Microcosm by Carl Zimmer

Posted on December 26, 2009 No Comments

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Related: Bacteriophages: The Most Common Life-Like Form on EarthForeign Cells Outnumber Human Cells in Our BodiesAmazing Designs of LifeAmazing Science: RetrovirusesOne Species’ Genome Discovered Inside Another’s

People are Superorganisms With Microbiomes of Thousands of Species

Posted on February 25, 2013 6 Comments

In a recent article in National Geographic Carl Zimmer has again done a good job of explaining the complex interaction between our bodies and the bacteria and microbes that make us sick, and keep us healthy.

The damage done by our indiscriminate use of antibiotics is not just the long term resistance that we create in bacteria (making the future more dangerous for people) that I have written about numerous times but it also endangers the person taking the anti-biotics in the short term. Sometimes the other damage is a tradeoff that should be accepted. But far too often we ignore the damage taking antibiotics too often does.

When You Swallow A Grenade

While antibiotics can discriminate between us and them, however, they can’t discriminate between them and them–between the bacteria that are making us sick and then ones we carry when we’re healthy. When we take a pill of vancomycin, it’s like swallowing a grenade. It may kill our enemy, but it kills a lot of bystanders, too.

If you think of the human genome as all the genes it takes to run a human body, the 20,000 protein-coding genes found in our own DNA are not enough. We are a superorganism that deploys as many as 20 million genes.

Before he started taking antibiotics, the scientists identified 41 species in a stool sample. By day 11, they only found 13. Six weeks after the antibiotics, the man was back up to 38 species. But the species he carried six weeks after the antibiotics did not represent that same kind of diversity he had before he took them. A number of major groups of bacteria were still missing.

They found that children who took antibiotics were at greater risk of developing inflammatory bowel disease later in life. The more antibiotics they took, the greater the risk. Similar studies have found a potential link to asthma as well.

The human body contains trillions of microorganisms — outnumbering human cells by 10 to 1. Because of their small size, however, microorganisms make up only about 1% to 3% of the body’s mass, but play a vital role in human health.

Where doctors had previously isolated only a few hundred bacterial species from the body, Human Microbiome Project (HMP) researchers now calculate that more than 10,000 microbial species occupy the human ecosystem. Moreover, researchers calculate that they have identified between 81% and 99% of all microorganismal genera in healthy adults.

“Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, Ph.D., NHGRI’s HMP program manager. “Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds, like vitamins and anti-inflammatories that our genome cannot produce.” Anti-inflammatories are compounds that regulate some of the immune system’s response to disease, such as swelling.

“Enabling disease-specific studies is the whole point of the Human Microbiome Project,” said Barbara Methé, Ph.D., of the J. Craig Venter Institute, Rockville, MD, and lead co-author of the Nature paper on the framework for current and future human microbiome research. “Now that we understand what the normal human microbiome looks like, we should be able to understand how changes in the microbiome are associated with, or even cause, illnesses.”

Read the full NIH press release on the normal bacterial makeup of the body

Related: Tracking the Ecosystem Within UsWhat Happens If the Overuse of Antibiotics Leads to Them No Longer Working?Antibacterial Products May Do More Harm Than GoodAntibiotics Too Often Prescribed for Sinus Woes

Evolution Follows a Predictable Genetic Pattern

Posted on November 1, 2012 No Comments

Far from random, evolution follows a predictable genetic pattern

The researchers carried out a survey of DNA sequences from 29 distantly related insect species, the largest sample of organisms yet examined for a single evolutionary trait. Fourteen of these species have evolved a nearly identical characteristic due to one external influence — they feed on plants that produce cardenolides, a class of steroid-like cardiotoxins that are a natural defense for plants such as milkweed and dogbane.

Though separated by 300 million years of evolution, these diverse insects — which include beetles, butterflies and aphids — experienced changes to a key protein called sodium-potassium adenosine triphosphatase, or the sodium-potassium pump, which regulates a cell’s crucial sodium-to-potassium ratio. The protein in these insects eventually evolved a resistance to cardenolides, which usually cripple the protein’s ability to “pump” potassium into cells and excess sodium out.

Andolfatto and his co-authors examined the sodium-potassium pump protein because of its well-known sensitivity to cardenolides. In order to function properly in a wide variety of physiological contexts, cells must be able to control levels of potassium and sodium. Situated on the cell membrane, the protein generates a desired potassium to sodium ratio by “pumping” three sodium atoms out of the cell for every two potassium atoms it brings in.

Cardenolides disrupt the exchange of potassium and sodium, essentially shutting down the protein, Andolfatto said. The human genome contains four copies of the pump protein, and it is a candidate gene for a number of human genetic disorders, including salt-sensitive hypertension and migraines. In addition, humans have long used low doses of cardenolides medicinally for purposes such as controlling heart arrhythmia and congestive heart failure.

