Recently in Prebiotic Chemistry Category

Expanding the genetic alphabet

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By Gert Korthof.

“It is a very, very hard problem. Getting all the pieces to work means re-engineering 3.5 billion years of evolution. It’s so ambitious.” These are the words of a scientist 14 years ago [1]. He was talking about the project of inventing new bases to include in DNA and let the new DNA function in a living cell. Now an important milestone has been reached towards that goal. Scientists have succeeded in adding a new base pair, d5SICS (call it X) and dNaM (call it Y), to the DNA of the bacterium E. coli and let it replicate its DNA [2]. Furthermore, the growth rate of the bacterium was not significantly slowed down, and the DNA-repair system did not remove the new bases. These results give us hope for realistic answers to the so far speculative questions as to why evolution settled on only two base pairs in DNA. Could there be superior bases and superior DNA?

Plasmid_modified_from_wiki.jpg

Plasmid, modified from Wikipedia. The yellow dot is the new base pair.

by Gert Korthof

Origin of life researcher and Nobel Prize winner Jack Szostak has made an important step towards creating a prebiotically plausible protocell (prebiotic implies that it did not originate from pre-existing forms of life, but its components could have self-assembled from raw materials available under physical and chemical conditions of the early earth). The protocell is a fatty acid vesicle, which is a simpler form of a cell membrane, in which RNA replication occurs autonomously without the help of enzymes. The results have been published in Science Nov 29 2013.

This is the first time that nonenzymatic RNA copying succeeded inside a fatty acid vesicle. The big obstacle has always been that magnesium ion Mg2+ was necessary for RNA copying, but two negative side-effects of high Mg2+ levels frustrated success. Firstly, high Mg2+ levels break down the simple, fatty acid membranes that probably surrounded the first living cells. Secondly, Mg2+ catalyses degradation of single-stranded RNA. After a long trial-and-error process, Szostak et al. discovered that citrate removes these two side-effects. Citrate efficiently protects fatty acid membranes from the disruptive effects of high Mg2+ ion concentrations, while both allowing RNA copying and protecting single-stranded RNA from Mg2+-catalyzed degradation.

KorthofFig2.jpg

An illustration of a protocell, composed of a fatty acid membrane encapsulating RNA ribozymes. © Exploring Life’s Origins.

Over at Science in Pen and Ink Lelia Battison has an in-depth discussion of Richard Hoovers’ paper on alleged “fossil” bacteria in CI1 Carbonaceous Meteorites in the Journal of Cosmology. It is an excellent article that covers a lot of issues not previously covered, and brings together some other information that has been scattered around. I’m referenced as well. Go have a read of Microbes on a Moonbeam, disentangling the Meteorite Microbe claims.

(for reference my posts on the subject are here and here)

The Journal of Cosmology has now posted 21 commentaries on the “Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites” paper by Richard Hoover that I have critiqued in my “Life from Beyond Earth on a Meteorite, or Pareidolia?” post.

The majority are uncritical (some don’t even seem to have read the actual paper), and zoom off on tangents assuming the Hoover’s paper is valid. Two posts are critical (commentary 5 and commentary 9), and bring up the same issue I do (but with more references), that abiotic minerals can imitate the shapes of bacteria, and that without further tests, there is no way to say these filaments are fossils of any sort.

As for the majority, well, largely I think they are sad. The near complete absence of any critical engagement with the paper is very telling, and there is much leaping to unsupported conclusions. I would dearly love for extra-terrestrial life to be found, but I’m not going to grasp at epsonite straws to pretend it’s been found. Hoover’s flawed paper is not evidence of extra-terrestrial life.

Oh, and the journal has added a long rant to before the main article:

Have the Terrorist(sic) Won? Only a few crackpots and charlatans have denounced the Hoover study. NASA’s chief scientist was charged with unprofessional conduct for lying publicly about the Journal of Cosmology and the Hoover paper. The same crackpots, self-promoters, liars, and failures, are quoted repeatedly in the media. However, where is the evidence the Hoover study is not accurate?

