Science on Morgan Bye

You deserve better

Tue, 23 Sep 2025 15:45:00 -0400

This post was originally written in July 2016 but was never published. Nearly a decade later it still rings true. I revisit it now for anyone still in grad school, thinking about life outside.

“You don’t climb mountains without a team… you don’t climb mountains without being prepared… you never climb a mountain on accident.”

– Mark Udall, US Senator

Stop me if you’ve heard this before.

Every day you go to work. You don’t just give your time, your attention… you give a piece of yourself. Sometimes you work late and lose track of time because you’re too invested. The people who love you say you work too much. They don’t get it.

Personalized cancer therapy

Fri, 17 May 2024 14:00:00 +0500

All cells have genomes (DNA genetic codes) that govern their existence. Cancer occurs when the genomes of cells change, leading to uncontrolled cell growth and replication.

The Personalized Onco-Genomics (POG) Program is BC Cancer’s flagship study in precision medicine and the first program of its kind to deploy whole genome analysis to inform individual treatment planning for patients.

For each patient, 2 samples are taken, one of “normal” cells, and one from the cancer. The sequences are then compared in an effort to find variations and mutations between the two which represent the cancer.

Organic food is a lie

Fri, 12 Feb 2016 22:00:00 +0000

Walking into a supermarket has become a bombardment on your senses. A barrage of words and terms that sound somewhere between science-fiction and extreme farming.

Eggs come with terms with “caged” or “barn-raised” to “free-range” or “grain-fed”. Some eggs even come from happy chickens! I mean, are these eggs or aren’t they?

These eggs are whiter than my laundry detergent.

Heck! I’m suspicious every time I look at eggs in North America and they come with perfectly white shells. Something isn’t quite right there. These eggs are whiter than my laundry detergent.

The problem with reading about cancer

Fri, 29 Jan 2016 21:00:00 +0000

Cancer. The scariest word in the world. For many people, cancer is the last word that they ever want to hear. In living memory, cancer was not a word that was dared to be spoken aloud. In this modern world, most people still read cancer as a death sentence. Despite all of modern medicine, despite the number of cancer survivors, the only question that matters is “How long?”

Cancer is perhaps the scariest of all topics. When confronted with cancer, most people respond with blind, rigid panic. A rabbit in headlights. The only question that matters is not one of “how are we going to defeat it?” but “when will it defeat me?”

Drug delivery

Fri, 15 Jan 2016 21:30:00 +0000

When you’re sick with headache or flu, you likely reach for the aspirin and the Tylenol. At your lowest point. When you feel like things can’t get any worse. With your head pounding. Your nose running a marathon. You reach for pills.

You don’t even think about it. But, culturally, it is ingrained in us. Pills are medicine.

This is something every supplement maker in the world is all too happy to jump on. Your nutritional supplement of choice, whether that’s multivitamins, cod liver oil or anything else comes in pill format. It doesn’t matter if it has any benefit for you, because the instinctively *feel *better for it.

The dangers of positivity, or "Why we shouldn't ignore bad news"

Fri, 01 Jan 2016 19:00:00 +0000

Everywhere you go. Everything you read. All that you see. Everything is positive results. “Science finds this new thing!” they exclaim. Lives will be changed! What a breakthrough!

What no press release tells you is the blood, the sweat, the tears. No one tells you about the ruined lives. The failed marriages. The missed bedtimes and children longing for affection. Misery doesn’t make for a feel-good headline. Besides, what does all this… emotion got to do with an academic subject?

Antibiotic Armageddon

Fri, 27 Nov 2015 20:30:00 +0000

Some experts say we are moving back to the pre-antibiotic era. No. this will be a post-antibiotic era. In terms of new replacement antibiotics, the pipeline is virtually dry. A post-antibiotic era means, in effect, an end to modern medicine as we know it.

– Dr. Margaret Chan, Director-General of the World Health Organization

Antibiotics might not seem as pressing as global terrorism or healthcare reforms. Bacteria don’t even, seem that scary. You can’t really see them, and yes there’s a scary Mission Impossible movie every now and then. But really, the worst experience most of us have from bacteria, is a bit of food poisoning.

Personalized medicine

Fri, 13 Nov 2015 20:45:00 +0000

It seems that the latest buzz phrase to be going around the medical world is the notion of “personalized medicine”. Which sounds like a bit of a joke, because isn’t all medicine personal? I mean, I’m the only sick person here, and I’m the only one putting medicine inside of my body. Doesn’t that already feel quite personal? But, if this isn’t, what is personalized medicine?

we should not treat everybody the same way

What is Big Data?

Fri, 23 Oct 2015 20:00:00 +0000

The world is being reshaped by the convergence of social, mobile, cloud, big data, community and other powerful forces. The combination of these technologies unlocks an incredible opportunity to connect everything together in a new way and is dramatically transforming the way we live and work.

– Marc Benioff

Big data is a feeling. The feeling that the future is an uncertain place. The feeling that we can make decisions today, that although we might not understand them now, in tomorrow’s future, they might be the most important decisions we ever made.

