Abiogenesis & Evolution

In the Beginning was Abiogenesis

2008-12-31T23:59:00.003-08:00

In current biological terminology "abiogenesis" refers to the emergence of life as self-replicating assemblages of chemicals from non-life assemblages of chemicals. This is the hypothesis that primordial life originated within the first 10 million years of Earth's history as a result of chemical reactions that generated larger and larger organic polymers, which ultimately attained the property of chemical self-replication.

This modern conceptualization is reasonable in view of what we now know of the demonstrable biochemical basis of all life. The modern conceptualization replaces earlier notions of "spontaneous generation" that viewed life as arising fully formed from non-living matter, or de novo. Such Aristotelian notions of archebiosis probably arose because much of life exists at the microscopic level of prokaryotes and unicellular eukaryotes, and some organisms living on detritus reach visible proportions after having been of microscopic size.

The term 'life' in relation to abiogenesis embraces the notion of utilization of energy sources to drive biochemical self-replication. This requires that an assembly of molecules and macromolecules acquired the ability to convert energy into growth and self-replication directed by informational macromolecules. A basic understanding of physical chemistry, biochemistry, biochemical energetics, and informational macromolecules is necessary to apprehend this concept.

Is the overall process depicted in the concept of abiogenesis one of pure chance? Of course not, rather the processes would have been governed by the non-random physical laws of chemistry, specifically those physical properties related to organic molecules. Since the processes involved would be widespread across the primordial planet, an enormous numbers of molecules and macromolecules would have been generated in the first 10 million years of Earth history. According to most theorists, conditions on Earth are no longer suitable for abiogenesis to occur. Abiogenesis requires a reducing environment, and oxygenic photosynthesis in Cyanobacteria converted the atmosphere to an oxidizing environment.

The exact elucidation/replication of abiogenetic mechanisms would be of enormous interest, yet this has never been a particularly active area of research because it has limited applications. The advent of space exploration has infused life into Astrobiology and the search for the Origin of Life. However, recent work, published in Nature, has demonstrated formation of activated pyrimidine nucleotides in a system consistent with early-Earth geochemical models.

Creationists, deliberately or out of ignorance, confuse the term abiogenesis with the term "evolution", which refers (in this context) to changes in the biology of living organisms over time. Creationists deceptively or mistakenly claim that evolution is not a fact. Biological evolution is a fact. That is, the fossil record and genomes demonstrate accumulated biological change over time. Denial or ignorance of a fact does not eliminate that fact.

Evolutionary theory deals with postulated mechanisms that explain the observed biological changes over time. Scientists do not claim that research on mechanisms of abiogenesis or biological evolution provide all the answers that they seek. This is not the problem that creationist love to claim it is, rather it one of the valuable features of scientific thinking. Proof exists only within mathematics, while most scientific reasearch employs empiricism and experimentation in order to disprove inaccurate theories – and thus to eliminate all but the best hypothesis. Basically, scientists seek the best possible explanation for an observed phenomenon, then move on to the next unanswered question. It is expected of scientists that they will abandon outmoded hypotheses.

Some creationists claim that evolution of biological forms cannot be explained without first accounting for the origin of life. This, like other creationist claims, is not a valid argument. The processes of abiogenesis and evolution affect two distinct areas of life. An analogy would be the construction of an automobile in a factory (origin) followed, independently of construction, by mechanical wear and tear (evolution). So, the mechanisms of biological evolution can be studied separately from the origin of life. Scientists may study the evolution of biological forms without any reference to the origin of life as assemblages of self-replicating chemicals.

From NASA's Astrobiology Institute
Spitzer Telecope Data Suggest that Life's Building Blocks are Abundant
Finding Life in Mars Analog Sites on Earth
More on Astrobiology:
Evolution and Ecology Beyond the Planet of Origin
Evolution and Development Workshop
New York Center for Studies on the Origins of Life
Ad Astra Magazine: Astrobiology Issue (January/February 1999)
The Astrobiology Web
Free audio on WAMC's Origins of Life Segments
Origins on Abiogenesis

Recommended on the Talk Origins Archive:
Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations
Borel's Law and the Origin of Many Creationist Probability Assertions
Spontaneous Generation and the Origin of Life

Before the Beginning

2008-12-31T23:58:00.001-08:00

Based on radio-dating of meteorites, the solar system is about 4600 Ma – 4600 million years, or 4.6 billion years old (Ga). This occurred 10 Ga after the Big Bang. The sun and planets condensed from a large, hot accretion disk.

When early Earth was cooling from its molten state, conditions would have been like hell on Earth – hence the term "hadean" for this earliest segment of the precambrian. Meteors rained down on the hot Earth, ultraviolet radiation was unchecked by an ozone belt, and volcanos belched fumes into a reducing atmosphere, which sparked with lightning. Life, of course, had not yet evolved, but it may have had an earlier start than thought previously (see below).

The term "hadean" was coined to designate the time before the earliest known rocks. However, rocks have been found that are older than the 4550-3800 Ma time-frame of the Hadean.

The oldest rocks so far discovered on Earth are:

Jack Hills, Western Australia, a 4.4 Ga detrital zircon (sample W74) in the Jack Hills metaconglomerate, Eranondoo Hill. More at Earliest Piece of Earth
The Acasta Gneisses near Canada’s Great Slave Lake (4.03 Ga)
The Isua Supracrustal rocks of West Greenland (3.7 to 3.8 Ga)
Northern Michigan (3.5-3.7 Ga)
Swaziland (3.4-3.5 Ga)

“No known rocks have survived from the first 500 million years of Earth history, but studies of single zircons suggest that some continental crust formed as early as 4.4 Ga, 160 m.y. after accretion of the Earth, and that surface temperatures were low enough for liquid water. Surface temperatures are inferred from high d18O values of zircons. The range of d18O values is constant throughout the Archean (4.4-2.6 Ga) suggesting uniformity of processes and conditions. The hypothesis of a Cool Early Earth suggests long intervals of relatively temperate surface conditions from 4.4 to 4.0 Ga that were conducive to liquid-water oceans and possibly life. Meteorite impacts during this period may have been less frequent than previously thought.”A Cool Early Earth

More: Introduction to the Hadean / Palaeos Hadean: The Hadean Eon / Geol 2C Hadean lecture / Evolution: Change: Deep Time / Geologic Time: Age of the Earth /

image "evolutionist

LUCA

2008-12-31T23:58:00.000-08:00

The last universal common ancestor, or universal cenancestor is hypothesized as being at the ancestral root of all living organisms. Not the earliest or simplest living organism, and not necessarily the sole example of its type, LUCA possessed the genetic material that diverged (about 3.5 Ga) into all currently living organisms. So, the last universal common ancestor sits at the first point of divergence of any cladogram that groups living organisms according to evolutionary-genetic relationships.

A number of terms are employed to refer to the universal cenancestor – last universal ancestor (LUA), last common ancestor (LCA), or last universal common ancestor (LUCA).

Timeline of Life

2008-12-31T23:57:00.000-08:00

Timeline for life in billions of years (Ga): click to enlarge image.

Based on radio-dating of meteorites, the solar system is about 4600 Ma – 4600 million years, or 4.6 billion years old (Ga). The formation of the earth occurred 10 Ga after the Big Bang. The sun and planets condensed from a large, hot accretion disk.

The earliest atmosphere of H2 and He was lost to space, and was replaced by a reductive atmosphere with a composition probably similar to outgassing of modern volcanoes – H₂O, CO₂, SO₂, S₂, Cl₂, N₂, NH₃, and CH₄

Oxygen levels began to rise after the evolution of oxygenic photosynthesis by the Cyanobacteria, which evolved at least at least 3450 million years ago (3.45 Ga) and formed the earliest microfossils as stromatolite reefs.

There is considerable evidence that the earliest eukaryotes evolved through serial endosymbiosis. Chloroplasts resulted from endosymbiotic transfers of Cyanobacteria, and mitochondria originated from endosymbiotic transfers of alpha-proteobacteria (purple bacteria). Mitochondria are the site of oxidative phosporylation in eukaryotes.

What Is Life?

CHONSP and RNA world

2008-12-31T23:56:00.001-08:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Asked about primordial conditions, participant UCLA paleobiologist William Schopf answered: 'We know the overall sequence of life's origin, from CHONSP (carbon, hydrogen, oxygen, nitrogen, sulfur, phosphorus), to monomers, to polymers, to cells; we know that the origin of life was early, microbial, and unicellular; and we know that an RNA world preceded today's DNA-protein world. "

Miller-Urey & Beyond

2008-12-31T23:56:00.000-08:00

In 1953, graduate student Miller set up an experiment in which he passed an electrical current (to simulate lightning discharges in the primordial atmosphere) through the gases then believed to constitute the primordial atmosphere – methane (CH4), ammonia (NH3), hydrogen (H2), and water (H2O). After a WEEK, Miller assayed the resulting chemicals and found that up to 15% of the carbon had been converted to organic compounds. Two percent of the carbon had formed amino acids, including 13 of the 21 that comprise the proteins of living cells. The smallest amino acid, glycine, was the most abundant.

It turns out that Miller’s and Urey’s guess about the composition of the primordial atmosphere was wrong, yet the Miller-Urey products and many more products (including nucleotides) have repeatedly been generated in similar experiments that more accurately replicate the early atmosphere.

The salient point is that in a very short time, a variety of life-related chemicals will generate themselves from simple molecules provided that some energy is supplied to the system. Considering the billions of years before recognizable life appeared on the entire planet, it is clear that chemical evolution could yield cellular life. In fact, the earliest discovered microfossils date from about 3 ½ billion years ago, and this is a minimum 1 billion years since the origin of the planet.

Similar processes to those above must be occurring in the energy-riddled immensity of space, because many organic compounds have been identified spectroscopically in space and have been found in meteorites.

