Doe Science news source
The DOE Science News Source is a Newswise initiative to promote research news from the Office of Science of the DOE to the public and news media.
  • 2015-07-28 10:05:00
  • Article ID: 637835

New Computer Model Could Explain how Simple Molecules Took First Step Toward Life

Two Brookhaven researchers developed theoretical model to explain the origins of self-replicating molecules

  • Credit: Brookhaven National Laboratory

    Brookhaven researchers Sergei Maslov (left) and Alexi Tkachenko developed a theoretical model to explain molecular self-replication.

  • Credit: Brookhaven National Laboratory

    A schematic drawing of template-assisted ligation, shown in this model to give rise to autocatalytic systems.

New Computer Model Could Explain how Simple Molecules Took First Step Toward Life

Two Brookhaven researchers developed theoretical model to explain the origins of self-replicating molecules

July 28, 2015

UPTON, NY—Nearly four billion years ago, the earliest precursors of life on Earth emerged. First small, simple molecules, or monomers, banded together to form larger, more complex molecules, or polymers. Then those polymers developed a mechanism that allowed them to self-replicate and pass their structure on to future generations.

We wouldn't be here today if molecules had not made that fateful transition to self-replication. Yet despite the fact that biochemists have spent decades searching for the specific chemical process that can explain how simple molecules could make this leap, we still don't really understand how it happened.

Now Sergei Maslov, a computational biologist at the U.S. Department of Energy's Brookhaven National Laboratory and adjunct professor at Stony Brook University, and Alexei Tkachenko, a scientist at Brookhaven's Center for Functional Nanomaterials (CFN), have taken a different, more conceptual approach. They've developed a model that explains how monomers could very rapidly make the jump to more complex polymers. And what their model points to could have intriguing implications for CFN's work in engineering artificial self-assembly at the nanoscale. Their work is published in the July 28, 2015 issue of The Journal of Chemical Physics.

To understand their work, let's consider the most famous organic polymer, and the carrier of life's genetic code: DNA. This polymer is composed of long chains of specific monomers called nucleotides, of which the four kinds are adenine, thymine, guanine, and cytosine (A, T, G, C). In a DNA double helix, each specific nucleotide pairs with another: A with T, and G with C. Because of this complementary pairing, it would be possible to put a complete piece of DNA back together even if just one of the two strands was intact.

While DNA has become the molecule of choice for encoding biological information, its close cousin RNA likely played this role at the dawn of life. This is known as the RNA world hypothesis, and it's the scenario that Maslov and Tkachenko considered in their work.

The single complete RNA strand is called a template strand, and the use of a template to piece together monomer fragments is what is known as template-assisted ligation. This concept is at the crux of their work. They asked whether that piecing together of complementary monomer chains into more complex polymers could occur not as the healing of a broken polymer, but rather as the formation of something new.

"Suppose we don't have any polymers at all, and we start with just monomers in a test tube," explained Tkachenko. "Will that mixture ever find its way to make those polymers? The answer is rather remarkable: Yes, it will! You would think there is some chicken-and-egg problem—that, in order to make polymers, you already need polymers there to provide the template for their formation. Turns out that you don't really."

Instilling memory

Maslov and Tkachenko's model imagines some kind of regular cycle in which conditions change in a predictable fashion—say, the transition between night and day. Imagine a world in which complex polymers break apart during the day, then repair themselves at night. The presence of a template strand means that the polymer reassembles itself precisely as it was the night before. That self-replication process means the polymer can transmit information about itself from one generation to the next. That ability to pass information along is a fundamental property of life.

"The way our system replicates from one day cycle to the next is that it preserves a memory of what was there," said Maslov. "It's relatively easy to make lots of long polymers, but they will have no memory. The template provides the memory. Right now, we are solving the problem of how to get long polymer chains capable of memory transmission from one unit to another to select a small subset of polymers out of an astronomically large number of solutions."

According to Maslov and Tkachenko's model, a molecular system only needs a very tiny percentage of more complex molecules—even just dimers, or pairs of identical molecules joined together—to start merging into the longer chains that will eventually become self-replicating polymers. This neatly sidesteps one of the most vexing puzzles of the origins of life: Self-replicating chains likely need to be very specific sequences of at least 100 paired monomers, yet the odds of 100 such pairs randomly assembling themselves in just the right order is practically zero.