Few legitimate scientists have come forward to contest Hoover’s findings. Why is that? Because the evidence is solid. But why have so few scientist come forward to attest to the validity? The answer is: They are afraid. They are terrified. And for good reason.

Apparently I am a crackpot and charlatan (sighs expressively), at least I’m in good company with Phil Plait, PZ Myers and Rosie Redfield (and really, read commentary #9 carefully).

Fossils of life or inorganic fibers? Image of alleged “microfossils” from “Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites: Implications to Life on Comets, Europa, and Enceladus Richard B. Hoover Journal of Cosmology, 2011, Vol 13, xxx.

A recent paper published in the Journal of Cosmology has claimed to have discovered evidence of fossil bacteria in a rare subclass of carbonaceous meteorite. The implications of this paper, should it be correct, are enormous and the blogosphere has gone into overdrive discussing it. There are interesting analyses by the Bad Astronomer, PZ Myers and Rosie Redfield.

Rosie Redmond’s analysis is more detailed (and Rosie being the microbiologist who burst the “Arsenic Bacteria” bubble, knows she her stuff), but all posts quickly get to the heart of the matter; the “evidence” is a bunch of squiggly stuff that bears little resemblance to actual bacterial fossils unless you obscure the details by rescaling the images.

(scroll down for an update)

Signature in the Cell?

(The following is a follow-up to a comment I made in this thread.) There is much abuzz in the ID-o-sphere regarding Stephen Meyer’s new book, “Signature in the Cell: DNA and the Evidence for Intelligent Design”. The book is a lengthy recapitulation of the main themes that ID proponents have been talking about for the past 15 years or so; indeed, there will be precious little that is new for seasoned veterans of the internet discussions and staged debates that have occurred over the years.

Long though the book is, it is built around one central theme - the idea that the genetic code harbors evidence for design. Indeed, the genetic code - the triplet-amino acid correspondence that is seen in life - is the “Signature in the Cell”. Meyer contends that the genetic code cannot have originated without the intervention of intelligence, that physics and chemistry cannot on their own accords account for the origin of the code.

It is this context that a recent paper by Yarus et al. (Yarus M, Widmann JJ, Knight R, 2009, RNA-Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol 69:406-429) merits discussion. This paper sums up several avenues of investigation into the mode of RNA-amino acid interaction, and places the body of work into an interesting light with respect to the origin of the genetic code. The bottom line, in terms that relate to Meyer’s book, is that chemistry and physics (to use Meyer’s phraseology) can account for the origin of the genetic code. In other words, the very heart of Meyer’s thesis (and his book) is wrong.

For details, follow this link, where comments may be left.

Ten Amino Acids Thermodynamically Favored

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One of the “criticisms” (scare quotes to indicate creationist blather) of science is that it doesn’t (and, some say, can’t) account for the emergence of life on earth. Now a new paper coming out in Astrobiology (pre-pub version online here) shows that 10 of the 20 amino acids in life on earth are thermodynamically favored, and would likely emerge under a variety of conditions.

The implications are profound, as Supernova Condensate notes. Among those implications is that life elsewhere is likely to have some characteristics in common with life on earth at the biochemical level. The abstract of the paper:

Of the twenty amino acids used in proteins, ten were formed in Miller’s atmospheric discharge experiments. The two other major proposed sources of prebiotic amino acid synthesis include formation in hydrothermal vents and delivery to Earth via meteorites. We combine observational and experimental data of amino acid frequencies formed by these diverse mechanisms and show that, regardless of the source, these ten early amino acids can be ranked in order of decreasing abundance in prebiotic contexts. This order can be predicted by thermodynamics. The relative abundances of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated. The remaining amino acids were incorporated into proteins after pathways for their biochemical synthesis evolved. This is consistent with theories of the evolution of the genetic code by stepwise addition of new amino acids. These are hints that key aspects of early biochemistry may be universal.