The evolution of the prebiotic atmosphere

2008-12-31T23:54:00.000-08:00

SpringerLink - Article: "High CO2 levels are required to warm the primitive earth in the face of decreased solar luminosity. The atmosphere should have had an effective stratospheric cold trap, which would have limited the abiotic production rate of oxygen to relatively low values. Photostimulated oxidation of ferrous iron in the oceans should have been the dominant source of atmospheric H2. Rainout of H2O2 would have kept the atmospheric H2 content high and the O2 content low, even if other sources of H2 were small." Article PubMed ChemPort

James F. Kasting
The evolution of the prebiotic atmosphere
Kasting, J. E. Origins of Life 14, 75−82 (1984).

Primordial Soup : Theories

2008-12-31T23:50:00.001-08:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Antonio Lazcano, President of the International Society for the Study of the Origins of Life and a scientist at the Universidad Autónoma de México, theorized that there were three sources for the primordial soup:
1. A reducing atmosphere from volcanic outgassing,
2. High-temperature submarine vents and fumaroles -- black smokers, and
3.Space--for example, the 4.6 billion-year-old Murchison meteorite, discovered in Australia in 1969 was loaded with amino acids, aliphatic and aromatic hydrocarbons, hydroxy acids, purines, pyrimidines, and other chemical building blocks of life.

'The evidence strongly suggests that prior to the origin of life the primitive Earth already had many different catalytic agents, polymers with sequences of nucleotides, and membrane-forming compounds,' Lazcano concluded. This prebiotic soup led to a catalytic and replicative RNA world, which led to the DNA world of today."

See: Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions

Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions

2008-12-30T14:54:00.000-08:00

Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions.
Powner MW, Gerland B, Sutherland JD

Nature. 2009 May 14;459(7244):239-42

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively, and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis-cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate-are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

See also:
Origins of life: Systems chemistry on early Earth.
Nature. 2009 May 14;459(7244):171-2

evolving

2007-12-01T01:00:00.000-08:00

Associated science sites • Abiogenesis and Evolution • Algorithms of Evolution • Archea Eubacteria • Cancer • Cell Biology • Complex Systems • Cyanobacteria • Diagrams Tables • Endosymbiosis • Enzymes • Evo Devo • Evolution in Action • Fat • Geology • Glossary • Immunology • Life Chemistry • Medical Science • Mechanisms of Evolution • Molecule • Molecular Biology • Molecular Paths • Neurosciences • Organics • Origin of Life • Paleogeology • Pathways • Photosynthesis • Protein • Receptor • Rocks & Minerals • SET • Signaling • Sleep • Stem & Progenitor Cells • Stromatolites • Taxonomy Phylogeny • Tissue • Virus • And some philosophy/general interest sites • A-Deistic • Adeistic • Black Out • cosmic • Eine Kleine Nattermusing • eMusings • eVolition • Galaria • Godborygmi • Godspell Follies • Gray Matters • MetaThoughts • Mimble Wimble • Naturalism • BLogodaedaly • palimpsest • Salient • Science of Evolution • Sechuam • Sintheist • Tabula Flexuosa • The Scarlet A • Weltschauung •

Top Down & Bottom Up

2006-12-31T23:35:00.000-08:00

Minimal Molecules

2006-12-31T23:20:00.000-08:00

Minimal Genome

2006-12-31T23:18:00.000-08:00

2001: Mycoplasma genitalium with 517 genes has the smallest gene complement of any independently replicating cell so far identified. Analysis suggests that 265 to 350 of the 480 protein-coding genes of M. genitalium are essential under laboratory growth conditions, including about 100 genes of unknown function. Science -- Abstracts: Hutchison et al. 286 (5447): 2165

2002: Here we show evidence of six species with a genome size smaller than Mycoplasma genitalium, the smallest bacterial genome reported thus far (580 kb). Our findings strongly suggest that the Buchnera genome is still experiencing a reductive process toward a minimum set of genes necessary for its symbiotic lifestyle. Extreme genome reduction in Buchnera spp.: Toward the minimal ...

2001: Genome Biology Full text The complexity of simplicity

Another Minimal Genome: Microbe Needs Just 271 Genes : Free Full Text : Modified:

"A minimal genome is the smallest set of genes that an organism needs to live in a particular environment. While most microbes have hundreds or thousands of genes, some use only a fraction of these at any one time, depending on their surroundings."

The bacterium Bacillus subtilis needs just 271 genes to live in an experimental environment that is rich in nutrients, a new study has found. The calculated minimum of 271 genes is a small fraction of the organism's roughly 4,100 genes. To arrive at the number 271, the researchers grew thousands of B. subtilis cells and systematically inactivated one gene per cell.

The ideal test of a minimal genome would be to inactivate every non-essential gene in a single cell, but the technology to accomplish this does not yet exist. The vast majority of essential genes in B. subtilis belong to one of five categories, such as “information processing” and “protein synthesis.” Only a few essential genes could not be categorized because so little was known about them.

“One of the interesting aspects of the study was that we found so few essential genes of unknown function,“ says Dusko. “This shows that there are fewer holes in our understanding of the living cell than early studies led us to believe.”

Researchers hope ultimately to construct a minimal genome, using information about different microbes. Hundreds of "essential" genes in bacteria have been identified in recent years, providing a rough idea of what minimal genomes might look like.

The minimal genomes published to date range in number from about 260 genes to 670 genes, depending upon the organism, the environment in which it grows, and the strategy used to calculate which genes are essential.

Kobayashi, K. et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100, 4678-4683 (April 15, 2003).

2005 : PEC (Profiling of E.coli Chromosome) : 250 genes minimal : 3,262,049 bp - genome map

GENETICS:Ethical Considerations in Synthesizing a Minimal Genome -- Cho et al. 286 (5447): 2087 -- Science: "Researchers are attempting to model and eventually to create 'minimal organisms,' organisms with the smallest set of genes that allow for survival and reproduction. Although the ability to create such an organism is beyond current technology, the work of Hutchison et al., reported in this issue, represents an important step in the path toward the creation of such an organism. Here we identify ethical, social, and religious issues raised by this research. Issues discussed include the potential abuse of the technology (biological weapons, environmental problems), as well as the challenge it poses to our conception of the meaning of life."

Archaea

2006-12-31T23:17:00.000-08:00

Max Planck Society - Press Release: "Archaea, small single-celled organisms, are particularly interesting for scientists because they are able to live under extreme environmental conditions, for instance under high salt concentrations, high pH-values, or high temperatures. Nature's masters of adaptation, they are model organisms from which researchers can draw conclusions about the first organisms on earth. "

Transcriptional response to DNA damage in the archaeon Sulfolobus solfataricus -- Salerno et al. 31 (21): 6127 -- Nucleic Acids Research: "Genomic sequencing has revealed the presence of archaeal genes homologous to components of the eucaryal nucleotide excision repair (NER) pathway, which is involved in the repair of ultraviolet (UV) light-induced DNA damage. . . The cell response to UV irradiation includes transcriptional regulation of genes encoding two DNA binding proteins involved in chromosome dynamics. Moreover, several of these genes are also strongly induced by the intercalating agent actinomycin D. Thus, response to DNA damage in S.solfataricus has features essentially conserved in all three domains of life. "

archeal/eukaryal replication fork
"Interestingly, phylogenetic data suggest that the specific attributes of the eukaryal machinery could date back to an archaeal ancestor containing a rudimentary form of chromatin structure. Since nucleosomes form only on double stranded DNA, greater symmetry of the ancestral eukaryal/archaeal replication fork could facilitate the emergence of chromatin structure. "

Illogical Deceit theory

2006-12-31T20:59:00.000-08:00

For brevity, intelligent design theory will be abbreviated “idism”. In so far as religion appeals to the emotions and to faith-despite-absence-of-direct-evidence the term 'id' seems appropriate because it refers to the feeling, non-rational part of the brain.

For brevity, those who promote idism will be abbreviated “idists”. Internet debaters who are pro-idism will be abbreviated “proids”. For accuracy the purported intelligent designer will be referred to as God. The ultimate point being philosophers can speculate about the existence of God, but that science cannot, by its naturalist nature examine the supernatural.

The arguments of idism belong in the realm of philosophy and not in the science curriculum. Therefore, discussion of idism ought to be confined to university level philosophy courses. There the principles of critical thinking are within the intellectual grasp of most students. Further, the dissection of fallacies of logic is pertinent to the course curriculum in philosophy.

In the more than 10 years since idism has been attracting the donations of proids, the idists have not performed a scientific investigation nor produced a single peer-reviewed scientific publication. Below are selected opinions of scientists on ‘intelligent design theory’, or what I regard as “Illogical Deceit theory”.

Why “illogical”? See the Fallacies of Logic section, a dissection of the fallacies of logic to be found in many arguments, specifically the arguments of creationists, proids and idists.

Why “deceit”? The claims of idists that idism does not speculate on the nature of the ‘designer’ are deceitful in view of all the evidence that links idism to religion. Any doubts concerning such evidence should be dispelled by googling abiogenesis, or "intelligent design", and observing the number of religion oriented websites.

Claims that idism is science and not theology are also deceitful in view of the anti-evolutionist and religious stance taken by proids. God cannot be examined by science, so idism is religious both in subject matter and in approach. See also The Wedge Document and On the teaching of pseudoscience. (On the Teaching of Pseudoscience and The Wedge Document.)

For more comments, articles, and refutations of creationists', anti-evolutionists', proids and idists' favorite fallacies see the Godspell Follies section.

RNA world

2006-11-30T20:59:00.000-08:00

RNA has been put forward as the chemical candidate for the transition from primordial soup to self-replicating cells.

