She got a place at one university, it was too far and priced out of our range.

My postdoc contract is for two years. Surprise is shelving her dreams for another two years. I want to settle down after the postdoc. I want to live in a country where my wife and kids can get a good education.

By now, my wife could be holding a master’s degree in education, seven years teaching experience, and a career. Fulbright might have paid for my grad school tuition using cash, my wife paid for my career by sacrificing her dream.

Image by Joanna Kosinska

Why early career researchers should care about teaching

Teaching is the art of enabling learning. For that reason, knowledge of the subject matter is not an adequate impetus to learning. A good teacher understands knowing how people learn is critical in facilitating learning. Sadly, many universities across the world are staffed by subject experts who have no formal training in higher education.

After completing my PhD studies in the US, I returned home and took a position as a lecturer. I enjoyed teaching but there was one problem; I had no idea how students learn. Of course, like most instructors in higher education, I knew how I learned. And I assumed that’s how everyone else learned.

No one taught me how to prepare course materials that addressed the learning objectives. But I had to. No one showed me how to draft a course schedule that guarantees students would master the subject content. But I had to. Importantly, no one showed me how to create a lesson plan, deliver a lecture or assess the students’ performance. But I had to.

Each day, as I stood in front of my zealous students, I became more aware of my inadequacy. My students deserved better. Although I had an impressive resume, a Fulbright Fellow, numerous awards, and a couple of papers in reputable journals, I had zero qualifications in education. How would I enable learning if I didn’t know how people learned?

I had to learn how people learn.

1. Enroll for a postgraduate certificate in higher education

After teaching in Zimbabwe for one academic year, I decided to take a postdoc position. It has been a year now since I started my postdoc. In January, I enrolled for a postgraduate certificate in higher education at Falmouth University. I realized that if I want to return to the classroom, I had to be better equipped.

2. Take online classes on teaching

They’re numerous MOOCs offering courses on teaching for free. During the Christmas holidays, I enrolled for a class on inclusive learning offered by University of Southampton at FutureLearn. The good news was studying for a certificate was free for learners in developing nations.

3. Take advantage of the free faculty prep courses on your campus

When I was doing my PhD at the University of California Riverside, I failed to enroll for the certificate in university teaching. I regret it because I ended up getting a postdoc at university that didn’t offer the certificate. Some universities offer it, and it’s probably wise enrolling in the course.

4. Reflect on your teaching practice

One of the best ways to learn how people learn is by stopping and reflecting on your practice. I learned this during in my PGCHE class. In the past week, I went back to an online discussion and peer review assignment I gave my students when I was still a lecturer. Reading the comments, I learned a lot about student engagement. I never realized I was sitting on a gold mine all along.

There’s much to learn, and even more when it comes to learn about learning. As an early career researcher, you probably need to learn about learning if you want to be an academic. I know the jobs in academia are scarce, but it never hurts to learn. Does it?

5 Things I Learned After Publishing In A Predatory Journal

Like thousands of young African researchers, I am a victim of a predatory journal. I published my first research paper in a predatory journal. I was young, I was ignorant and I was looking for validation. And a predatory journal took advantage of all of this.

Predatory journals are con artists. They pry on your ignorance and take advantage of your pride. But what is a predatory journal? A predatory journal is a journal that charge researchers submission fees but offers little or no peer review or editorial support. Hence, the primary goal of a predatory journal is profit rather than advancement of sound scholarship.

How I published in a predatory journal and why I regret it

In undergrad, I studied the occurrence of acrylamide in traditional foods consumed in Zimbabwe. Since I didn’t have the right equipment, I collected my samples and sent them to Sweden for analysis. The study confirmed traditional foods had acrylamide, a cancer-causing chemical although at a lower concentration than French fries or cookies.

1. People publish in predatory journals out of ignorance

I decided to publish my study on acrylamide in food. But I didn’t know anything about publishing manuscripts. Researchers at my university in Zimbabwe often published at Academic Journals. So, I sent my manuscript to African Journal of Food Science, which is published by Academic Journals.

2. Predatory journals only want your money

A week after submission, I received an email saying my paper had been submitted. I had to pay about $350 for my paper to be published. One of my co-authors paid, “Edmond, I have published many articles but I have never paid for publication. Be careful.” I didn’t listen, I only wanted to list a publication on my resume.

3. Predatory journals lack a robust peer review system

After reading Beall’s List of Predatory Journals, I realized the African Journal of Food Science was a predatory journal. They had a shady peer review system and only cared about their profits. I think my research was good. But with a good peer review system, my paper could have been better. Editorial support could have removed the grammatical and spelling mistakes I made.

4. Predatory journals can ruin your career

Publishing in a predatory journal put a stain on my resume. I think when recruiters see that I published in a predatory journal they assume I’m a shady scientist. As a result, I often think of removing the paper on my CV when I submit job applications.

5. Predatory journals survive from the greed and pride of researchers

A recent study found in the past decade the South African government lost between $7 million and $23 million subsidizing articles published in predatory journals. Out of greed and probably ignorance, most researchers resorted to paying $350 to predatory journals. After all, the South African government would give them $7,700 in return. Researchers at my school knew Academic Journals was a predatory publisher but they wanted the pride that comes with listing a dozen papers on your CV.