Hot drinks cool you faster - fact or fiction?

Fri, 09 Oct 2015 19:30:00 +0000

Imagine you’re sat on a tropical beach. The sort of beach they only have in magazines and nature documentaries. The sun beating down on paradise. The humidity and cooling sea breeze is just enough to make anything other than another cocktail unbearable. Rather than decided to top up your tan a little further you decide that you really must keep up your marathon training. After all, those unfortunate orphans cannot raise the money to save their orphanage without your fundraising efforts.

10 steps to making your graphs not suck

Fri, 18 Sep 2015 19:30:00 +0000

Recently I wrote about how your graphs suck. It even generated a little bit of a stir over on LinkedIn. I am not however, the kind of person that points at a problem and walks away. I taught lab classes full of trainee chemists, biochemists and pharmacists for over 4 years. Over the years, I’ve read and marked more experiment reports than I want to think about and let me tell you, I have seen some truly shocking graphs. Including one quick hand sketch in a printed report with an apology post-it attached, “Trust me, it looked a bit like this.”

Your graphs suck!

Fri, 04 Sep 2015 19:30:00 +0000

Your graphs suck! Bold statement huh? I don’t even know you, Mr or Ms Anonyomous Internet Reader. Yet I know that your graphs suck. I know that when things get tough, and you really need a graph, you’ll suck the air between your teeth, quietly swear to yourself, before admitting defeat. Then, you’ll go open up Excel.

“What’s wrong with Excel?” I hear you cry!

Ah-ha! I’ve got you! You’re already on the defensive. Trying to justify that Excel is a perfectly good piece of software used by millions of people every day.

3x deadlier than ISIS

Fri, 21 Aug 2015 20:00:00 +0000

The cholera had broken out at the post, and five or six men were dying daily.

– Buffalo Bill

We are in the middle of a global pandemic. In one small country, population 10 million, 4000 dead. Another 200,000 infected. All in under 3 months. International efforts have had little effect. 5 years later, 9000 lie dead. Almost three-quarters of a million infected. The sick are highly infectious. Food and water are not safe from infection. This pandemic, by World Health Organisation numbers, is claiming up to 142,000 lives EVERY YEAR.¹ 3 years of civil war in Syria and the rise of ISIS is estimated at 170,000 deaths.²

Vaccination doesn't cure fear

Fri, 07 Aug 2015 17:10:00 +0000

Trust is not simply a matter of truthfulness, or even constancy. It is also a matter of amity and goodwill. We trust those who have our best interests at heart, and mistrust those who seem deaf to our concerns.

– Gary Hamel

The year is 1998, a respected British surgeon, Dr. Andrew Wakefield, publishes a paper in the prestigious medical journal, The Lancet. In this paper, Dr. Wakefield and coauthors make a claim that they have seen a link between children receiving the measles, mumps and rubella (MMR) vaccine and their development of autism and bowel disease.¹ To quote paper’s introduction

Eugenics – From designer babies to the Holocaust

Fri, 24 Jul 2015 20:50:00 +0000

You can tell when something’s not moving forward anymore. When the doubts you have about it don’t go away.

– Jeffrey Eugenides

18,000 children die every day from starvation.¹ The fact of the matter is the world is only so big. We live in a world of dwindling resources and massive overpopulation. We are approaching a transhumanist era. A moment in time when science and technology will fundamentally change the human experience. Indefinite lifespans, cloning and technology integrating our bodies. Perhaps then, it might be time to reconsider human breeding.

Pluto - the planet of surprises

Fri, 17 Jul 2015 20:45:00 +0000

We explore because we are human

– Prof. Stephen Hawking

Pluto is in the news this week and with good reason. Pluto, as most people are aware, is more than just a beloved Disney character or Roman God of the underworld. However, most people would struggle to tell you whether Pluto is even a planet - which it is… sort of. For most, we remember the science textbooks of a long forgotten youth, telling us that Pluto was the last thing of significance in our solar system before the long journey to our next nearest star (Alpha Centauri at 4.4 light years away. If your mind does not work in light years in kilometres that is 41 followed by 12 zeroes).

The rise of artificial intelligence

Fri, 10 Jul 2015 20:50:00 +0000

The development of full artificial intelligence could spell the end of the human race

– Prof. Stephan Hawking

Elon Musk, co-founder of PayPal, founder of a solar power company, founder of an electric car company, founder of a company with a mission to put a human colony on Mars in his lifetime, described artificial intelligence, or AI, as “summoning the devil”. He’s not alone, Bill Gates, urges people to be wary of artificial intelligence.

Vitamin pills and the hard to swallow truth

Fri, 26 Jun 2015 21:50:00 +0000

There is a major problem with reliance on placebos, like most vitamins and antioxidants. Everyone gets upset about Big Science, Big Pharma, but they love Big Placebo.