RNA can:
- be transcribed into DNA
- self-replicate
- act as an enzyme (ribozyme) – peptide-bond formation is catalyzed solely by RNA

"The first stage of evolution proceeds, then, by RNA molecules performing the catalytic activities necessary to assemble themselves from a nucleotide soup. The RNA molecules evolve in self-replicating patterns, using recombination and mutation to explore new niches. ... they then develop an entire range of enzymic activities. At the next stage, RNA molecules began to synthesize proteins, first by developing RNA adaptor molecules that can bind activated amino acids and then by arranging them according to an RNA template using other RNA molecules such as the RNA core of the ribosome. This process would make the first proteins, which would simply be better enzymes than their RNA counterparts. ... These protein enzymes are ... built up of mini-elements of structure.Finally, DNA appeared on the scene, the ultimate holder of information copied from the genetic RNA molecules by reverse transcription. ... RNA is then relegated to the intermediate role it has today—no longer the center of the stage, displaced by DNA and the more effective protein enzymes."
Walter Gilbert, "The RNA world," p 618 v 319, Nature, 1986.
More links: RNA World Website

protein catalysts and ribozymes

2006-11-30T20:33:00.000-08:00

BIO.COM: Biotechnology & Pharmaceutical News, Jobs, Software, Reports, Books, Events: "Protein enzymes are polymer strings made up of the 20 different amino acid building blocks, many of which have reactive side chains that can participate in biocatalysis. RNA polymers are made up of only four different building blocks, the RNA nucleotides, which lack the chemical versatility and reactivity of the protein functional groups.

After the discovery that RNA could act as a biocatalyst, many scientists began to theorize and discuss the possibility of an RNA world, the notion that at one time the world was ruled by RNA-based life forms in which RNA enzymes were the chief catalytic molecules and RNA nucleotides were the building blocks that stored genetic information. This raised a number of questions, such as where catalysis came from and how the world transitioned from an RNA-based form to the current DNA-RNA-protein form."

A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase.

2006-11-13T23:50:00.000-08:00

Entrez PubMed: "The modified nucleoside 1-methyladenosine (m(1)A) is found in the T-loop of many tRNAs from organisms belonging to the three domains of life (Eukaryota, Bacteria, Archaea). In the T-loop of eukaryotic and bacterial tRNAs, m(1)A is present at position 58, whereas in archaeal tRNAs it is present at position(s) 58 and/or 57, m(1)A57 being the obligatory intermediate in the biosynthesis of 1-methylinosine (m(1)I57). In yeast, the formation of m(1)A58 is catalysed by the essential tRNA (m(1)A58) methyltransferase (MTase), a tetrameric enzyme that is composed of two types of subunits (Gcd14p and Gcd10p), whereas in the bacterium Thermus thermophilus the enzyme is a homotetramer of the TrmI polypeptide. Here, we report that the TrmI enzyme from the archaeon Pyrococcus abyssi is also a homotetramer. However, unlike the bacterial site-specific TrmI MTase, the P.abyssi enzyme is region-specific and catalyses the formation of m(1)A at two adjacent positions (57 and 58) in the T-loop of certain tRNAs. The stabilisation of P.abyssi TrmI at extreme temperatures involves intersubunit disulphide bridges that reinforce the tetrameric oligomerisation, as revealed by biochemical and crystallographic evidences. The origin and evolution of m(1)A MTases is discussed in the context of different hypotheses of the tree of life."Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 2004 Jan 22;32(2):465-76. Print 2004. Free Full Text article

genome and proteome

2006-10-31T20:58:00.000-08:00

Important features of the genome and proteome:

1) Segments of nucleic acid that code for a useful sequence can be re-used, and need not arise de novo for each protein in an organism’s proteome.

2) The original genetic code probably employed 2 not 3 bases to code for each amino acid, and there were probably less than 20 constituent amino acids in primordial proteomes.

3) Many codons – the 2 or 3 base coding sequences – overlap with one another. That is, several sequences may code for a single amino acid within the polypeptide. This redundancy feature protects the proteome from random point mutations in the genome. For example, these are the triplet codons for arginine: CGU CGC CGA CGG AGA AGG

4) The function of proteins depends upon their tertiary and quaternary (3D) structure, and not on the primary (amino acid sequence) structure.

5) Homologous proteins, those that perform similar functions in different organisms, share sequences that are evolutionarily invariant, or conserved. Other amino acids may be substituted into the sequences whose sole function is to connect the important sequences without altering the 3D configuration or function of a protein.

6) Many small RNAs are important as enzymes and in epigenetic regulation – these RNAs are coded for by segments of DNA that do not code for proteins. Translation of RNA to protein is orchestrated by RNA and proteins.

7) Because the sequences of bases in RNA and one strand of DNA are complementary, the sequences of bases in RNA are equivalent to those in the other strand of DNA (with RNA's U switched to DNA's T). This means that RNA could have provided the template for encoding of its own sequences, thus eliminating any need for re-invention of a DNA code from which to transcribe RNAs.

8) The enormous number of different sequences of bases in the hypothetical 26 base RNA strand in the example demonstrates the possible ‘experiments’ that could be performed in a primordial soup mix. Remember that the example merely examined permutations and combinations for a 26 base nucleic acid polymer.

Evidence Found for Origin of Genes

2006-10-31T20:50:00.000-08:00

Evidence Found for Origin of Genes: "Evidence compiled by a team, led by Nobel laureate Walter Gilbert, supports the theory that all genes in all organisms that ever lived on Earth consist of a small number of basic building blocks. These blocks were shuffled and recombined during the past 3-4 billion years to form a dazzling variety of simple and complex proteins that make up life as we know it. The genes carry instructions for making proteins that do everything from allowing bacteria to metabolize methane gas to aiding humans to think."

mtDNA

2006-10-31T20:15:00.000-08:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): University of Cambridge professor Peter Forster, is an expert in archaeogenetics and states that prehistoric human migrations can be traced by mitochondrial DNA (mtDNA) through the maternal line of modern humans. These mtDNA samples are obtained by taking cheek swabs.

Mitochondrial DNA is passed down the maternal line because the oocyte contains mitochondria within the cytoplasm. Because spermatozoa contain almost no cytoplasm, and hence no mtDNA containing mitochondria, the Y chromosome is employed to trace lineages of human males.

See also, Fossil Hominids: mitochondrial DNA The Great DNA Hunt NOVA Online Neanderthals on Trial Tracing Ancestry with MtDNA Genetics and Genealogy: Y Polymorphism and mtDNA Analyses Genetics and Human Migration Patterns

Ancient DNA

2006-10-30T20:48:00.000-08:00

McMaster Ancient DNA Center: "Once an organism dies, presumably the single most important factor in the long-term preservation of its DNA is the rate at which specific cellular enzymes, called nucleases, can be stopped. These endonucleases are efficient and can rapidly cleave DNA into small fragments. However as these are energy requiring functions, and a cell without oxygen will deplete its energy sources quickly, nuclease degradation may cease relatively soon post mortem. The organism must then face the bacterial, fungal and insect onslaught which can be quite effective but often incomplete. Once bacterial onslaught has slowed, the DNA molecule is still subject to chemical degradation via hydrolysis and oxidation. To understand the processes which degrade the DNA molecule in the fossil record and under what conditions these reactions are minimized, one needs to look briefly at the molecule itself and its susceptible sites."

DNA evolutionary connections

2006-10-30T20:40:00.000-08:00

UCSD Study Shows 'Junk' DNA Has Evolutionary Importance: "In the October 20 issue of Nature, Peter Andolfatto, an assistant professor of biology at UCSD, shows that non-coding regions play an important role in maintaining an organism's genetic integrity. In his study of the genes from the fruit fly Drosophila melanogaster, he discovered that these regions are strongly affected by natural selection, the evolutionary process that preferentially leads to the survival of organisms and genes best adapted to the environment."

Intron functions: "Although some introns, such as those in globin genes, appear to be inserted at what are structural domain boundaries in the polypeptide, many intron insertion positions bear no relation to structural or functional domains. The theory that introns serve an evolutionary function in allowing the shuffling of exons is still being debated."

Group II introns: "Some group II introns have a second remarkable property: they encode reverse transcriptase (RT) ORFs and are active mobile elements. Such mobile group II introns can insert into defined sites at high efficiencies (called retrohoming), or can invade unrelated sites at low frequencies (retrotransposition).Group II introns were discovered and first studied in organellar genomes, where they are relatively abundant. However, group II introns are now being found in unexpected numbers in bacterial genomes"

evolution and organogenesis

2006-10-30T20:38:00.000-08:00

MOLECULAR BIOLOGY: ON HEDGEHOG PROTEINS: "It is now widely accepted that similar sets of factors are shared by different animal species and also by distinct processes in the course of early patterning of organogenesis. During animal evolution, a 'prepattern' of fundamental organs apparently emerged relatively early."

Darwin

2006-09-30T20:59:00.000-07:00

Darwin in the Galapagos

2006-09-30T20:52:00.000-07:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): U.C. Berkeley Darwin scholar Frank J. Sulloway debunked the myth that Darwin discovered natural selection while in the Galapagos and became an evolutionist on the Beagle voyage. Darwin was a creationist from start to finish of the expedition, and he did not fully realize the importance of the Galapagos islands until he began work on his extensive specimen collection following his return to England. Because Darwin had not recorded the island locations from which most of his specimens came, he was forced to rely on the notes taken by other Beagle crew members, including Captain Fitz-Roy.

MicroRNAs Have Shaped The Evolution Of The Majority Of Mammalian Genes

2006-09-30T20:00:00.000-07:00

MicroRNAs Have Shaped The Evolution Of The Majority Of Mammalian Genes: "In a paper published last January in the journal Cell, Bartel's lab, in collaboration with Chris Burge's lab at MIT, presented evidence that one third of human genes are regulated by microRNAs. In this new study, published online Nov. 24 in Science, the researchers demonstrate that microRNAs affect the expression or evolution of the majority of human genes.

Nearly all genes, the authors explain, contain short sequences that match portions of microRNAs. Some of these potential microRNA target sites are evolutionarily "conserved," meaning that they show up in the same spot on the same gene across species as disparate as the mouse and the chicken. The authors of last January's Cell paper showed that thousands of human genes contain microRNA sites that are conserved in this way. To the extent that evolution has preserved these sites more than would be expected by chance, scientists have regarded them as sites that microRNAs target.