Cool stuff. It makes sense to me which is nice (it is nice to get confirmation that I find what actually exists is sensible). When things that are true just seem crazy it is a bit disconcerting – like quantum mechanics. It is fun to read stuff that totally shakes up preconceived notions, but even then it is nice once I think understand it to find it sensible.

Related: All present-day Life on Earth Has A Single AncestorCambrian Explosion SongBacteriophages: The Most Common Life-Like Form on EarthMicrocosm by Carl Zimmer

The Information: A History, a Theory, a Flood by James Gleick

Posted on March 6, 2012 2 Comments

book cover image of The Information

James Gleick is a great science writer. I remember first reading his book, Chaos, which I loved. He continues to write engaging and entertaining books on science. His 2011 release The Information: A History, a Theory, a Flood, is now available in paperback.

From the invention of scripts and alphabets to the long-misunderstood talking drums of Africa, Gleick tells the story of information technologies that changed the very nature of human consciousness. Gleick provides portraits of the key figures contributing to the inexorable development of our modern understanding of information: Charles Babbage, the idiosyncratic inventor of the first great mechanical computer; Ada Byron, the brilliant and doomed daughter of the poet, who became the first true programmer; pivotal figures like Samuel Morse and Alan Turing; and Claude Shannon, the creator of information theory itself.

And now the information age arrives. The Information is the story of how we got here and where we are heading.

Related: science booksWhat Dogs Reveal About EvolutionMicrocosm by Carl ZimmerThe Last Lecture Book

How Bee Hives Make Decisions

Posted on February 28, 2012 1 Comment

The Secret Life of Bees by Carl Zimmer

The decision-making power of honeybees is a prime example of what scientists call swarm intelligence. Clouds of locusts, schools of fish, flocks of birds and colonies of termites display it as well. And in the field of swarm intelligence, Seeley is a towering figure. For 40 years he has come up with experiments that have allowed him to decipher the rules honeybees use for their collective decision-making. “No one has reached the level of experimentation and ingenuity of Tom Seeley,” says Edward O. Wilson of Harvard University.

Enthusiasm translates into attention. An enthusiastic scout will inspire more bees to go check out her site. And when the second-wave scouts return, they persuade more scouts to investigate the better site.

The second principle is flexibility. Once a scout finds a site, she travels back and forth from site to hive. Each time she returns, she dances to win over other scouts. But the number of dance repetitions declines, until she stops dancing altogether. Seeley and his colleagues found that honeybees that visit good sites keep dancing for more trips than honeybees from mediocre ones.

This decaying dance allows a swarm to avoid getting stuck in a bad decision. Even when a mediocre site has attracted a lot of scouts, a single scout returning from a better one can cause the hive to change its collective mind.

“Bees are to hives as neurons are to brains,” says Jeffrey Schall, a neuroscientist at Vanderbilt University. Neurons use some of the same tricks honeybees use to come to decisions. A single visual neuron is like a single scout. It reports about a tiny patch of what we see, just as a scout dances for a single site. Different neurons may give us conflicting ideas about what we’re actually seeing, but we have to quickly choose between the alternatives. That red blob seen from the corner of your eye may be a stop sign, or it may be a car barreling down the street.

To make the right choice, our neurons hold a competition, and different coalitions recruit more neurons to their interpretation of reality, much as scouts recruit more bees

Very cool stuff.

Related: Honeybees Warn Others of RisksWasps Used to Detect ExplosivesStudy of the Colony Collapse Disorder Continues as Bee Colonies Continue to Disappear

Our Genome Has Adopted Virus Genes Critical to Our Survival

Posted on February 16, 2012 No Comments

Mammals Made By Viruses by Carl Zimmer

Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years. They typically have gotten there by infecting eggs or sperm, inserting their own DNA into ours. There are 100,000 known fragments of viruses in the human genome, making up over 8% of our DNA. Most of this virus DNA has been hit by so many mutations that it’s nothing but baggage our species carries along from one generation to the next. Yet there are some viral genes that still make proteins in our bodies. Syncytin appeared to be a hugely important one to our own biology. Originally, syncytin allowed viruses to fuse host cells together so they could spread from one cell to another. Now the protein allowed babies to fuse to their mothers.

The big picture that’s now emerging is quite amazing. Viruses have rained down on mammals, and on at least six occasions, they’ve gotten snagged in their hosts and started carrying out the same function: building placentas.

Some mammals that scientists have yet to investigate, such as pigs and horses, don’t have the open layer of cells in their placenta like we do. Scientists have come up with all sorts of explanations for why that may be, mainly by looking for differences in the biology of each kind of mammals. But the answer may be simpler: the ancestors of pigs and horses might never have gotten sick with the right virus.

