misciwriterseditors blog, evolution, genetics

Where Do Genes Come From? Part 2: De novo Genes

Author: Belle Moyers

Editors: Theresa Mau, Alex Taylor, and Kevin Boehnke

“The probability that a functional protein would appear de novo by random association of amino acids is practically zero.” ~ Francois Jacob, 1977

If you’ve ever gotten into arguments about evolution, you may have heard the argument that goes something like this: A new gene randomly forming is as improbable as a tornado blowing through a junkyard and assembling a working 747. The above quote by Francois Jacob shows that scientists have been pretty skeptical about this idea, too.

But something seeming unlikely doesn’t mean that it doesn’t happen. As we learned last time, most mutations are harmful, and most gene duplications are lost—but the rare times when they are beneficial, a new gene can have a huge effect on species survival.

So, is it possible that a protein-coding gene might form randomly?

Continue reading “Where Do Genes Come From? Part 2: De novo Genes” →
misciwriterseditors Biodiversity, Biology, blog, evolution, genetics

Of Sporks and Scorpions: Where Do Genes Come From? (Part 1)

Author: Belle Moyers

Editors: Theresa Mau, Alex Taylor, and Kevin Boehnke

What exactly separates us from other animals?  For that matter, what makes any species or group of species special?  How is life so diverse?  How can cephalopods camouflage themselves so well, and how did platypuses become so bizarre?

Part of the answer is in genes.  Genes are sections of DNA that perform a specific function, usually after being translated into proteins by special cellular machinery.  Every species has genes that code for proteins, but different species have different numbers of genes. Humans have around 20,000, fruit flies have around 18,000, and the tiny water-flea has around 31,000 genes. Different sets of genes produce animals with different structures and functions.

Continue reading “Of Sporks and Scorpions: Where Do Genes Come From? (Part 1)” →
misciwriterseditors blog, Cancer, genetics, Public health

What Does Smoking Do to Your DNA?

Authors: Shweta Ramdas

Editors: Irene Park and Kevin Boehnke

Smoking 1
Figure 1. Smoking is known to cause at least 14 different types of cancers, although it is not clear how or why.

 

We have known tobacco to be a cause of many cancers for decades now. It is associated with it least 14 types of cancers (see Figure 1). Less understood is how tobacco causes cancer. The short answer—it causes mutations. Tobacco smoke is a mixture of many chemicals, including at least 60 carcinogens (cancer-causing chemicals).

A trans-national team of researchers has begun unearthing the distinct types of mutations caused by tobacco smoke to better understand the biological pathways leading to tobacco-induced cancer. They found that tobacco causes specific types of DNA damage in organs directly exposed to smoke (like the lungs) and that smoking tobacco generally leads to higher rates of mutation in all tissues. Understanding how the chemicals in tobacco smoke cause mutations can help scientists identify new and emerging mutagens and design better treatment strategies.

Continue reading “What Does Smoking Do to Your DNA?” →

misciwriterseditors Biochemistry, blog, Chemistry, Computer Science, Technology

Computing Levinthal’s Paradox: Protein Folding, Part 2

Author: Sarah Kearns

Editors: David Mertz, Zuleirys Santana Rodriguez, and Scott Barolo

In a previous post, we discussed how proteins fold into unique shapes that allow them to perform their biological functions. Through many physical and chemical properties, like hydrogen bonding and hydrophobicity, proteins are able to fold correctly. However, proteins can fold improperly, and sometimes these malformed peptides aggregate, leading to diseases like Alzheimer’s.

How can we figure out when the folding process goes wrong? Can we use computers to figure out the folding/misfolding process and develop methods to prevent or undo the damage done by protein aggregates?

Continue reading “Computing Levinthal’s Paradox: Protein Folding, Part 2” →

misciwriterseditors blog, Education, Psychology

Homework: a Necessity or an Age-Old Brain Drain?