In the new study, scientists in the Bartel lab designed an experiment that zeroed in on these nonconserved targets. Grimson took mRNAs whose target sequences were not conserved and exposed them to microRNAs, which latched on without a problem. The experiment proved that a matching sequence is generally sufficient to disrupt mRNA's ability to make protein.

Kyle Kai-How Farh, a graduate student in Bartel's lab, found that mRNAs with nonconserved sites were generally absent in cells with corresponding microRNAs--more absent than statistical models suggested. The researchers concluded that over the course of evolution many mRNAs, in order to maintain their functions and ensure fitness of the organism, have quickly lost sites that pair up with microRNAs.

In addition to the thousands of cases where genes have avoided microRNA targeting, Farh also investigated the opposite extreme, cases where genes have maintained microRNA target sites over the course of evolution. He found that as immature muscle cells stop dividing and become mature muscle cells, microRNAs are activated and suppress genes that are no longer needed at such high levels in the mature muscle. "Many of these evolutionarily conserved microRNA targets are known to be active in the processes of cell proliferation, development, and cancer," says Farh. "Our genomes have good reason to maintain the microRNA targeting sites necessary for turning down these genes at the appropriate place and time."

An emerging idea is that microRNAs often act to reduce the quantity of protein a gene produces without shutting it off all together. "We think the microRNAs are sometimes having what you can call a dampening effect," says Bartel, who is also a Howard Hughes Medical Institute investigator and MIT professor of biology. "They appear to be helping cells achieve optimal levels of proteins.""

Diversity

2006-08-31T20:59:00.000-07:00

Selection

2006-07-31T20:59:00.000-07:00

Analyses of physiological evolutionary response.

2006-07-31T20:50:00.000-07:00

Entrez PubMed: "Selection studies are useful if they can provide us with insights into the patterns and processes of evolution in populations under controlled conditions. In this context it is particularly valuable to be able to analyze the limitations of and constraints on evolutionary responses to allow predictions concerning evolutionary change. The concept of a selection pathway is presented as a means of visualizing this predictive process and the constraints that help define the population's response to selection. As pointed out by Gould and Lewontin, history and chance are confounding forces that can mask or distort the adaptive response. Students of the evolutionary responses of organisms are very interested in the effects of these confounding forces, since they play a critical role not only in the laboratory but also in natural selection in the field. "

Analyses of physiological evolutionary response. Bradley TJ, Folk DG. Physiol Biochem Zool. 2004 Jan-Feb;77(1):1-9.

Multi-Level Selection

2006-07-31T20:18:00.000-07:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Leticia Aviles, a zoologist at the University of British Columbia, summarized the evidence for 'multilevel selection.'

Stephen Jay Gould coined the deliberately pejorative term 'Darwinian fundamentalists' for those who believe that the individual organism is the sole target of natural selection. Aviles said that selection may occur at the level of genes, chromosomes, organelles, and cells. Selection may occur at the level of social groups, demes, species, and multispecies communities. In a sense, Aviles said, 'individual' depends on the frame of reference.

optimization

2006-07-30T19:25:00.000-07:00

EVOLUTION: ON OPTIMIZATION: "Optimization has its critics. The most common objection centers on the mistaken belief that the aim of this method is to test whether organisms are optimal. Actually, it is the assumptions of optimality that are tested. The failure to find support for a prediction can be used to determine whether an assumption is wrong. For example, if animals do not select the diet that maximizes energy intake, it may be because they are choosing a diet that optimizes a balance of different components, or that avoids the costs associated with obtaining larger prey. Once such possibilities have been identified, a new theory can be devised and its predictions tested. It has been argued that this process is circular but in practice it is no different from the successive predicting and testing that underlies most science.["

Logic & Science

2006-06-30T20:59:00.000-07:00

“Reasonable reflective thinking that is focused on deciding what to believe or do. More precisely, it is assessing the authenticity, accuracy, and/or worth of knowledge claims and arguments. It requires careful, precise, persistent and objective analysis of any knowledge claim or belief to judge its validity and/or worth.” Source: definition of critical thinking

The practice of critical thinking sets out to assess the validity of premises, logic of arguments, and reliability of conclusions. In practice, discerning the truth of an argument is not always a simple task. Core Concepts in Critical Thinking Introduction to Statements or Claims

An argument is a set of statements. The premises – facts or propositions – are intended to provide support for the conclusion. The conclusion is asserted to be true on the basis of the premises. If an argument is cogent, then a true conclusion follows logically from true premises.

Logic can be symbolic or informal. Symbolic logic examines the precise symbolic representation of logical concepts, the abstract relationships between these concepts, and the systematization of these relationships. Informal logic involves the application of logical principles to assessment the types of informal arguments and claims that we encounter in daily life.

Propositional logic is a branch of symbolic logic dealing with propositions as units and with their combinations and the connectives that relate them – if, then compound statements. Propositional Logic Terms and Symbols Proposition evaluator. Categorical logic and categorical syllogisms are more concrete than is propositional logic – some, all, and/not. Venn diagram evaluator. An understanding of Fallacies of Logic – recognized structural errors in argumentation – provides a shortcut to assessing the cogency of an argument.

We most often encounter prepositional arguments in daily life, while the logic of science, and of mathematics in particular, is more often categorical. In special cases such as the behavior of gases, at different temperatures, and under pressure, the “problem of induction” can be disregarded and predictive equations are termed Laws (The Gas Laws).

Scientific predictions, however, represent a subset of experimentation and are propositional – if this hypothesis is correct, then we will observe such and such a phenomenon. Failure to observe the predicted phenomenon might be taken to disprove the hypothesis. However, the failure might be a result of experimental or observational error, or might result from faulty predictions based upon a reasonable hypothesis. Alternatively, the hypothesis may be incorrect, but the predicted phenomenon is observed because of a mechanism not yet hypothetically considered.

For these reasons peer-reviewed scientific papers include analyses of current thinking, descriptions of methods, and statements of results so that other researchers might attempt replication. In science, unlike the case for mathematics, proof is not possible, while disproof – falsification – is possible. For this reason, hypotheses to be experimentally tested are ideally framed in such a way that they may be disproved – falsifiable hypotheses. When an empirically based, logical hypothesis, which has not been disproved after repeated testing, is deemed satisfactory by consensus within the scientific community, then the hypothesis graduates to the status of Theory (capitalized to differentiate the scientific term from its vernacular usage). In practice, much of science proceeds upon positive results – repeated observations of a phenomenon under particular conditions. In the softer sciences, such as the social sciences, statistical analyses of results play an important role. Some sciences, such as paleontology are by their nature outside the possibility of experimentation – we cannot resurrect dinosaurs and recreate meteor impacts – and must proceed on the basis of accumulated evidence.

Neo-Darwinism

2006-05-31T20:59:00.000-07:00

Stephen Jay Gould

2006-05-31T20:56:00.000-07:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): "Prediction made by Stephen Jay Gould in the late 1980s: 'We know about three coexisting branches of the human bush. I will be surprised if twice as many more are not discovered before the end of the century.' "

Computer Modeling

2006-04-30T20:59:00.000-07:00

PLoS Genetics: The Evolutionary Value of Recombination Is Constrained by Genome Modularity

2006-04-30T20:29:00.000-07:00

PLoS Genetics: The Evolutionary Value of Recombination Is Constrained by Genome Modularity: "Genetic recombination may predate the evolution of cellular life [1] and is the basis of ubiquitous biological processes such as DNA repair and sexual reproduction. The combinatorial nature of recombination can provide organisms with vastly more evolutionary options than are available through mutation alone [2–4]. However, kingdom-wide analyses of bacterial recombination [5] and DNA-shuffling studies [6,7] have indicated that the evolutionary value of recombination can vary depending on both the genes and the sub-gene modules transferred. In bacteria, the complexity hypothesis has been proposed to explain an imbalance in detectable informational and operational gene transfers between species [5]. Similarly, the schema hypothesis has been proposed to explain patterns of sequence mosaics observed in DNA-shuffling experiments [7]. Although the complexity hypothesis concerns genes within the context of genomes, the schema hypothesis concerns amino acids within the context of proteins. Both hypotheses are conceptually related and propose that the functionality of sequence fragments in foreign genetic backgrounds is inversely correlated with the complexity of interaction networks within which they must function.

The complexity hypothesis [5] was proposed to explain the disparity in informational (those involved in transcription, translation, and related processes) and operational (those involved in housekeeping) gene transfer rates in bacteria. It states that because informational genes are generally involved in more complex interactions than operational genes, they are less likely to continue functioning well after horizontal transfer. The functional genes produced by shuffling three or more distinct sequences (i.e., 60%–85% identical) are usually derived predominantly from either one sequence or combinations of the most similar sequences [2,6,23,24].

The schema hypothesis proposes that these imbalances are due to the probability of recombinant protein-fold disruption increasing with increasing divergence of parental sequences [6,7]. The probability of the normal network of intragenome interactions being disrupted by recombination increases with increasing divergence of the exchanged fragments The successful inheritance of genomic fragments through recombination is expected to depend on the maintenance of important intragenome interactions. After all, the exchange of a genome fragment could be seen as a simultaneous introduction of multiple mutations. Negative or purifying selection should remove those recombinants that break the epistatic interactions that define the architecture of a particular genome, whereas genetic drift might permit the survival and spread of “neutral” recombinants. Alternatively, positive selection should favour the spread of rare recombinants with improved genomic interactions. The genomic interactions in the (natural) parental viruses used in these experiments have most likely been optimised through selection over long evolutionary periods. None of the recombinants generated from these viruses was more fit than the fitter of its parents, which is expected if negative selection is the dominant force that now maintains the integrity of these genomes.