Summary

Three years after publishing in a predatory journal, I published my first article in a reputable journal. I dreaded the peer review but it made my manuscript better.

To date, I have published in Journal of Chromatography AEnvironmental Pollution and Water Research. I have a manuscript under review in Environmental Pollution and another in Integrated Environment Assessment and Management.

My email is flooded daily with emails from predatory journals. They want to me to submit a manuscript or become an editor. I mark all the emails as spam. And continue with my work, reviewing manuscripts or editing my own manuscripts.

Image by Eric MacDonell from Unsplash

Good Research Ethics Will Make You A Better Scientist

Besides a handful online classes, I have never taken a formal class in research ethics. And I think that’s a serious bummer. I believe graduate schools should offer formal classes in research ethics, especially students pursuing a career in natural sciences.

In the past five months, I have been working on a review manuscript that I plan to submit this summer. Review articles are demanding but sometimes the pay-off is high. Especially when your manuscript is reviewing an emerging research area.

But you must be willing to read at least 200 articles, with a red highlight and a thick notebook. Above all, you should brace for abrasive encounters with academic dishonesty. In the past five months, I had my fair share of such encounters.

As a combed through the 274 papers for my review, I came across serious cases of academic dishonesty. It was easy for me to blame the editors and reviewers for not noticing the unethical research practices. After all, scientific journals should be beacons for promoting research ethics.

However, expecting journal editors and reviewers to fork manuscripts with questionable research ethics is farfetched. It’s like expecting palladium catalyst to convert water into bronze. It ain’t gonna happen.

I believe the best place to teach research ethics is in undergrad. And in this article, I want to show you why research ethics is important and identify some common, yet less talked about, practices that are unethical.

What is research ethics and why is it important?

I learned the importance of research ethics when I was an analytical chemist intern at a national laboratory. The lab was mandated by the state to test and approve agrochemicals used in the country. One day, my boss came to our lab fuming. There was a problem with one of the agrochemicals we had approved – it was out of spec and was destroying crops.

A witch hunt immediately began. As an ISO17025 certified lab, our paper trail was exceptional. In less than two hours, we had found the culprit. A chromatogram showed the concentration of the target compound was higher than recommended. But the analyst wrote on the approval certificate that it was within range.

That small act of dishonesty resulted in a national crisis as many tobacco seedlings were destroyed. Unethical practices in science research may cause unexpected catastrophe. The lady who fudged the results of the pesticides did so out of pressure from the bosses. But most of the time people doctor results so that their results can fit a cute theory.

I learned my first lesson on research ethics from my mother. Our family was on the bottom of the societal rank. She was a widow and we were very poor. So, we sold fruits and vegetables to supplement her monthly meagre pension.

My mother used to send me to the farmer’s market to research on the current practices of fruits and vegetables. The prices rarely changed, so sometimes I would not go to the market and tell her the previous week’s prices. Sometimes it worked, but most of the time it didn’t. And the result was, mom would go to the farmer’s market with money that wasn’t enough.

So, what is research ethics? Research ethics is the appropriate application of moral principles in planning, conducting and reporting research. Above all, research ethics define scientifically acceptable norms. Hence, research ethics can be learned from your parents, friends, spiritual leader or professor.

5 common practices in science research that are unethical

As I wrote my review manuscript, I came across 4 practices that looked like prototypes of poor research ethics. The 5th practice I heard about in lobbies at national conferences – it’s the most disgusting.

1. Paraphrasing same paper, publish in different journal

A group of researchers published the same data set twice in different journals. But they were slick. This how they did it; they changed the title of their paper. And then added two new target compounds to their initial 15+.

2. Pick a sub-sample of study, make it an independent paper

Another research team played around with sampling period. They carried out a ten-year survey and published in 2015. Then using a different first author, they published another paper for a 5-year survey in a different journal. And guess what? The 5-year survey was a sub-sample of the first 10-year survey. Slick.

3. Outlier, out of paper

Sometimes researchers use statistics to justify their questionable research ethics practices. You probably have encountered several papers that state they removed certain treatments because they would skew the results. Isn’t that supposed to read: we removed results of treatment A because it didn’t fit well with our hypothesis?

4. Poor research design, poor research ethics

I once heard a talk from a researcher who set out to investigate the degradation of 10 organic pollutants in sediments but discussed on 6. When quizzed about this, she said, “I did my sampling on day 1, 3, 7, 14, 21, 42 and 63. Those four compounds disappeared in the sediment after day 3.” Instead of redesigning her experiment she redesigned her results.

5. The unethical rings of research publishing

You probably heard of citation rings – a group of research cite each other to increase their citation index. But there’s a more pervasive ring; review ring. This is the most dangerous form of academic dishonesty. A group of researchers forms an extensive ring that review each other’s manuscripts and grants.

However, considering ethics in science research are built on individual values and experiences, these researchers might not have been aware of what they did. It is the responsibility of academic institutions to instill good research ethics.

What are other unethical practices you have encountered in your research?