Tag Archives: things that blow Diana’s mind

The (Mostly) Untold Story of the Oxygen Revolution

[Cyanobacteria–green, brown, and orange streaks–grow in hot spring at Yellowstone National Park. Photo by Harvey Barrison via Flickr & Creative Commons 2.0] 

The troublemakers were hardly new to the neighborhood. For 300 million years, they had lived in the water column, floating in the sunlight near the surface, sending tiny plumes of toxic gas into the air. That was how they ate: sunlight in, poison out. But it was nothing the ecosystem couldn’t handle. The atmosphere was vast, and the troublemakers were microscopic. The poison diffused. Life went on.  

Until something changed. For some reason, there were more of the green troublemakers. Quadrillions more. So many more that their poison became the air itself. An entire world’s atmosphere transformed. Those that could tolerate the miasma grew and spread. Others survived in pockets of the planet where the new air couldn’t reach them. Uncountable numbers died.

The sunlight-eating oxygen-makers inherited the Earth.

In other words, 2.3 billion years ago, photosynthesis caused a mass extinction.

Continue reading “The (Mostly) Untold Story of the Oxygen Revolution” »

Why You Can Blame Your Metabolism on Liver Proteomics Instead of Your Genes

Blaming things on genetics–everything from lateness to diet quirks–is wildly popular these days. However, DNA’s role in your body’s overall destiny has been greatly exaggerated. Sure, DNA is the “master blueprint”, but any one gene from that blueprint can contain instructions for making hundreds or thousands of tiny cell parts. And even so, there are plenty of cell parts that defy the master template.

Proteins–tiny biological machines made from proteins that you eat– are key players in pretty much every biological process that happens. Yet, their behavior remains almost impossible to decipher. Scientists have gotten pretty good at decoding genes and RNA snippets, and tracking a single type of protein is pretty doable. Also, since RNA snippets are templates for building proteins, scientists often use RNA data to estimate the total number of proteins. But there are thousands of different protein forms in every cell; tracking all of them at once remains basically impossible.

However, variations in those proteins can make an enormous difference in processes like weight gain. And according to a new study, our most-used method for estimating protein numbers–counting the RNAs–only works about 30% of the time. 

As in, according to science’s latest numbers, at least 2/3rds of all “genetic bad luck” happens outside of genes. 

Continue reading “Why You Can Blame Your Metabolism on Liver Proteomics Instead of Your Genes” »

Hybrid Problems: Chimerism, Synthetic Life, and Mixed Heritage

[A hybrid orchid. Photo by Mark Freeth.] 

[“Molecularization of Identity” Workshop Recap, Part 2]

Genomes of indigenous people, which often include genes found nowhere else in the world, can be powerful symbols for nations that want to showcase their uniqueness. 

But when the Mexico’s Instituto Nacional de Medicina Genómica  (INMEGEN)  set out to find examples of Mexico’s indigenous genome, they ran into problems. Namely, that pretty much every population in Mexico, no matter how remote, includes people of mixed ethnic ancestry.

INMEGEN’s attempts to reconstruct an indigenous identity were the focus of not one, but two talks at Harvard STS’s “Molecularization of Identity Conference“, one by Vivette García Deister–who teaches in the Science & Technology Studies department at Universidad Nacional Autónoma de México– and one by Ernesto Schwartz Marin of Durham University.  Since that conference was chock-full of important studies on the social dynamics around science, I’m writing a 3-part recap, of which this post is part 2. (See Part 1 here).

García Deister began her presentation by introducing the concept of Mestizaje, a blend of Native American, Spanish/European, and African heritage that characterizes Latin American countries. The majority of Mexicans are of Mestizo–or “mixed” descent–so naturally, the Mexican government wanted to know the ratios of  “Amerindian”, “European”, and “African” genes in their country’s population.

To do that, they had to try to establish a baseline “Indigenous” genome to compare to their representative “Mestizo” genome. García Deister calls these hypothetical representative genomes “Genetic Avatars”. 

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[Interestingly, the “avatars” in the uber-successful movie Avatar are literally synthetic genetic hybrids, with human DNA spliced into Na’vi genome. Image by Michael Kordahl.]

Colonist outsiders love to look for “Genetic Avatars” because it gives them a way to quantify and tell stories about Latin American hybridity, or MestizajeGarcía Deister argued.  Scientists and policy makers  justify it by arguing that it’s important to know their country’s history and vital to look for genetic clues to various diseases.

But does any of that make the Mexican Genome Project any less of a colonial enterprise? Not really…

Continue reading “Hybrid Problems: Chimerism, Synthetic Life, and Mixed Heritage” »

“Perceive. Identify. Regulate.” How to be Racist with 21st Century Science

[Image via Brockhaus and Efron Encyclopedic Dictionary & Creative Commons]

[“Molecularization of Identity” Workshop Recap, Part 1]

The diagram of racism was shockingly simple: four highlighted brain regions with black arrows between them, forming an almost-isosceles triangle.

racism_brain_diagram

[Diagram by Elizabeth Phelps’ group at NYU via The Brain Bank blog]

Perception. Identification. Regulation. 