"If conditions are right, there is what we call a first-order transition, where you go from this soup of completely dispersed monomers to this new solution where you have these long chains appearing," said Tkachenko. "And we now have this mechanism for the emergence of these polymers that can potentially carry information and transmit it downstream. Once this threshold is passed, we expect monomers to be able to form polymers, taking us from the primordial soup to a primordial soufflé."

While the model's concept of template-assisted ligation does describe how DNA—as well as RNA—repairs itself, Maslov and Tkachenko's work doesn't require that either of those was the specific polymer for the origin of life.

"Our model could also describe a proto-RNA molecule. It could be something completely different," Maslov said.

Order from disorder

The fact that Maslov and Tkachenko's model doesn't require the presence of a specific molecule speaks to their more theoretical approach.

"It's a different mentality from what a biochemist would do," said Tkachenko. "A biochemist would be fixated on specific molecules. We, being ignorant physicists, tried to work our way from a general conceptual point of view, as there's a fundamental problem."

That fundamental problem is the second law of thermodynamics, which states that systems tend toward increasing disorder and lack of organization. The formation of long polymer chains from monomers is the precise opposite of that.

"How do you start with the regular laws of physics and get to these laws of biology which makes things run backward, which make things more complex, rather than less complex?" Tkachenko queried. "That's exactly the jump that we want to understand."

Applications in nanoscience

The work is an outgrowth of efforts at the Center for Functional Nanomaterials, a DOE Office of Science User Facility, to use DNA and other biomolecules to direct the self-assembly of nanoparticles into large, ordered arrays. While CFN doesn't typically focus on these kinds of primordial biological questions, Maslov and Tkachenko's modeling work could help CFN scientists engaged in cutting-edge nanoscience research to engineer even larger and more complex assemblies using nanostructured building blocks.

"There is a huge interest in making engineered self-assembled structures, so we were essentially thinking about two problems at once," said Tkachenko. "One is relevant to biologists, and second asks whether we can engineer a nanosystem that will do what our model does."

The next step will be to determine whether template-aided ligation can allow polymers to begin undergoing the evolutionary changes that characterize life as we know it. While this first round of research involved relatively modest computational resources, that next phase will require far more involved models and simulations.

Maslov and Tkachenko's work has solved the problem of how long polymer chains capable of information transmission from one generation to the next could emerge from the world of simple monomers. Now they are turning their attention to how such a system could naturally narrow itself down from exponentially many polymers to only a select few with desirable sequences.

"What we needed to show here was that this template-based ligation does result in a set of polymer chains, starting just from monomers," said Tkachenko. "So the next question we will be asking is whether, because of this template-based merger, we will be able to see specific sequences that will be more 'fit' than others. So this work sets the stage for the shift to the Darwinian phase."

This work was supported by the DOE Office of Science.

Brookhaven National Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. Brookhaven is operated and managed for DOE's Office of Science by Brookhaven Science Associates, a limited-liability company founded by the Research Foundation for the State University of New York on behalf of Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit applied science and technology organization.

Related Links

Scientific Paper: "Spontaneous emergence of autocatalytic information-coding polymers" http://scitation.aip.org/content/aip/journal/jcp/143/2/10.1063/1.4922545

Media contact: Peter Genzer, 631-344-3174, genzer@bnl.gov

X
X
X
  • Filters

  • × Clear Filters

The Challenge of Estimating Alaska's Soil Carbon Stocks

A geospatial analysis determined the optimal distribution of sites needed to reliably estimate Alaska's vast soil carbon.

Strain-Free Epitaxy of Germanium Film on Mica

Germanium was the material of choice in the early history of electronic devices, and due to its high charge carrier mobility, it's making a comeback. It's generally grown on expensive single-crystal substrates, adding another challenge to making it sustainably viable for most applications. To address this aspect, researchers demonstrate an epitaxy method that incorporates van der Waals' forces to grow germanium on mica. They discuss their work in the Journal of Applied Physics.

Unplugging the Cellulose Biofuel Bottleneck

Molecular-level understanding of cellulose structure reveals why it resists degradation and could lead to cost-effective biofuels.

Detailed View of Immune Proteins Could Lead to New Pathogen-Defense Strategies

Biologists at Berkeley Lab and UC Berkeley used cryo-EM to resolve the structure of a ring of proteins used by the immune system to summon support when under attack, providing new insight into potential strategies for protection from pathogens. The researchers captured the high-resolution image of a protein ring, called an inflammasome, as it was bound to flagellin, a protein from the whiplike tail used by bacteria to propel themselves forward.