Author: Amira Aker

Editors: Shweta Ramdas, Zena Lapp, and David Mertz

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Everyone hates homework. It’s boring, annoying, and takes you away from a million other things you’d rather be doing. But I always thought it was a necessary part of learning. How else could you learn without effort and a little struggle? As a Ph.D. student (so, somewhat academically inclined) and a mother of two, I was distraught by the growing phenomenon of schools banning homework. But the logical part of me thinks that there must be more to this than just pandering to student laziness and teacher burnout.

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misciwriterseditors Biology, blog, Cancer, Disease research, Public health, Research

Training T Cell Assassins

Author: John Charpentier

Editors: Zena Lapp, Theresa Mau, and David Mertz

 

t_cell_assassin
Figure 1. An encounter between a CAR-T cell and a cancer cell

 

The assassins have a description of their targets, who are hiding in plain sight among the non-combatants. The targets are guerillas who’ve infiltrated the neighborhood, overwhelming the local authorities and fomenting chaos. After only minutes on patrol, the assassins go on the attack, quickly identifying and eliminating the enemy without harming a single bystander.

This scenario may sound like the plot of a Hollywood blockbuster, but it’s also a good metaphor to describe the activity of engineered immune cells against cancer cells. The assassins are called CAR-T (Chimeric Antigen Receptor-T) cells, and they receive their elite training at the hands of physicians and scientists, who teach them to recognize particular molecules on the surface of tumors.

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misciwriterseditors blog, Psychology, Uncategorized

The Science of What Keeps Us Apart

Author: Kaitlin Weskamp

Editors: Shweta Ramdas, Alex Taylor, and Kevin Boehnke

“… in diversity there is beauty and there is strength.” 
             ― Maya Angelou

Over time, there has been a general trend towards acceptance and inclusivity in the civil rights laws of the United States. From the abolition of slavery in 1865, to granting women the right to vote in 1920, to the legalization of gay marriage in 2015, we are making torturously-slow-but-steady progress towards the promise that “all men [and women] are created equal.”

Today, the majority of people in the U.S. agree with Maya Angelou that diversity lends strength to our community. However, racism, sexism, and homophobia remain enormous societal issues. Is there a neurological basis for these ideas? If so, how can we combat it?

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misciwriterseditors Biochemistry, blog

How to Fold (and Misfold) a Protein (Part 1)

Author: Sarah Kearns

Editors: David Mertz, Zulierys Santana-Rodriguez, and Scott Barolo

Proteins do most of the work in your body: Depending on their shape, they can digest your food, fire your neurons, give color to your eyes and allow you to see colors. Proteins follow instructions encoded in your DNA to fold into their shape, but how do they “know” what shape to fold into to perform their biological functions? What happens when they fold incorrectly?

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misciwriterseditors blog, Physics

String Theory: Worth the Wait or Just Stringing Us Along? (Part 2)

Author: Molly Kozminsky

Editors: Theresa Mau, Jimmy Brancho, and Alisha John

In my previous post, I discussed what string theory is, how it has not been experimentally verified, and how the existence of Higgs boson was proved fifty years after it was first proposed. In this post, I will continue to discuss the lengthy process of validating the theory of gravitational waves and where we stand with string theory research.

Continue reading “String Theory: Worth the Wait or Just Stringing Us Along? (Part 2)” →

misciwriterseditors blog, Physics

String Theory: Worth the Wait or Just Stringing Us Along? (Part 1)

Author: Molly Kozminsky

Editors: Theresa Mau, Jimmy Brancho, and Alisha John

July 2016 was all about taking potshots at string theorists. First, Belle Moyers pointed out that people questioned if their field is really science. Then they showed up in the Ghostbusters reboot as the villains.

But what is it about string theory that inspires such vitriol? String theory suffers from a number of problems that inspire strong feelings and entire books. Over forty years of research have passed without yielding the promised “Theory of Everything,” with many scientists questioning whether it is even possible to confirm the theory. But before we write off string theory entirely, it might help to think about other long-shot theories such as the Higgs boson and gravity waves, and more generally about string theory itself.

So, what is string theory anyway?

Continue reading “String Theory: Worth the Wait or Just Stringing Us Along? (Part 1)” →