Those are the three steps in the cognition of racism, according to a handful of neuroscientists.

The diagram’s presenters weren’t the neuroscientists themselves, but a pair of sociologists who study neuroscientistsOliver Rollins of Penn and Torsten Heinemann of University of Hamburg.  The neuroscientists who try to spot neural patterns of racism in fMRI argue that  before a racist action occurs, several things happen in a person’s brain: First, they have to see or hear the other person, which triggers a response in the amygdala, a brain structure that contributes to people becoming jumpy and/or aggressive. Next, the signal moves to the anterior cingulate cortex, which identifies the other person as a threat or a non-threat. Finally, the signal moves to the prefrontal cortex, which makes a conscious decision: “Do I hurt or try to escape from this person?” 

The neuroscientists who study racism tend to be optimistic about the possibility of changing racist individuals’ cognition patterns via social interaction or even through medication, Rollins and Heinemann explained. However,  though the neuroscientists’ approach is commendable, it doesn’t address systemic racism. 

“If there’s a racist ‘Stop-and-Frisk‘ policy in place that allows you to stop any black men, it may not matter whether the individual cop has a racial bias,” Rollins said.

Continue reading ““Perceive. Identify. Regulate.” How to be Racist with 21st Century Science” »

5 Amazing Feats Performed by “Meta-Genes”

[Image via the NIH Image Gallery. Photo by Alex Ritter, Jennifer Lippincott Schwartz, and Gillian Griffiths. Full video, complete with narration here.] 

Under the Radar: A series of listicles about biology concepts you definitely won’t find in newspaper headlines.

#1: Be a Navigation App for Immune Cells

Natural killer cells, or “NK cells” are the human body’s best defense against cancer.  While other types of immune cells often ignore tumor cells, natural killer cells specialize in finding and destroying human cells that look either infected or like cancer mutants. In leukemia patients,  a higher number of active natural killer cells ups the patient’s chances for survival, so much so that  researchers are experimenting with transfusing NK cells into patients.

Just one problem there: Active natural killer cells die without a strong support network.

Dormant NK cells can survive in the bloodstream for a long time, but once activated, natural killers have to make a b-line for cells carrying a marker called IL-15 or die,  but until a study in Monday’s edtion of PNAS , no one knew how natural killers knew to look for IL-15. The study, led by Vanderbilt immunologist Eric Sebzda and grad student Whitney Rabacal, traced NK cells’ IL-15 homing ability back to a biochemical with the horrendous name “Kruppel-like Factor 2” (KLF2).

KLF2, oddly enough, also exerts a strong navigational influence on the immune system’s T-cells and B-cells.  Even though all three types of cells fall under the “white blood cell” umbrella, the notion that one protein could control navigation in all three is pretty weird.  Crawling and navigating are complex tasks, requiring coordination between dozens of genes. “[NK cell migration] is totally different from how t-cells and b-cells circulate,” Sebzda said.

Additionally, taking away KLF2 has distinctive effects on each type of cell: KLF2-less t-cells vacate the central body and crawl out to lab mice’s fingers and toes, KLF2-less b-cells all congregate at the spleen (which creates some serious problems for those lab mice), and KLF2-less natural killers end up dying alone.

So KLF2 could be super-useful for improving cancer immunotherapy. But why is KLF2 so versatile in the first place?

The answer lies in KLF2’s ability to bind to a certain recurring DNA base pair sequence, one that presumably earmarks the genes needed in each immune system navigation system, and it’s far from the only protein with such abilities…

Continue reading “5 Amazing Feats Performed by “Meta-Genes”” »

Splice of Life: 3 Examples of How Nature Edits Its Own Genes

About the “Under the Radar” series: Some scientific concepts come up again and again in interviews with scientists but never find their way into newspaper headlines. Each post in this series follows one of those biology “bogeys” that fly under journalism’s radar through 3 different mini-stories.

Story #1: Scientists splice up a CRISPR chicken…and find an evolutionary shortcut

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Birds’ brains have all of the tools to make mammal-like neurons, according to a study in Science from August And, incredibly, the researchers behind the study only had to tinker with one gene  that changes how chicken cells edit their RNA to unlock several seemingly unrelated mammal neuron traits in chicken neural precursor cells.

It was as if the chicken cells instantly acquired a whole bunch of mutations at once, instead of just one. 

Researchers think that this gene editing process– aka “alternative splicing”–may explain why some traits seem to have evolved at such high speeds.

“This is a process that has diverged very rapidly during evolution to produce different versions of proteins,” University of Toronto geneticist Ben Blencowe explained in a phone interview.

500 million years is a long time to evolve, but it’s still hard to account for all of the diversity in vertebrates based on variation in DNA base pairs alone.

The key to animal diversity lies in an aspect of biology that your high school biology class kinda sorta covered, but lots of people forget all the steps after they’re done cramming for the test.