Unlocking the Secrets of Ebola

Scientists have identified a set of biomarkers that indicate which patients infected with the Ebola virus are most at risk of dying from the disease. The results come from one of the most in-depth studies ever of blood samples from patients with Ebola.

Scientists Make First Observations of How a Meteor-Like Shock Turns Silica Into Glass

Studies at the Department of Energy's SLAC National Accelerator Laboratory have made the first real-time observations of how silica - an abundant material in the Earth's crust - easily transforms into a dense glass when hit with a massive shock wave like one generated from a meteor impact.

How Fungal Enzymes Break Down Plant Cell Walls

Lignocellulose-degrading enzyme complexes could improve biofuel production.

Stretching to Perfection of 2-D Semiconductors

Scientists use heat and mismatched surfaces to stretch films that can potentially improve the efficient operation of devices.

Simple is Beautiful in Quantum Computing

Defect spins in diamond were controlled with a simpler, geometric method, leading to faster computing.

Replace or Wait? Study Says Swap All Incandescent Bulbs Now, but Hold on to CFLs, older LEDs

LED light bulbs are getting cheaper and more energy efficient every year. So, does it make sense to replace less-efficient bulbs with the latest light-emitting diodes now, or should you wait for future improvements and even lower costs?


  • Filters

  • × Clear Filters

Argonne to Install Comanche System to Explore ARM Technology for High-Performance Computing

Argonne National Laboratory is collaborating with Hewlett Packard Enterprise (HPE) to provide system software expertise and a development ecosystem for a future high-performance computing (HPC) system based on 64-bit ARM processors.

CANDLE Shines in 2017 HPCwire Readers' and Editors' Choice Awards

Argonne National Laboratory has been recognized in the annual <em>HPCwire</em> Readers' and Editors' Choice Awards, presented at the 2017 International Conference for High Performance Computing, Networking, Storage and Analysis (SC17), in Denver, Colorado.

SLAC's Helen Quinn Honored with 2018 Benjamin Franklin Medal in Physics

Helen Quinn, a professor emerita at the Department of Energy's SLAC National Accelerator Laboratory and Stanford University, will receive the 2018 Benjamin Franklin Medal in Physics - one of eight prestigious Franklin Institute Awards that will be handed out in Philadelphia next April.

PPPL Honors Grierson and Greenough for Distinguished Research and Engineering Achievements

Article describes PPPL's presentation of 2017 Kaul Prize and Distinguished Engineering Fellow awards.

INCITE Grants of 5.95 Billion Hours Awarded to 55 Computational Research Projects

The U.S. Department of Energy's Office of Science announced 55 projects with high potential for accelerating discovery through its Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program. The projects will share 5.95 billion core-hours on three of America's most powerful supercomputers dedicated to capability-limited open science and support a broad range of large-scale research campaigns from infectious disease treatment to next-generation materials development.

Former SLAC Director Jonathan Dorfan Awarded Japan's Order of the Rising Sun

Former SLAC Director and Stanford University Professor Emeritus Jonathan Dorfan has been awarded Japan's Order of the Rising Sun, Gold and Silver Star for his contributions as founding president of the Okinawa Institute of Science and Technology Graduate University (OIST). It is the highest award Japan bestows on university presidents.

Jefferson Lab Staff Scientist Honored with APS Fellowship

Fulvia Pilat, a staff scientist at the Department of Energy's Thomas Jefferson National Accelerator Facility, has been named a fellow of the American Physical Society. The honor is bestowed by members of APS on their peers for exceptional contributions to their fields.

First Northwest Theoretical Chemistry Conference Is a Hit!

The first Northwest Theoretical Chemistry Conference was a success. The event offered ~50 early career theorists and students opportunities to present talks in a nurturing environment that developed and advanced collaborations.

Argonne Forms New Divisions to Focus on Computation and Data Science Strengths

Argonne has formed two new research divisions to focus its lab-wide foundational expertise on computational science and data science activities.

Hermann Grunder Recognized by IEEE Nuclear and Plasma Sciences Society

Dr. Hermann Grunder, Founding Director of Jefferson Lab, has been selected as one of two recipients of the 2018 IEEE NPSS Particle Accelerator Science and Technology (PAST) Award.