The relative degree of modularity that we demonstrated experimentally for each genome component appears to be reflected in the recombination events detected within the same regions in natural viruses represented in GenBank. This correlation is surprising because the natural recombinants—unlike the recombinants we constructed in the laboratory—involve exchanges of fragments of genes or intergenic regions. Such exchanges may disrupt intraprotein or intra-intergenic region interactions as well as interaction networks amongst whole genes and intergenic regions. Survival of the natural viruses with detectable recombination events in coding regions presumably depended on their inheritance of sequences that did not overly disrupt either intraprotein or intergene/intergenic region interaction networks; survival of natural intergenic region recombinants and those we generated in the laboratory would have been subject only to the latter constraint. The correlation between our experimental results and the inferred natural recombinants may indicate that maintenance of intergenome component interactions is the principal determinant of recombination tolerance (at least for MSV and closely related viruses). Alternatively, a requirement for the preservation of both intergenome component, and intragene, interaction networks has a net effect that is difficult to distinguish from either constraint operating alone.

We have provided experimental support for the complexity hypothesis by demonstrating a relationship between the relative modularity of defined genomic regions and the complexity of interactions in which they are involved. The striking correlation between our experimental results and the types of recombination observed in nature lends credence to the notion that these detectable modularity differences are evolutionarily relevant. Our results also suggest that the degree of similarity between an inherited sequence and the sequence it replaces is an important additional determinant of recombinant fitness. Whereas recombination can substantially increase the evolutionary options of an organism, the obligatory maintenance of co-evolved interaction networks may severely restrict its evolutionary value."

Evolutionary Distance Analysis & Maximum Parsimony Analysis

2006-04-30T20:05:00.000-07:00

Prokaryote Systematics: The Evolution of a Science: "Two main types of analysis are used today to infer phylogenetic trees from sequence alignments, evolutionary distance analysis (Fitch and Margoliash, 1967; Felsenstein, 1982) and maximum parsimony analysis (Fitch, 1971; Felsenstein, 1982). The former takes into account only the number of positions that differ in composition between pairs of sequences - this pair-wise difference being formally a distance. The latter looks at the quality of the difference between sequences, i.e., at which positions have different compositions in different sequences and the nature of these differences. Evolutionary distance analysis uses less of the information in an alignment than does maximum parsimony analysis. A crude analogy that to some extent captures the distinction between the two is that of a person arriving at a city from some far-away place, having traveled by some arbitrarily chosen circuitous route. A distance measurement would concern itself only with how far the person has traveled, not the route, the travel time or where the traveler began. A parsimony analysis attempts to reconstruct the actual route taken."

Tree of Life

2006-03-31T20:59:00.000-08:00

Western religion adopted the concept of a “Great Chain of Being”, which was borrowed from the ancient Greek Neoplatonists, in particular from Aristotle. The concept held that everything was part of a divinely orchestrated hierarchical order with God above all, followed by angels, humans, lower animals, plants, and so on down to inanimate objects. This notion persisted through the works of 17th and 18th century philosophers. 16th century illustration of "Great Chain of Being" concept From Didacus Valades, Rhetorica Christiana (1579).

Almost all later philosophers and scientists abandoned the notion in the face of a greater understanding of the nature of matter based upon empirical evidence. However, remnants of the concept persist in theology and in creationism. Scientific evidence supports the view that life inheres self-replication, and that living and extinct organisms are interrelated on a branching “Tree of Life”.

Tree of Life Project
"One of the most profound ideas to emerge in modern science is Charles Darwin's concept that all of life, from the smallest microorganism to the largest vertebrate, is connected through genetic relatedness in a vast genealogy. This "Tree of Life" summarizes all we know about biological diversity and underpins much of modern biology, yet many of its branches remain poorly known and unresolved."

Tree of Life or Fuzzy Bush of Life

2006-03-31T20:55:00.000-08:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Peter Gogarten is a professor of molecular and cell biology at the University of Connecticut. During his presentation at the World Summit on Evolution, he asked 'Is the 'Tree of Life' a Tree?'

Horizontal gene transfer between organisms allows us to understand genealogical relationships in prokaryote evolution. 'Over long periods of time gene transfer makes organisms existing in the same environment more similar to one another. This is most clearly seen in the case of organisms that live in environments that are otherwise inhabited by distant relatives only.' Thus, Gogarten concluded, 'the boundaries between prokaryotic species are fuzzy. Therefore the principles of population genetics need to be broadened so that they can be applied to higher taxonomic categories.'

See also: Genomes and the Tree of Life Tree of Life Horizontal Gene Transfer in Prokayotes

Comparing Gene Trees and Genome Trees: A Cobweb of Life?

2006-03-31T20:39:00.000-08:00

PLoS Biology: Comparing Gene Trees and Genome Trees: A Cobweb of Life?: "The tree of life has long served as a useful tool for describing the history and relationships of organisms over evolutionary time. One species is represented as a branching point, or node, on the tree, and the branches represent paths of descent from a parental node. The tree diagram carries an implicit assumption that genes are transferred vertically, from parent to child, and that all the genes in a new species come from the ancestral species. In theory, one should be able to trace the origin of each gene in a species back to its ancestor. In practice, however, the ancestral gene is rarely available, so researchers look for the gene in a closely related species. (These similar genes, which diverge slightly after a speciation event, are called orthologs.)

But as the tools of genome analysis became more refined, searches for similar genes sometimes turned up sequences that belonged to a species on a different branch of the evolutionary tree. Clearly, vertical gene transfer was not the only mechanism of genetic transmission. Organisms, it turns out, can acquire genes from non-ancestral species through a mechanism called horizontal gene transfer (HGT).

Such genetic exchanges, most common among bacteria and other microbes, are not represented in the tree of life—no single branch connects the two unrelated species. Initial studies suggested that HGT events were extremely common, prompting some to say it was time to replace the tree with a netlike diagram. Other studies have since suggested that methods used to calculate HGT overestimated its frequency: researchers detect HGT events by finding inconsistencies between gene trees and organism, or whole-genome, trees, but statistical errors can artificially increase the number of HGT events."
(2005) Comparing Gene Trees and Genome Trees: A Cobweb of Life? PLoS Biol 3(10): e347

Genomes and the Tree of Life

2006-03-31T20:35:00.000-08:00

EVOLUTION: GENOMES AND THE TREE OF LIFE: "Although we have not yet counted the total number of species on our planet, biologists in the field of systematics are assembling the 'Tree of Life' (1,2). The Tree of Life aims to define the phylogenetic relationships of all organisms on Earth.

Computer simulation studies (5) recently showed that, contrary to the prevailing view, phylogenetic accuracy depends more on having sufficient characters (such as amino acids) than on whether data are missing. Clearly, building a super-tree allows for an abundance of characters even though there are many missing entries in the resulting matrix." K.A. Crandall and J.E. Buhay (Science 2004 306:1144)

5. J. Wiens, Syst. Biol. 52, 528 (2003)

Protozoa

2006-02-28T20:59:00.000-08:00

Horizontal Gene Transfer in Prokayotes

2006-02-28T20:40:00.000-08:00

Horizontal gene transfer - gene swapping - has blurred the evolutionary relationships (phylogeny) of prokaryotes (image), and continues to provide a mechanism for the sharing of antibiotic resistance between bacteria.
(see The net of life: Reconstructing the microbial phylogenetic networkV. Kunin, L. Goldovsky, N. Darzentas, and C. A. OuzounisGenome Res. 1 July 2005. pdf)

Three mechanisms of horizontal (lateral) gene transfer are recognized: direct bacterial conjugation, bacteriophage mediated transduction between bacteria, and bacterial transformation by uptake of DNA fragments.

A major form of vertical gene transfer followed serial endosymbiotic events, in which ingested purple bacteria and Cyanobacteria became eukaryotic mitochondria and chloroplasts respectively. The ingested prokaryotes are believed to have relinquished certain genes to the nuclei of their host cells, a process known as endosymbiotic gene transfer.

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Margaret Riley is a colleague of Lynn Margulis at the University of Massachusetts-Amherst. She provided the commentary on Gogarten's presentation (Tree of Life or Fuzzy Bush of Life), suggesting that we need a modification of Ernst Mayr's definition of a species to accommodate microbes. Ernst Mayr defined a species as: 'A group of actually or potentially interbreeding natural populations reproductively isolated from other such populations.'

The problem with applying this definition to microbes is that separate species are not truly reproductively isolated, and yet they still retain distinct features that keep them phenotypically apart. 'Although horizontal gene transfer can and does occur, it does not obliterate the phenotypic groupings of organisms,' Riley concluded."

Protists in Evolution, and Symbiogenesis

2006-02-28T20:07:00.000-08:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): "Australian botanist Geoff McFadden, from the University of Melbourne, lectured on 'Protists and Cellular Phenomena in Evolution.'

Darwin ignored protists, but Ernst Haeckel included them in his comprehensive tree of life. Constantin Mereschkowsky was the first to appreciate the significance of protists in early eukaryotic evolution. A.F.W. Schimper noted that chloroplasts in plant cells very much resembled cyanobacteria. The the ultimate theoretical model was provided by Lynn Margulis: the key step was the endosymbiosis of cyanobacteria within a phagotrophic eukaryotic host, a process she calls symbiogenesis. The symbiotic theory of mitochondrial origin is supported by the different nature of internal and external membranes in mitochondria. In primary endosymbiosis, 1,000 genes were acquired by the nucleus from an incorporated cyanobacteria. A second round of gene transfer involved the engulfment of another plastid-containing eukaryote in secondary endosymbiosis. See also, Endosymbiosis and The Origin of Eukaryotes Illustration Endosymbiosis in Evolution

Proterozoic and Archaean

2006-01-31T20:59:00.000-08:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): "The Proterozoic and Archean Eons extend back to more than 3.6 billion years ago and cover the first microfossils and stromatolite fossils. Mikhail Fedonkin, head of the Laboratory of the Precambrian Organisms at the Paleontological Institute in Moscow suggested that a fall of global temperatures and the oxygenation of the biosphere secondary to photosynthesis played a major role in the dramatic change in the availability of heavy metals, which he believes were crucial in the metabolic processes that led to the evolution of complex life. This metal-rich environment served as a catalyst: 'Over 70 percent of known enzymes contain metal ions as a cofactor of an active site. Fast catalyzed reactions segregated life first dynamically and then structurally from the mineral realm.' Once prokaryotes gave rise to eukaryotes through symbiogenesis, life was off and running, exploding in the Cambrian with complex hard-bodied organisms.