More amazing facts from science. This stuff is so interesting. Carl Zimmer is a fantastic science writer and he has written several great science books.

Related: Amazing Science, RetrovirusesMicrocosm by Carl ZimmerTen Things Everyone Should Know About ScienceParasite Rex

Evolution in New York City Wildlife

Posted on July 31, 2011 No Comments

Evolution Right Under Our Noses by Carl Zimmer

White-footed mice, stranded on isolated urban islands, are evolving to adapt to urban stress. Fish in the Hudson have evolved to cope with poisons in the water. Native ants find refuge in the median strips on Broadway. And more familiar urban organisms, like bedbugs, rats and bacteria, also mutate and change in response to the pressures of the metropolis. In short, the process of evolution is responding to New York and other cities the way it has responded to countless environmental changes over the past few billion years. Life adapts.

Dr. Wirgin and his colleagues were intrigued to discover that the Hudson’s population of tomcod, a bottom-dwelling fish, turned out to be resistant to PCBs. “There was no effect on them at all,” Dr. Wirgin said, “and we wanted to know why.”

In March, he and his colleagues reported that almost all the tomcod in the Hudson share the same mutation in a gene called AHR2. PCBs must first bind to the protein encoded by AHR2 to cause damage. The Hudson River mutation makes it difficult for PCBs to grab onto the receptor, shielding the fish from the chemical’s harm.

The AHR2 mutation is entirely missing from tomcod that live in northern New England and Canada. A small percentage of tomcod in Long Island and Connecticut carry the mutation. Dr. Wirgin and his colleagues concluded that once PCBs entered the Hudson, the mutant gene spread quickly.

Carl Zimmer again does a good job of explaining science in an engaging way. It is interesting to learn about science and evolution in urban environments. Lots of life manages to survive the challenges of urban life and it is interesting to learn what scientists are finding about that life.

Related: Trying to Find Pest Solutions While Hoping Evolution Doesn’t Exist Doesn’t WorkMicrocosm by Carl ZimmerNew Yorkers Help Robot Find Its Way in the Big CityParasite RexBackyard Wildlife: Great Spreadwing Damselfly

Trying to Find Pest Solutions While Hoping Evolution Doesn’t Exist Doesn’t Work

Posted on May 5, 2010 2 Comments

How To Make A Superweed

Melander wondered why some populations of scales were becoming able to resist pesticides. Could the sulfur-lime spray trigger a change in their biology, the way manual labor triggers the growth of callouses on our hands? Melander doubted it. After all, ten generations of scales lived and died between sprayings. The resistance must be hereditary, he reasoned. He sometimes would find families of scales still alive amidst a crowd of dead insects.

This was a radical idea at the time. Biologists had only recently rediscovered Mendel’s laws of heredity. They talked about genes being passed down from one generation to the next, yet they didn’t know what genes were made of yet. But they did recognize that genes could spontaneously change–mutate–and in so doing alter traits permanently.

In the short term, Melander suggested that farmers switch to fuel oil to fight scales, but he warned that they would eventually become resistant to fuel oil as well. In fact, the best way to keep the scales from becoming entirely resistant to pesticides was, paradoxically, to do a bad job of applying those herbicides. By allowing some susceptible scales to survive, farmers would keep their susceptible genes in the scale population. “Thus we may make the strange assertion that the more faulty the spraying this year the easier it will be to control the scale the next year,” Melander predicted.

What’s striking is how many different ways weeds have found to overcome the chemical. Scientists had thought that Roundup was invincible in part because the enzyme it attacks is pretty much the same in all plants. That uniformity suggests that plants can’t tolerate mutations to it; mutations must change its shape so that it doesn’t work and the plant dies. But it turns out that many populations of ryegrass and goosegrass have independently stumbled across one mutation that can change a single amino acid in the enzyme. The plant can still survive with this altered enzyme. And Roundup has a hard time attacking it thanks to its different shape.

Another way weeds fight off Roundup is through sheer numbers. Earlier this year an international team of scientists reported their discovery of how Palmer amaranth resists glyphosate. The plants make the ordinary, vulnerable form of the enzyme. But the scientists discovered that they have many extra copies of the gene for the enzyme–up to 160 extra copies, in fact.

What makes the evolution of Roundup resistance all the more dangerous is how it doesn’t respect species barriers. Scientists have found evidence that once one species evolves resistance, it can pass on those resistance genes to other species. They just interbreed, producing hybrids that can then breed with the vulnerable parent species.

Another great article from Carl Zimmer.

Related: Amazing Designs of LifeMicrocosm by Carl ZimmerParasite RexPigs Instead of Pesticides

Microbes Flourish In Healthy People

Posted on January 15, 2010 2 Comments

Bugs Inside: What Happens When the Microbes That Keep Us Healthy Disappear? by Katherine Harmon

The human body has some 10 trillion human cells—but 10 times that number of microbial cells. So what happens when such an important part of our bodies goes missing?