  • Filters

  • × Clear Filters

The Challenge of Estimating Alaska's Soil Carbon Stocks

A geospatial analysis determined the optimal distribution of sites needed to reliably estimate Alaska's vast soil carbon.

Unplugging the Cellulose Biofuel Bottleneck

Molecular-level understanding of cellulose structure reveals why it resists degradation and could lead to cost-effective biofuels.

How Fungal Enzymes Break Down Plant Cell Walls

Lignocellulose-degrading enzyme complexes could improve biofuel production.

Stretching to Perfection of 2-D Semiconductors

Scientists use heat and mismatched surfaces to stretch films that can potentially improve the efficient operation of devices.

Simple is Beautiful in Quantum Computing

Defect spins in diamond were controlled with a simpler, geometric method, leading to faster computing.

The Effect of Hurricanes on Puerto Rico's Dry Forests

More frequent storms turn forests from carbon source to sink.

A Chemical Thermometer for Tropical Forests

Monoterpene measures how certain forests respond to heat stress.

Where a Leaf Lands and Lies Influences Carbon Levels in Soil for Years to Come

Whether carbon comes from leaves or needles affects how fast it decomposes, but where it ends up determines how long it's available.

Twisting Molecule Wrings More Power from Solar Cells

Readily rotating molecules let electrons last, resulting in higher solar cell efficiency.

Rules Are Only Suggestions in Heavy Elements

The arrangement of electrons in an exotic human-made element shows that certain properties of heavy elements cannot be predicted using lighter ones.


Spotlight

Tuesday October 03, 2017, 01:05 PM

Stairway to Science

Argonne National Laboratory

Thursday September 28, 2017, 12:05 PM

After-School Energy Rush

Argonne National Laboratory

Thursday September 28, 2017, 10:05 AM

Bringing Diversity Into Computational Science Through Student Outreach

Brookhaven National Laboratory

Thursday September 21, 2017, 03:05 PM

From Science to Finance: SLAC Summer Interns Forge New Paths in STEM

SLAC National Accelerator Laboratory

Thursday September 07, 2017, 02:05 PM

Students Discuss 'Cosmic Opportunities' at 45th Annual SLAC Summer Institute

SLAC National Accelerator Laboratory

Thursday August 31, 2017, 05:05 PM

Binghamton University Opens $70 Million Smart Energy Building

Binghamton University, State University of New York

Wednesday August 23, 2017, 05:05 PM

Widening Horizons for High Schoolers with Code

Argonne National Laboratory

Saturday May 20, 2017, 12:05 PM

Rensselaer Polytechnic Institute Graduates Urged to Embrace Change at 211th Commencement

Rensselaer Polytechnic Institute (RPI)

Monday May 15, 2017, 01:05 PM

ORNL, University of Tennessee Launch New Doctoral Program in Data Science

Oak Ridge National Laboratory

Friday April 07, 2017, 11:05 AM

Champions in Science: Profile of Jonathan Kirzner

Department of Energy, Office of Science

Wednesday April 05, 2017, 12:05 PM

High-Schooler Solves College-Level Security Puzzle From Argonne, Sparks Interest in Career

Argonne National Laboratory

Tuesday March 28, 2017, 12:05 PM

Champions in Science: Profile of Jenica Jacobi

Department of Energy, Office of Science

Friday March 24, 2017, 10:40 AM

Great Neck South High School Wins Regional Science Bowl at Brookhaven Lab

Brookhaven National Laboratory

Wednesday February 15, 2017, 04:05 PM

Middle Schoolers Test Their Knowledge at Science Bowl Competition

Argonne National Laboratory

Friday January 27, 2017, 04:00 PM

Haslam Visits ORNL to Highlight State's Role in Discovering Tennessine

Oak Ridge National Laboratory

Tuesday November 08, 2016, 12:05 PM

Internship Program Helps Foster Development of Future Nuclear Scientists

Oak Ridge National Laboratory

Friday May 13, 2016, 04:05 PM

More Than 12,000 Explore Jefferson Lab During April 30 Open House

Thomas Jefferson National Accelerator Facility

Monday April 25, 2016, 05:05 PM

Giving Back to National Science Bowl

Ames Laboratory

Friday March 25, 2016, 12:05 PM

NMSU Undergrad Tackles 3D Particle Scattering Animations After Receiving JSA Research Assistantship

Thomas Jefferson National Accelerator Facility

Tuesday February 02, 2016, 10:05 AM

Shannon Greco: A Self-Described "STEM Education Zealot"

Princeton Plasma Physics Laboratory

Monday November 16, 2015, 04:05 PM

Rare Earths for Life: An 85th Birthday Visit with Mr. Rare Earth

Ames Laboratory

Tuesday October 20, 2015, 01:05 PM

Meet Robert Palomino: 'Give Everything a Shot!'