Prokaryote Systematics: The Evolution of a Science

2006-01-31T20:58:00.000-08:00

Prokaryote Systematics: The Evolution of a Science: "The "evolutionary clock" (Kimura, 1983) is one of the great discoveries of the 20th century: The fact that in different organisms different (but clearly related) molecular sequences correspond to what appears to be the very same molecular function implies that most of the (net) changes that become fixed over time in any given molecular sequence are selectively neutral; they are of no phenotypic consequence (Kimura, 1983). Such changes must happen more or less randomly in time, and so can be used to measure time in a relative sense. In other words, on the genotypic level a more-or-less steady pace of evolutionary change occurs that is quasi-independent of the sporadic �real� evolutionary changes happening in the overlying phenotype. This independent �evolutionary clock� embedded in the genotype gives the biologist the capacity to infer evolutionary histories and relationships (Woese, 1987); and it has also freed the bacteriologist from the phenotypic quagmire of ill-defined, confusing, or conflicting, and generally phylogenetically uninterpretable morphological and physiological characters."

Prokaryote Systematics: The Evolution of a Science

2006-01-31T20:04:00.000-08:00

Prokaryote Systematics: The Evolution of a Science: "The most useful molecular chronometers actually are molecules like the ribosomal RNAs - molecules with universal, constant, and highly constrained functions that were established at early stages in evolution, functions that are not affected by changes in the organism's environment (except for changes in basic physical parameters such as intracellular pH and temperature). (A strong indicator of the constancy of rRNA function is the near constancy of the molecule's secondary structure within each of the primary kingdoms, and the approximate constancy that holds even between kingdoms [Gutell et al., 1985]). Because rRNAs are large molecules, they contain considerable information; their size also makes them less erratic chronometers than smaller molecules (Woese, 1987). Moreover, rRNAs are easy to isolate in relatively large quantities; they seem not to be subject to lateral gene transfer; and they can be sequenced directly (without resort to gene cloning).

The fact that a precisely functioning molecule such as RNA is under strict functional constraints is both an advantage and a disadvantage. The advantage lies in the constancy of the constraints on the various positions in the sequence and the fact that some positions change far more slowly than others; this last makes the molecule like a clock that includes both a second hand and a calendar—i.e., it can measure a wide range of time intervals. The disadvantage is that the stringent constraints lead to more (local) sequence convergence than otherwise, and the vast differential in rates at which positions change makes analysis more problematic than it would be for a uniform rate situation. (Another of its advantages would appear to be that RNA is a “nonlinear” chronometer and so is potentially capable of distinguishing rapidly vs. slowly evolving lineages, and, therefore, localizing the root of a tree without the need to resort to the use of outgroup sequences [Woese, 1987]).

Full text | A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

2006-01-30T20:37:00.000-08:00

BioMed Central Full text A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land: "A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land"

Why I'm Happy I Evolved - New York Times

2006-01-22T10:48:00.000-08:00

Why I'm Happy I Evolved - New York Times: "Some people want to think of humans as the product of a special creation, separate from other living things. I am not among them; I am glad it is not so. I am proud to be part of the riot of nature, to know that the same forces that produced me also produced bees, giant ferns and microbes that live at the bottom of the sea."

EVOLUTION: ON PLACOZOA -- THE SIMPLEST KNOWN ANIMAL

2006-01-08T10:28:00.000-08:00

EVOLUTION: ON PLACOZOA -- THE SIMPLEST KNOWN ANIMAL: "Often described as the simplest known animal, the unassuming marine placozoan Trichoplax adhaerens is one of a handful of 'lower' metazoans that have so far defied being pigeonholed. "

New cellular evolution theory rejects single cell beginning

2006-01-05T17:34:00.000-08:00

New cellular evolution theory rejects single cell beginning: "In the late 1970s Woese identified the Archaea, a group of microorganisms that thrive primarily in extremely harsh environments, as a separate life form from the planet�s two long-accepted lines � the typical bacteria and the eukaryotes (creatures like animals, plants, fungi and certain unicellular organisms, whose cells have a visible nucleus). His discovery eventually led to a revision of biology books around the world.

The three primary divisions of life now comprise the familiar bacteria and eukaryotes, along with the Archaea. Woese argues that these three life forms evolved separately but exchanged genes, which he refers to as inventions, along the way. He rejects the widely held notion that endosymbiosis (which led to chloroplasts and mitochondria) was the driving force in the evolution of the eukaryotic cell itself or that it was a determining factor in cellular evolution, because that approach assumes a beginning with fully evolved cells.

"The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different," Woese wrote in his introduction. "As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance."Woese calls this critical point in a cell’s evolutionary course the Darwinian Threshold, a time when a genealogical trail, or the origin of a species, begins. From this point forward, only relatively minor changes can occur in the evolution of the organization of a given type of cell.To understand cellular evolution, one must go back beyond the Darwinian Threshold, Woese said.His argument is built around evidence "from the three main cellular information processing systems" – translation, transcription and replication – and he suggests that cellular evolution progressed in that order, with translation leading the way.The pivotal development in the evolution of modern protein-based cells, Woese said, was the invention of symbolic representation on the molecular level – that is, the capacity to "translate" nucleic acid sequence into amino acid sequence.

The advent of translation, he said, caused various archaic nucleic-based entities to begin changing into proteinaceous ones, emerging as forerunners of modern cells as genes and other individual components were exchanged among them. The three modern types of cellular organization represent a mosaic of relationships: In some ways one pair of them will appear highly similar; in others a different pair will.This, Woese said, is exactly what would be expected had they individually begun as distinct entities, but during their subsequent evolutions they had engaged in genetic cross-talk – they had indulged in a commerce of genes."

Fossils

2005-12-31T20:59:00.000-08:00

Dinosaur Fossils Predict Body Temperatures

Shanidar Protein

2005-12-31T20:20:00.000-08:00

Max Planck Society - Press Release: "An international team, led by researchers at the Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, in Leipzig, Germany, have extracted and sequenced protein from a Neanderthal from Shanidar Cave, Iraq dating to approximately 75,000 years old. It is rare to recover protein of this age, and remarkable to be able to determine the constituent amino acid sequence. This is the oldest fossil protein ever sequenced. Protein sequences may be used in a similar way to DNA, to provide information on the genetic relationships between extinct and living species. As ancient DNA rarely survives, this new method opens up the possibility of determining these relationships in much older fossils which no longer contain DNA (PNAS Online Early Edition, March 8, 2005)."

New Study Shows Animal Family Tree Looking Bushy In Places

2005-12-26T11:52:00.000-08:00

New Study Shows Animal Family Tree Looking Bushy In Places: "Writing this week (Dec. 23, 2005) in the journal Science, a team of UW-Madison scientists led by Antonis Rokas, now of the Broad Institute of MIT and Harvard, suggests that a branch-by-branch account of animal relationships over a vast expanse of time is difficult to reconstruct because early animal evolution occurred in bunches."

Science's Breakthrough Of The Year: Watching Evolution In Action

2005-12-25T12:15:00.000-08:00

Science's Breakthrough Of The Year: Watching Evolution In Action: "In 2005, scientists piled up new insights about evolution at the genetic level and the birth of species, including information that could help us lead healthier lives in the future. Ironically, these often-startling discoveries occurred in a year when backers of 'intelligent design' and other opponents of evolution sought to renew challenges to this fundamental concept."

Scientists Narrow The Time Limits For The Human And Chimpanzee Split

2005-12-22T09:30:00.000-08:00

Scientists Narrow The Time Limits For The Human And Chimpanzee Split: "The scientists estimated the time of divergence between species by studying the sequential arrangement of nucleotides that make up the chain-like DNA molecules of each species. The number of mutations in the DNA sequence of a species, compared with other species, is a gauge of its rate of evolutionary change. By calibrating this rate with the known time of divergence of a species on another branch of the tree-like diagram that shows relationships among species, scientists can estimate the time when the species they are studying evolved. In this case, the calibration time the scientists used was the split of Old World monkeys -- including baboons, macaques, and others -- from the branch of the phylogenetic tree that led to humans and apes, which fossil studies have shown is at least 24 million years ago. Using this calibration time, the team estimated that the human-chimp divergence occurred at least 5 million years ago, proportionally about one-fifth of the calibration time."

Scientists Sequence DNA Of Woolly Mammoth

2005-12-21T15:40:00.000-08:00

Scientists Sequence DNA Of Woolly Mammoth: "A team of genome researchers at Penn State University and experts in ancient DNA at McMaster University in Canada has obtained the first genomic sequences from a woolly mammoth, a mammal that roamed grassy plains of the Northern Hemisphere until it became extinct about 10,000 years ago. The team's research on bones preserved in Siberian permafrost will be published on 22 December 2005 by the journal Science on the Science Express website. The project also involved paleontologists from the American Museum of Natural History (USA) and researchers from Russia, the United Kingdom, France, and Germany."

Geologists Link the "Great Dying" to Volcanism

2005-12-11T09:38:00.000-08:00

Science & Technology at Scientific American.com: Geologists Link the "Great Dying" to Volcanism: Modified:
"Life on Earth almost died out about 252 million years ago. Roughly 90% of marine life and 70% of terrestrial life died out. At roughly the same time, a vast up swelling of magma on land that became Siberia covered between one million and four million cubic kilometers. Eruption continued for about a million years, with basaltic lava and poisonous gases emerging through cracks in Siberia's mantle. Rocks from Italy may have linked the extinctions with the massive upwellings of magma.