Continue reading “Splice of Life: 3 Examples of How Nature Edits Its Own Genes” »

Gaia Theory, “Irresponsible Heroes”, & Why We’re Like Cyanobacteria- Recap of talk by Dr. Andrew Knoll & Dr. David Grinspoon

The Talk:

“Planetary Changes from Deep Time to the 4th Kind”

In Plain English:

Life doesn’t just adapt to geochemical features; it transforms them simply by…living.

The Speaker:

Andrew Knoll of Harvard and David Grinspoon of the Planetary Science Institute

The Sponsor:

Planet and Life Series, sponsored by MIT Earth, Atmospheric, and Planetary Sciences dept. (EAPS)

What it covered:

Climate shapes life. This is a fact. But when you get right down to it, life is not a fragile, softly-treading phenomenon; every living cell is an interlocking network of chemical reactions. Nutrients and resources are taken in; other chemicals get spewed out.

It would be rather amazing if all those living organisms didn’t have some effect on the non-living environment. But what kinds of impacts? And how can we, as humans with advanced technology, understand and predict the effects our actions will have on the environment?

These are the questions being addressed by The Planets and Life Series at MIT, and the kick-off event, held back in September (unfortunately, I do not get paid to write this blog) was a doozy. Continue reading “Gaia Theory, “Irresponsible Heroes”, & Why We’re Like Cyanobacteria- Recap of talk by Dr. Andrew Knoll & Dr. David Grinspoon” »

BICEP2 & Gravitational Waves 101: Recap of Panel Discussion ft. Alan Guth, John Kovac, Scott Hughes, & Max Tegmark

The Talk:

The BICEP2 Results and What They Mean: The First Observation of Gravitational Waves from the Early Universe

In Plain English:

The guys who came up with gravitational wave theory explain the gravitational wave story that’s been blowing up everybody’s Facebook feed in terms undergrads can understand

The Speakers:

Alan Guth of MIT (the guy who came up with repulsive gravity theory), Scott Hughes of MIT, Max Tegmark of MIT, and John Kovac of Harvard (the Primary Investigator on the telescope in question)

The Sponsor:

MIT Physics Department

What it covered:

When the BICEP2 team announced that they had found b-mode-style (aka “swirly pattern”) gravitational waves that confirmed inflation model of universe-formation, the internet exploded. The video feed for the press conference crashed. When the team posted their paper on arXiv, the it got 3.5 million hits in the first 11 hours.

That’s for the formal academic research write-up (and the average academic research write-up is lucky if 35 people read it all the way through). In the first 11 hours. Continue reading “BICEP2 & Gravitational Waves 101: Recap of Panel Discussion ft. Alan Guth, John Kovac, Scott Hughes, & Max Tegmark” »

Investigating neural patterns in the younger siblings of autistic children – Recap of talk by Dr. Charles Nelson

The Talk:

A Cognitive Neuroscience Approach to the Early Identification of Autism

In Plain English:

A scientist investigates the patterns of neural wiring in infants whose older siblings have autism

The Speaker:

Charles Nelson of Boston Children’s Hospital

The Sponsor:

Simons Center for the Social Brain at MIT

What it covered:

Dr. Charles “Chuck” Nelson is one of the best known (and judging from the way he was introduced and addressed at this colloquium, he’s also one of the best-liked and most-respected) researchers in the field of neurological development. Before coming to Boston Children’s Hospital, he made a name for himself by working on face recognition in infants.

He stopped by the MIT Simons Center for the Social Brain colloquium to tell other researchers about his team’s latest findings in  neurological development in autistic infants (and their siblings).

He prefaced his talk by saying that he was really torn about whether this talk should focus on the more mechanistic aspects of his work (“Which neurons are firing?” & “What neurotransmitters are making them do that?” type questions) or the more descriptive aspects (questions about overall statistical trends in “at-risk” populations) of his work. Continue reading “Investigating neural patterns in the younger siblings of autistic children – Recap of talk by Dr. Charles Nelson” »

Bioelectric signals tell organisms when to grow limbs (among other things) – Recap of talk by Dr. Michael Levin

[This post is part of a series called “Brown Bag Lunch Reports” where I recap some of the academic talks given at college campuses in and around the city of Boston. Let me know what you think of the post format and what kinds of talks you think I should recap next!]

The Talk’s Title:

Manipulating natural bioelectric gradients to control growth and form in embryogenesis, regeneration, and cancer

In Plain English:

Changing the ways electric signals flow through living tissues alters the organisms’ growth in profound ways, including (but not limited to) the regeneration of complex organs like eyes and limbs.

The Speaker:

Michael Levin, Ph.d. of the Tufts Center for Regenerative Medicine and Developmental Biology

The Location:

Northeastern University’s Center for Interdisciplinary Research on Complex Systems

What it covered:

Dr. Michael Levin’s lab investigates a little-known (and if half of what he says is true, very underappreciated) topic in biology: the effect of variation in the electric charges of cells on morphological development. If that last sentence sounded like a random string of sciencey-sounding words from different disciplines, there’s a reason for that: Dr. Levin’s work draws heavily from both physics and molecular biology. Continue reading “Bioelectric signals tell organisms when to grow limbs (among other things) – Recap of talk by Dr. Michael Levin” »