“Someone who didn’t have their microbes, they’d be naked,” says Martin Blaser, a professor of microbiology and chair of the Department of Medicine at New York University Langone Medical Center in New York City.

Even though it is such an apparently integral and ancient aspect of human health, scientists are still grasping for better ways to study human microbiota—before it changes beyond historical recognition. Borrowing models from outside of medicine has helped many in the field gain a better understanding of this living world within us. “The important concept is about extinctions,” Blaser says. “It’s ecology.”

The first step in understanding these systems is simply taking stock of what archaea, bacteria, fungi, protozoa and viruses are present in healthy individuals. This massive micro undertaking has been ongoing since 2007 through the National Institutes of Health’s (NIH) Human Microbiome Project. So far it has turned up some surprisingly rich data, including genetic sequencing for some 205 of the different genera that live on healthy human skin.

Despite the flood of new data, Foxman laughs when asked if there is any hope for a final report from the Human Microbiome Project any time soon. “This is the very, very beginning,” she says, comparing this project with the NIH’s Human Genome Project, which jump-started a barrage of new genetic research. “There are basic, basic questions that we don’t know the answers to,” she says, such as how different microbiota are between random individuals or family members; how much microbiota change over time; or how related the microbiota are to each other on or inside a person’s body.

Related: Microcosm by Carl ZimmerTracking the Ecosystem Within UsAlligator Blood Provides Strong Resistance to Bacteria and VirusesBeneficial Bacteria

Dennis Bray Podcast on Microbes As Computers

Posted on October 13, 2009 1 Comment

Carl Zimmer interviews Dennis Bray in an interesting podcast:

Dennis Bray is an active professor emeritus in both the Department of Physiology and Department of Neuroscience at the University of Cambridge. He studies the behavior of microbes–how they “decide” where to swim, when to divide, and how best to manage the millions of chemical reactions taking place inside their membranes. For Bray, microbes are tiny, living computers, with genes and proteins serving the roles of microprocessors.

Related: E. Coli IndividualityWetware: A Computer in Every Living Cell by Dennis Bray – Programing BacteriaMicro-robots to ‘swim’ Through Veins

The Nobel Prize in Chemistry 2008

Posted on October 8, 2008 2 Comments

The Nobel Prize in Chemistry 2008 is evenly shared by Osamu Shimomura, Boston University Medical School, USA; Martin Chalfie, Columbia University, New York, USA and Roger Y. Tsien, University of California, San Diego, USA for discovery and work with glowing green fluorescent protein.

The remarkable brightly glowing green fluorescent protein, GFP, was first observed in the beautiful jellyfish, Aequorea victoria in 1962. Since then, this protein has become one of the most important tools used in contemporary bioscience. With the aid of GFP, researchers have developed ways to watch processes that were previously invisible, such as the development of nerve cells in the brain or how cancer cells spread.

Tens of thousands of different proteins reside in a living organism, controlling important chemical processes in minute detail. If this protein machinery malfunctions, illness and disease often follow. That is why it has been imperative for bioscience to map the role of different proteins in the body.

This year’s Nobel Prize in Chemistry rewards the initial discovery of GFP and a series of important developments which have led to its use as a tagging tool in bioscience. By using DNA technology, researchers can now connect GFP to other interesting, but otherwise invisible, proteins. This glowing marker allows them to watch the movements, positions and interactions of the tagged proteins.

Researchers can also follow the fate of various cells with the help of GFP: nerve cell damage during Alzheimer’s disease or how insulin-producing beta cells are created in the pancreas of a growing embryo. In one spectacular experiment, researchers succeeded in tagging different nerve cells in the brain of a mouse with a kaleidoscope of colors.


Osamu Shimomura
, a Japanese citizen, was born 1928 in Kyoto, Japan. He received his Ph.D. in organic chemistry 1960 from Nagoya University, Japan. first isolated GFP from the jellyfish Aequorea victoria, which drifts with the currents off the west coast of North America. He discovered that this protein glowed bright green under ultraviolet light.

Martin Chalfie demonstrated the value of GFP as a luminous genetic tag for various biological phenomena. In one of his first experiments, he coloured six individual cells in the transparent roundworm Caenorhabditis elegans with the aid of GFP.

Roger Y. Tsien contributed to our general understanding of how GFP fluoresces. He also extended the colour palette beyond green allowing researchers to give various proteins and cells different colours. This enables scientists to follow several different biological processes at the same time.

Related: 2007 Nobel Prize in ChemistryNobel Laureate Initiates Symposia for Student ScientistsNobel Prize in Chemistry (2006)Webcasts by Chemistry and Physics Nobel Laureates