In a paper in the Dec '05 issue of Geology, Mark Sephton of Imperial College London and his colleagues reveal that sedimentary rocks from that period, formed on the bottom of a shallow sea, contain unusually elevated levels of organic material from soil and plants. Typically microbes break down suchmaterial immediately. However, these rocks suggest, that a great flood of such terrestrial organic matter reached the sea, swamping it and suffocating marine life. "Similar to the 'dead zone' nowadays spreading in the Gulf of Mexico, the soil crisis could have caused a worldwide expanse of uninhabitable low-oxygen conditions in shallow waters," explains team member Henk Visscher of Utrecht University in the Netherlands.

The researchers argue that deadly gases emitted during the Siberian eruption killed vegetation across the globe. Without roots to hold the soil in place, rivers and streams would have carried most of the dead vegetation to the sea where it then blocked the sun's light and consumed all the oxygen. "What began on land ended in the sea," Visscher says. "It seems there was no place to hide at this time of great dying."

Although this postulated linkage may not end the debate over what caused the earth's greatest mass extinction, it stands to shed light on the loss of life the planet is currently experiencing. "Land degradation is a worsening global problem thanks to human activity and soil erosion [that] has caused the loss of a third of arable land over the last 40 years," Sephton notes. "Identifying the nature of the end of Permian soil crisis may help us understand what is in store for us in the years ahead.""

Acanthostega

2005-12-11T08:07:00.000-08:00

Science & Technology at Scientific American.com: Getting a Leg Up on Land -- [ EVOLUTION ] -- Recent fossil discoveries cast light on the evolution of four-limbed animals from fish: "Among the first fossil finds to pave the way for our modern conception of tetrapod origins were those of a creature called Acanthostega, which lived about 360 million years ago in what is now eastern Greenland. It was first identified in 1952 by Erik Jarvik of the Swedish Museum of Natural History in Stockholm on the basis of two partial skull roofs. But not until 1987 did my colleagues and I finally find specimens revealing the postcranial skeleton of Acanthostega. "

EVOLUTION: ON PHYLOGENETIC TREES

2005-12-07T07:44:00.000-08:00

EVOLUTION: ON PHYLOGENETIC TREES: "Phylogenetic trees show historical relationships, not similarities. Although closely related species tend to be similar to one another, this is not necessarily the case if the rate of evolution is not uniform: Crocodiles are more closely related to birds than they are to lizards, even though crocodiles are indisputably more similar in external appearance to lizards."

DNA Studies Show Microevolution In Penguins

2005-11-17T14:25:00.000-08:00

DNA Studies Show Microevolution In Penguins: "Comparison across thousands of years is possible because the extremely cold and dry conditions of the southernmost continent--conditions found almost nowhere else on Earth--preserved the ancient penguins' physical remains so well. The new study shows that the alleles -- slight variations in the coding of genes -- from ancient birds differ in several significant ways from those in modern populations in the same area. The researchers found that the DNA sequences for some of the genes had become longer over time, and that the frequency of some of the different genes had changed as well."

Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe

2005-11-16T15:26:00.000-08:00

PLoS Biology: Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe: "The 'Neanderthals' or Homo sapiens neanderthalensis (HN) constitute a group of hominids, whose particular morphology developed in Europe during the last 350,000 y under the effect of selection and genetic drift, reaching its final form approximately 130,000 y ago (Klein 2003). This subgroup of hominids populated Europe and western Asia until the arrival of the first modern humans, Homo sapiens sapiens (HS), approximately 45,000 y ago (Mellars 1992). This arrival coincided with the beginning of Neanderthal decline, a process that occurred in less than 15,000 y and that is still not fully understood (Stringer and Davies 2001). "

Evolution at Two Levels: On Genes and Form

2005-11-16T14:12:00.000-08:00

PLoS Biology: Evolution at Two Levels: On Genes and Form: "In their classic paper "Evolution at Two Levels in Humans and Chimpanzees," published exactly 30 years ago, Mary-Claire King and Allan Wilson described the great similarity between many proteins of chimpanzees and humans [1]. They concluded that the small degree of molecular divergence observed could not account for the anatomical or behavioral differences between chimps and humans. Rather, they proposed that evolutionary changes in anatomy and way of life are more often based on changes in the mechanisms controlling the expression of genes than on sequence changes in proteins."
Carroll SB (2005) Evolution at Two Levels: On Genes and Form. PLoS Biol 3(7): e245

Evolution of the entire arthropod Hox gene set predated the origin and radiation of the onychophoran/arthropod clade.

2005-11-16T14:06:00.000-08:00

Entrez PubMed: "Dramatic changes in body size and pattern occurred during the radiation of many taxa in the Cambrian, and these changes are best documented for the arthropods. The sudden appearance of such diverse body plans raises the fundamental question of when the genes and the developmental control systems that regulate these designs evolved. As Hox genes regulate arthropod body patterns, the evolution of these genes may have played a role in the origin and diversification of the arthropod body plan from a homonomous ancestor.

Despite the limited segmental diversity within myriapods and Onychophora, all insect Hox genes are present in both taxa, including the trunk Hox genes Ultrabithorax and abdominal-A as well as an ortholog of the fushi tarazu gene. Comparative analysis of Hox gene deployment revealed that the anterior boundary of expression of trunk Hox genes has shifted dramatically along the anteroposterior axis between Onychophora and different arthropod classes. Furthermore, we found that repression of expression of the Hox target gene Distal-less is unique to the insect lineage. So, a complete arthropod Hox gene family existed in the ancestor of the onychophoran/arthropod clade. No new Hox genes were therefore required to catalyze the arthropod radiation; instead, arthropod body-plan diversity arose through changes in the regulation of Hox genes and their downstream targets."
Grenier JK, Garber TL, Warren R, Whitington PM, Carroll S. Evolution of the entire arthropod Hox gene set predated the origin and radiation of the onychophoran/arthropod clade. Curr Biol. 1997 Aug 1;7(8):547-53.

'Perception' Gene Tracked Humanity's Evolution, Scientists Say

2005-11-15T19:30:00.000-08:00

'Perception' Gene Tracked Humanity's Evolution, Scientists Say: "Hahn said this 'evolutionary burst' is responsible for differences in gene expression rates. When induced, the human prodynorphin gene was 20 percent more active than the chimpanzee prodynorphin gene. Past research has also observed variation in expression levels within humans.
This report supports a growing consensus among evolutionary anthropologists that hominid divergence from the other great apes was fueled not by the origin of new genes, but by the quickening (or slowing) of the expression of existing genes."

The habitat and nature of early life : Nature

2005-11-15T14:17:00.000-08:00

The habitat and nature of early life : Nature: "Earth is over 4,500 million years old. Massive bombardment of the planet took place for the first 500−700 million years, and the largest impacts would have been capable of sterilizing the planet. Probably until 4,000 million years ago or later, occasional impacts might have heated the ocean over 100 °C. Life on Earth dates from before about 3,800 million years ago, and is likely to have gone through one or more hot-ocean 'bottlenecks'. Only hyperthermophiles (organisms optimally living in water at 80−110 °C) would have survived. It is possible that early life diversified near hydrothermal vents, but hypotheses that life first occupied other pre-bottleneck habitats are tenable (including transfer from Mars on ejecta from impacts there). Early hyperthermophile life, probably near hydrothermal systems, may have been non-photosynthetic, and many housekeeping proteins and biochemical processes may have an original hydrothermal heritage. The development of anoxygenic and then oxygenic photosynthesis would have allowed life to escape the hydrothermal setting. By about 3,500 million years ago, most of the principal biochemical pathways that sustain the modern biosphere had evolved, and were global in scope."

Copper and the biological evolution.

2005-11-15T08:53:00.000-08:00

Entrez PubMed: "Copper is contained in a number of enzymes and proteins. A remarkable feature is that except for the electron-carrying blue copper proteins (azurin and plastocyanin) and copper-containing cytochrome c oxidase found in some cyanobacteria and some aerobic bacteria, all copper enzymes and proteins are found only in eukaryotes. In the early and middle precambrian period when the stationary oxygen pressure in the atmosphere was quite low, copper existed as either metallic or cuprous sulfides which are very insoluble in aqueous media; thus copper might have been unavailable to organisms. The time when copper became Cu(II) upon rise of the atmospheric oxygen pressure and thus became available to organisms seems to be in the middle of Proteozoic era when first eukaryotic organisms seem to have appeared on earth. Thus copper may be considered to be an indicator element for the atmospheric evolution (switching from anoxygenic to oxygenic) and the evolution of higher organisms (eukaryotes)."

Ochiai EI. Copper and the biological evolution. Biosystems. 1983;16(2):81-6.

Theoretical Biology and Medical Modelling | Full text | Three subsets of sequence complexity and their relevance to biopolymeric information

2005-11-11T18:56:00.000-08:00

Theoretical Biology and Medical Modelling | Full text | Three subsets of sequence complexity and their relevance to biopolymeric information: "Nucleic acid instructions reside in linear, digital, resortable, and unidirectionally read sequences [46-49]. Replication is sufficiently mutable for evolution, yet conserved, competent, and repairable for heritability [50]. An exception to the unidirectionality of reading is that DNA can occasionally be read from both directions simultaneously. For example, the circular bacterial chromosome can be replicated in both directions at the same time [51] But the basic principle of unidirectionality of the linear digital flow of information nonetheless remains intact."

Digital Evolution

2005-11-11T18:30:00.000-08:00

PLoS Biology: Digital Evolution: "The research confronts evolutionary theory's long-standing challenge to explain how an organism can develop complex features simply as a result of random mutation and natural selection. The challenge remains a controversial one, too. Supporters of intelligent design, a branch of the creationist movement, promote the notion of �irreducible complexity� as evidence that Darwinian evolution is a flawed theory. The notion purports that a complex feature cannot evolve sequentially from its elements, and must have been designed in one step by some higher intelligence.
Traditional investigations, based on molecular biology and palaeontology, have yielded much evidence about the incremental evolution of the eye or the brain, for instance. But continuing ignorance about many developmental processes and the absence of key fossil records mean that accounts without missing links, to endorse the theory, may never be realised."

