biology

Mark Pallen

Mark Pallen is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Mark Pallen rather than just read about it. In short: Mark J. Pallen is a British microbiologist who is a research leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia.

Key takeaways

Mark Pallen belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Mark Pallen to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Mark Pallen from memory before moving on to harder problems.

Reference excerpt

Mark J. Pallen is a British microbiologist who is a research leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia. In recent years, he has been at the forefront of efforts to apply next-generation sequencing to problems in microbiology and ancient DNA research.

Education Pallen was educated at Wallington High School. He completed an undergraduate degree in medical sciences at Fitzwilliam College, Cambridge and gained his medical qualification from the London Hospital Medical College. During the early 1990s, he gained an MD while working at St Bartholomew's Hospital Medical College. In the mid-1990s, he worked for a PhD under the supervision of Gordon Dougan at Imperial College. During this time, he captained the winning team from Imperial College in the TV quiz show University Challenge, while also writing a series of articles for the British Medical Journal, introducing the medical profession to the Internet.

Microbial genomics, metagenomics and bioinformatics In 2011, Pallen led a crowdsourced analysis of the genome of the outbreak strain from the 2011 German E. coli O104:H4 outbreak, which had been genome-sequenced on the Ion Torrent platform by the BGI. Around the same time, he also led a project in which an isolate from the 2011 German E. coli O104:H4 outbreak was genome-sequenced on three new benchtop sequencing platforms, benchmarking these new platforms. He has also shown that whole-genome sequencing can be used to track the spread of resistant bacteria and to study the emergence of antimicrobial resistance . Through analyses of fecal samples from the 2011 German E. coli O104:H4 outbreak and sputum samples from The Gambia, Pallen showed that metagenomics can be used as a culture-independent approach to the diagnosis of bacterial infection. He has pioneered the use of metagenomics to open up new avenues in ancient DNA research, recovering 200-year-old Mycobacterium tuberculosis genomes from human remains and a medieval Brucella genome sequence. With Vince Gaffney and Robin Allaby, he has applied shotgun metagenomics to sedimentary ancient DNA samples, showing the presence of wheat in the British Isles 2000 years earlier than expected. Pallen has also used metagenomics to investigate the chicken gut microbiome, the gut microbiome of patients on the intensive care unit and the microbes that inhabit ticks. From 2014 to 2020, Pallen was Principal Investigator on the £8 million MRC-funded cloud-computing project the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) and now serves as director of the successor project CLIMB-BIG-DATA. In 2020, the CLIMB project received the HPCWire Readers' Best High Performance Computing Collaboration Award for supporting analysis and publication of coronavirus genome sequences during the COVID-19 pandemic.

Microbial nomenclature Pallen's studies on the chicken gut microbiome led him to propose over 800 new names for bacterial taxa found in this setting. Pallen then developed a system for automating the creation of taxonomic names for bacteria, which resulted in the publication of over a million new names available for use by the microbiology research community to name new bacterial genera. Subsequently, in an opinion piece in the journal New Microbes and New Infections

and an invited talk for Bergey's International Society for Microbial Systematics, Pallen outlined his ideas for making bacterial nomenclature more accessible. In 2022, Pallen published over 65,000 names for previously unnamed bacterial and archaeal taxa in the Genome Taxonomy Database, using Python scripts to create user-friendly arbitrary names that comply with the phonotactics and grammar of Latin. Pallen has also been active in viral nomenclature, starting with the creation of over 400 species epithets for the bacterial positive-sense single-stranded viruses in the family Leviviridae. In March 2021, Pallen suggested in an Opinion article in New Scientist that an alternative should be found to the use of geographical names for variants of SARS-CoV-2, raiding the classical world for options. In early 2021, Pallen participated in a WHO working group, priming adoption of a scheme for naming variants of SARS-CoV-2 after letters in the Greek alphabet. In recognition of Pallen's efforts in automating creation of names for microbes, in 2022 the name Palleniella was created for a new bacterial genus previously within the genus Prevotella.

Public understanding of science Pallen is the author of a popular science book, The Rough Guide to Evolution. In the wake of the 2005 Kitzmiller v. Dover Area School District trial, he wrote a review with Nick Matzke, outlining the evidence that the bacterial flagellum is an evolved rather than designed entity. He commissioned and peer-reviewed Baba Brinkman's Rap Guide to Evolution and was responsible for recruiting Alice Roberts to the role of Professor of Public Engagement in Science at the University of Birmingham. In June 2011, Pallen appeared in an episode of Melvin Bragg's In our Time radio programme. In 2018, Pallen self-published a book on the 1978 smallpox outbreak in the United Kingdom, The Last Days of Smallpox: Tragedy in Birmingham, which includes a mixture of popular science and a historical narrative of the outbreak and subsequent court case. Pallen has served alongside Alice Roberts on the advisory board of the Milner Centre for Evolution at the University of Bath

References

Worked examples

Example 1 — a first encounter with Mark Pallen

Start with the simplest possible case. Write down what Mark Pallen claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Mark Pallen before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Mark Pallen ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Mark Pallen

In research: Mark Pallen appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Mark Pallen in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Mark Pallen is common in secondary-school and first-year university syllabi. It links to neighbouring topics 1960 births, 20th-century British medical doctors, Academics of the University of East Anglia, so understanding it makes those chapters shorter.
In everyday life: Look for Mark Pallen outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Mark Pallen in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Mark Pallen means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Mark Pallen out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Mark Pallen in simple terms?

Mark J. Pallen is a British microbiologist who is a research leader at the Quadram Institute and Professor of Microbial Genomics at the University of East Anglia.

Why does Mark Pallen matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Mark Pallen?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Mark Pallen.