Brookhaven National Laboratory

Tuesday April 22, 2014, 11:30 AM

University of Utah Makes Solar Accessible

University of Utah

Wednesday March 06, 2013, 03:40 PM

Student Innovator at Rensselaer Polytechnic Institute Seeks Brighter, Smarter, and More Efficient LEDs

Rensselaer Polytechnic Institute (RPI)

Friday November 16, 2012, 10:00 AM

Texas Tech Energy Commerce Students, Community Light up Tent City

Texas Tech University

Wednesday November 23, 2011, 10:45 AM

Don't Get 'Frosted' Over Heating Your Home This Winter

Temple University

Wednesday July 06, 2011, 06:00 PM

New Research Center To Tackle Critical Challenges Related to Aircraft Design, Wind Energy, Smart Buildings

Rensselaer Polytechnic Institute (RPI)

Friday April 22, 2011, 09:00 AM

First Polymer Solar-Thermal Device Heats Home, Saves Money

Wake Forest University

Friday April 15, 2011, 12:25 PM

Like Superman, American University Will Get Its Energy from the Sun

American University

Thursday February 10, 2011, 05:00 PM

ARRA Grant to Help Fund Seminary Building Green Roof

University of Chicago

Tuesday December 07, 2010, 05:00 PM

UC San Diego Installing 2.8 Megawatt Fuel Cell to Anchor Energy Innovation Park

University of California San Diego

Monday November 01, 2010, 12:50 PM

Rensselaer Smart Lighting Engineering Research Center Announces First Deployment of New Technology on Campus

Rensselaer Polytechnic Institute (RPI)

Friday September 10, 2010, 12:40 PM

Ithaca College Will Host Regional Clean Energy Summit

Ithaca College

Tuesday July 27, 2010, 10:30 AM

Texas Governor Announces $8.4 Million Award to Create Renewable Energy Institute

Texas Tech University

Friday May 07, 2010, 04:20 PM

Creighton University to Offer New Alternative Energy Program

Creighton University

Wednesday May 05, 2010, 09:30 AM

National Engineering Program Seeks Subject Matter Experts in Energy

JETS Junior Engineering Technical Society

Wednesday April 21, 2010, 12:30 PM

Students Using Solar Power To Create Sustainable Solutions for Haiti, Peru

Rensselaer Polytechnic Institute (RPI)

Wednesday March 03, 2010, 07:00 PM

Helping Hydrogen: Student Inventor Tackles Challenge of Hydrogen Storage

Rensselaer Polytechnic Institute (RPI)

Thursday February 04, 2010, 02:00 PM

Turning Exercise into Electricity

Furman University

Thursday November 12, 2009, 12:45 PM

Campus Leaders Showing the Way to a Sustainable, Clean Energy Future

National Wildlife Federation (NWF)

Tuesday November 03, 2009, 04:20 PM

Furman University Receives $2.5 Million DOE Grant for Geothermal Project

Furman University

Thursday September 17, 2009, 02:45 PM

Could Sorghum Become a Significant Alternative Fuel Source?

Salisbury University

Wednesday September 16, 2009, 11:15 AM

Students Navigating the Hudson River With Hydrogen Fuel Cells

Rensselaer Polytechnic Institute (RPI)

Wednesday September 16, 2009, 10:00 AM

College Presidents Flock to D.C., Urge Senate to Pass Clean Energy Bill

National Wildlife Federation (NWF)

Wednesday July 01, 2009, 04:15 PM

Northeastern Announces New Professional Master's in Energy Systems

Northeastern University

Friday October 12, 2007, 09:35 AM

Kansas Rural Schools To Receive Wind Turbines

Kansas State University

Thursday August 17, 2006, 05:30 PM

High Gas Prices Here to Stay, Says Engineering Professor

Rowan University





Showing results

0-4 Of 2215