– Michael Specter

Study after study show vitamins do not lower cancer or heart-disease risk. In fact, they vitamins may be creating more problems than they solve.

More than half the population is regularly taking vitamins in Canada¹ and the US², with similar levels across the rest of the Western world.³ Most common is the multivitamin and mineral supplement (MVM), popularized in the US in 1941.⁴. Multivitamins are now estimated to be consumed, regularly, by 1 in 3 Americans.⁵

You, pot, and politics

Fri, 19 Jun 2015 21:45:00 +0000

Winners don’t use drugs – William S. Sessions, Director, FBI

Ever noticed how a bad hangover feels like your body is dying? The truth is, it sort of is. What you did the night before was knowingly load your body full of a poison. Anyone that has ever taken that “one drink too many” knows all too well the symptoms of what amounts to mild poisoning.

The weak heartbeat, tiredness, muscle fatigue, dehydration, headache, bad breath. We even know what long-term alcoholism looks like either thanks to the media or our own personal experience (the UK’s National Health Service reported 9 % of adult males as having alcohol dependence back in 2009¹).

Bacteria are going to kill you

Fri, 12 Jun 2015 20:57:00 +0000

The art of medicine consists in amusing the patient while nature cures the disease.

– Voltaire (1694-1778)

Bacteria ancestors were the first organisms on the planet. Bacteria have survived around 4 billion years on this lump of rock, flying through space. Homo sapiens by comparison have only turned up in the last 100,000 years or so.

Scientists estimate there to be around 5 quintillion bacteria on the planet (that is 5 followed by 30 zeroes)(or 5 nonillion for our US friends). Combined, the weight of bacteria in the world exceeds plants and animals combined.¹

The world is going to university

Fri, 05 Jun 2015 21:35:00 +0000

Knowledge is power. Information is liberating. Education is the premise of progress, in every society, in every family.

– Kofi Annan

In the last few years I have experienced many universities, all of them are building. New campuses, new buildings, more accommodation. From the casual observers perspective it looks like a great time to be in the education game.

I recently got to quiz a Vice Chancellor about why there was so much construction in his university. I asked why exactly he felt the need for constructing an entirely new university village on campus grounds?

Why trust is vital to science

Fri, 29 May 2015 12:00:00 +0000

To be trusted is a greater compliment than being loved. – George MacDonald

This week in America we have once again seen how difficult it is to build trust and how quickly it can be taken away. Four of the largest cancer charities in the US have been charged by the Federal Trade Commission (FTC) with bilking (an archaic word meaning to obtain or withhold money from someone by deceit or without justification) over $187 million from consumers.

Why I'm choosing to give up academic science

Tue, 19 Aug 2014 12:00:00 +0200

I have held off writing this blog post for some time now. It has been a long time in the making. A very long time. Part of my reason to hold off for so long is due to the very public nature of the medium and part of it has been that sitting down to write this forces me to confront the situation and think about it. The fact remains however, that it has been a little over a week since I walked into my boss’ office and told her that I would be leaving. Not this very second, not even in a month’s time, but soon. In my mind I had reached a conclusion and I respected her enough to tell her as soon as I knew - even if I did not yet understand what that decision meant.

PyMOL visualising binding interfaces

Fri, 24 Feb 2012 17:31:00 +0000

Today I’ve been trying to come up with a nice way of visualising the binding interface between protein-protein or protein-DNA complexes. What follows is a quick little walk-through mostly for my own purposes so that I can remember what I’ve done in the future.

Download PDB file from pdb.org, here XXXX will be your PDB accession code.

Point a terminal window at the download directory

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cd ~/Downloads

Run CCP4:

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ncont XYZIN XXXX.pdb >> XXXX.ncont << eof

source A [or whatever your protein chain is]

target E,F [or whatever the DNA chains are]

eof

This will give us a file XXXX.ncont in the Downloads folder which contains all the information about the binding interface

Copenhagen: who do we believe?

Fri, 09 Dec 2011 17:07:00 +0000

As a scientist I am trained nay indoctrinated to find the truth, whatever that may be. Right or wrong. And no matter what the out come ultimately the job requires a certain amount of starring at nature, observing what happens and trying to make educated conclusions from these observations that will perhaps allow for the prediction of further instances. The problem is, I’m not just a scientist. I am human. And with humanity comes a certain amount of shying away from the facts even when they are staring us in the face, simply because we don’t like what we see.

A future in science?

Sun, 23 Oct 2011 12:00:00 +0000

Approximately 2 months ago the first knock-ons from the Government’s spending decisions was announced to the research community. Whilst the Government as a response to the Science is Vital campaign acknowledged not to cut science research spending.

The problem with science is that almost all research that is conducted not by industry with the aim of direct marketable end product within 5 years (eg a drug to sell for a pharmaceutical company) is paid for by the Government and to a lesser extent charities (think Cancer Research UK and the like). And the problem with that is that all things take time, and there might be 20 years research behind an idea before industry gets interested, if not an entire professional lifetime of several teams.