More discussion at Supernova Condensate, where I found the story.

ribozyme.png Aminoacyl-tRNA synthetase ribozyme, an example of the RNA-based catalysts that may have preceded protein enzymmes during the origin of life.

The Museum of Science at Boston has a fantastic interactive web resource on the origins of life. Exploring Lifes Origins has a timeline of lifes evolution (with sliders), and pages on understanding the RNA world and building protocells, with a nice animation of protocell replication. The pages have been made in collaboration with ribozyme guru Jack Szostak and his laboratory, and there is a handy resources page for educators.

If you are interested in our current understanding of the origin of life, this is a very handy starting off point. You can explore ribozymes in more detail with proteopedia.

(Hat tip to Sandra Porter, biology educators should not miss her blog)

The Rockefeller University presents a two day symposium on “From RNA to Humans”

With videos of all the lectures

Session 1: Archaean Chemistry and Earliest Fossils

  • The RNA World and the Molecular Origins of Life Gerald F. Joyce, The Scripps Research Institute
  • The Origins of Cellular Life Jack W. Szostak, Harvard Medical School
  • Can the Distribution of Protein Domains Shed Light on the Tree of Life Russell F. Doolittle, University of California, San Diego
  • The Earliest Life on Earth Roger Buick, University of Washington
  • Proterozoic Life and Environments Andrew H. Knoll, Harvard University

Session 2: Cells, Cellular Evolution and Protein History

  • The Tree of Life and Major Transitions in Cell Evolution Thomas Cavalier-Smith, University of Oxford
  • The Origin of Eukaryotes Eugene V. Koonin, National Center for Biotechnology Information, National Institutes of Health
  • Barking up the Wrong Tree: The Dangers of Reification in Molecular Phylogenetics and Systematics W. Ford Doolittle, Dalhousie University
  • RNA Interference May Provide a Window on the RNA-to-DNA World Transition Phillip A. Sharp, Massachusetts Institute of Technology

Evening Lecture, 6 – 7 p.m.

Feeding and Gloating for More: The Challenge of the New Creationism Jerry A. Coyne, The University of Chicago

Session 3: Development of Eukaryotic Genetic Capacity and Multicellularity

  • The Deep Evolutionary History of Eukaryotes Andrew Roger, Dalhousie University
  • Demonstrating the Sufficiency of Microevolutionary Processes David Penny, Massey University
  • Genes and Development: A Comparison of Human and Amphioxus Genomes Peter W.H. Holland, University of Oxford
  • Cnidaria and the Evolution of the Bilaterian Body Plans: Insights from an Outgroup Ulrich Technau, University of Vienna

Session 4: Human Evolution through the Lens of DNA Sequences

  • Evolution of Human Populations L. Luca Cavalli-Sforza, Stanford University School of Medicine
  • Accelerated Evolution in the Human Genome Katherine S. Pollard, University of California, Davis
  • Probing Human Brain Evolution at the Genetic Level Bruce T. Lahn, The University of Chicago
  • A Neanderthal Perspective on Human Origins Fairfield Osborn Memorial Lecture , Svante Pääbo, Max Planck Institute for Evolutionary Anthropology

Cosmic Soup

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Here’s an interesting article from Nature News (subscription may be required):

Organic compound found in the stars

Astronomers have found the largest negatively charged molecule so far seen in interstellar space. The discovery, of an organic compound, suggests that the chemical building blocks of life may be more common in the Universe than had been previously thought.

The molecule is a chain of eight carbons and a single hydrogen called the octatetraynyl anion (C8H¯). Two teams of scientists have spotted it near a dying star and in a cloud of cold gas.

The discovery, along with that of three smaller organic molecules in the past year, opens up a suite of potential chemical reactions and products. It suggests that ‘prebiotic’ molecules such as amino acids, the building blocks of protein, could form all over the Universe, says Tony Remijan, an astronomer at the National Radio Astronomy Observatory (NRAO) in Charlottesville, Virginia.

Way cool.

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