Evolution at Two Levels: On Genes and Form

2005-11-11T18:27:00.000-08:00

Cro-Magnons Conquered Europe, but Left Neanderthals Alone

2005-11-11T18:08:00.000-08:00

PLoS Biology: Cro-Magnons Conquered Europe, but Left Neanderthals Alone: "An ongoing question concerns the possibility that Neanderthals and early humans mated, since they likely crossed paths during thousands of years of European cohabitation. In a new study, Mathias Currat and Laurent Excoffier present a simulation model based on what we know about the population density and distribution of Neanderthals and Cro-Magnons. Their results complement recent genetic and morphological evidence indicating that early human and Neanderthal interbreeding was unlikely.

Since no Neanderthal mitochondrial DNA has been found in modern-day Europeans, the authors modeled the maximum number of interbreeding events that would support this observation. The estimated maximum number of events, it turns out, falls between 34 and 120—extremely low values, Currat and Excoffier conclude, “given the fact that the two populations must have coexisted for more than 12,000 years.”

While the authors acknowledge their simulations suggest rather than reflect reality, their model does incorporate real historical data such as Cro-Magnon expansion over time and local population growth. At a value of only 0.1%, their new estimate of the rate of interbreeding is about 400 times lower than previous estimates and provides strong support that Neanderthals and Cro-Magnon didn't interbreed and may even have been different species."

Cro-Magnons Conquered Europe, but Left Neanderthals Alone. PLoS Biol 2(12): e449 Published: November 30, 2004

HGT: Genome-Scale Estimates of Horizontal Gene Transfer

2005-11-11T18:00:00.000-08:00

PLoS Biology: The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer: "The role of horizontal gene transfer (HGT) in speciation, adaptation, and evolution of life on earth has been studied intensively [1], and there has been a growing body of evidence of transfers of genes among species [2�4] and transfers from organelles to nuclei [5�7]. Whole genome analyses of different prokaryotes have been thought to indicate rampant HGTs [8,9] and suggest that HGT plays a pivotal role in prokaryotic evolution, producing dynamic and mosaic genomes. The speculation [10] that even genes involved in transcription and translation might have been subject to HGT has also led to the suggestion that HGT should be considered the essence of phylogeny and that HGT might have eroded the organismal genealogical trace. Therefore, life history cannot be properly represented by the traditional treelike form, but rather by a netlike form [4,11�13]."

Lipids or RNA world?

2005-10-31T20:56:00.000-08:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): University of Massachusetts theoretical biologist Lynn Margulis, asked Antonio Lazcano, President of the International Society for the Study of the Origins of Life, 'In your opinion what came first, cells or the RNA world?' Lazcano answered: 'If you define a cell as a membrane-enclosed system, then lipids-enclosed systems assisted in the polymerization of molecules, which led to RNA. Lipids and cells came first, then the RNA world.'"

capping by ancient eukaryotes

2005-10-30T10:17:00.000-08:00

UB Department of Biological Sciences: Kiong Ho: "Initial analysis of the mRNA capping apparatus of T. brucei and the malarial parasite P. falciparum has illuminated an evolutionary connection to fungi rather than metazoans. T. brucei and P. falciparum encode a triphosphatase that is structurally and mechanistically similar to the fungal enzymes. RNA triphosphatase is an attractive drug target because the mechanism of cap formation is completely different from the metazoan host and metazoan species encode no recognizable homologue of the fungal/protozoan enzymes. Thus, a mechanism-based inhibitor against triphophatase should be highly selective for the parasite and have minimal effect on the human host or arthropod vector."

ancient eukaryotic functions

2005-10-30T10:13:00.000-08:00

UB Department of Biological Sciences: Kiong Ho: "Parasitic protozoa are causative agents of widespread human diseases, including malaria (caused by Plasmodium falciparum), African sleeping sickness (Trypanosome brucei), and Chagas' disease (Trypanosome cruzi). Because these parasites diverged early from the main branch of the eukaryotic lineage, their unusual mechanisms of gene expression reflect ancient eukaryotic functions that have been preserved to present. By studying the process of gene expression, not only may we learn about the evolution of higher eukaryotes, but we can also identify parasite specific processes that can be exploited as targets for novel therapeutic intervention."

Cambrian Explosion

2005-10-26T18:00:00.000-07:00

"Stratigraphic sections spanning the Vendian-Cambrian boundary show a broadly similar pattern whereby the key events are bracketed by the 600-million-year (Myr)-old Neoproterozoic glacial deposits (tillites) and in the succeeding Cambrian diverse metazoan assemblages, typified by abundant skeletons, diverse trace fossils, and Burgess Shale-type faunas (Fig. 1). One key development is a series of accurate radiometric determinations (1). The Vendian-Cambrian boundary is now placed at 543 Myr, and the duration (45 Myr) of the Cambrian is substantially shorter than once thought. The preceding Ediacaran faunas have an approximate age range of 565-545 Myr. Accordingly, the overall time-scale for discussion is a relatively protracted 65 Myr, although the principal events of evolutionary interest are probably more tightly bracketed (550-530 Myr) between the diverse Ediacaran faunas of latest Neoproterozoic age (2) and the Chengjiang Burgess Shale-type faunas (3). Correlations are also assisted by emerging schemes of chemostratigraphy (2, 4), notably with reference to strontium (87Sr) and carbon (13C)." Simon Conway Morris The Cambrian "explosion": Slow-fuse or megatonnage? PNAS April 25, 2000 vol. 97 no. 9 4426-4429

Science & Technology at Scientific American.com: The Woodstock of Evolution -- The World Summit on Evolution, held in the Galapagos Islands, revealed a science rich in history and tradition, data and theory, as well as controversy and debate: "Stephen Jay Gould's Wonderful Life stimulated a lot of new ideas about the Cambrian explosion of life, he continued, and it soon became clear that there were a huge variety of organisms difficult to classify, such as those in the Burgess Shale. But there are a number of Cambrian fossil beds, such as in China, where important phyla such as Chordata evolved. 'But what does all this diversity mean?' Fortey asked. 'There are today 30 living phyla. In the Cambrian, some claim that there were as many as 100 phyla, but the evidence does not support this. We now believe that morphological diversity did not explode as much as Gould originally suggested, although the explosion in evolutionary experimentation was real. By the time we get to the Cambrian, like at the Burgess Shale, the systems are very complex, such as trilobite eyes. Evolution was experimenting with many wondrous varieties, such as all the armor on the heads of trilobites.' "

Homo Floresiensis: More Bones Support Mini Human Case

2005-10-26T17:37:00.000-07:00

Scientific American.com: More Bones Support Mini Human Case: "Now Morwood, Brown and their colleagues say that various arm, leg, jaw, toe and finger bones as well as a scapula and vertebra were excavated in 2004, bringing the estimated number of individuals represented thus far at Liang Bua to nine and casting doubt on those alternative interpretations. Analysis of the second jaw shows that it is very similar to the first one. Both notably lack a chin, which is a unique characteristic of Homo sapiens, even those that suffer from microcephaly. And further study of the leg and arm bones confirm that H. floresiensis was about a meter tall and had long arms. Modern adult pygmies have legs and arms that are proportional to their short stature. 'We can now reconstruct the body proportions with some certainty,' the researchers write in the October 13 issue of Nature."

Cambrian Explosion

2005-09-30T20:59:00.000-07:00

Stephen Jay Gould's in "Wonderful Life" stimulated a lot of new ideas about the Cambrian explosion of life. It soon became clear that there were a huge variety of organisms difficult to classify, such as those in the Burgess Shale. However, there are a number of Cambrian fossil beds, such as the lagerstatte in China, which contain evidence of important phyla such as Chordata.

Richard Fortey from the British Museum of Natural History asked, 'But what does all this diversity mean?'. "There are today 30 living phyla. In the Cambrian, some claim that there were as many as 100 phyla, but the evidence does not support this. We now believe that morphological diversity did not explode as much as Gould originally suggested, although the explosion in evolutionary experimentation was real. By the time we get to the Cambrian, like at the Burgess Shale, the systems are very complex, such as trilobite eyes. Evolution was experimenting with many wondrous varieties, such as all the armor on the heads of trilobites."
The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com).

"Stratigraphic sections spanning the Vendian-Cambrian boundary show a broadly similar pattern whereby the key events are bracketed by the 600-million-year (Myr)-old Neoproterozoic glacial deposits (tillites) and in the succeeding Cambrian diverse metazoan assemblages, typified by abundant skeletons, diverse trace fossils, and Burgess Shale-type faunas (Fig. 1, large). One key development is a series of accurate radiometric determinations (1). The Vendian-Cambrian boundary is now placed at 543 Myr, and the duration (45 Myr) of the Cambrian is substantially shorter than once thought. The preceding Ediacaran faunas have an approximate age range of 565-545 Myr. Accordingly, the overall time-scale for discussion is a relatively protracted 65 Myr, although the principal events of evolutionary interest are probably more tightly bracketed (550-530 Myr) between the diverse Ediacaran faunas of latest Neoproterozoic age (2) and the Chengjiang Burgess Shale-type faunas (3). Correlations are also assisted by emerging schemes of chemostratigraphy (2, 4), notably with reference to strontium (87Sr) and carbon (13C)." Cambrian taxonony & Phylogeny
Simon Conway Morris The Cambrian "explosion": Slow-fuse or megatonnage? PNAS April 25, 2000 vol. 97 no. 9 4426-4429

No safe ground for life to stand on during world's largest mass extinction

2005-08-31T22:59:00.000-07:00

Imperial College London - No safe ground for life to stand on during world's largest mass extinction: "Many scientists had previously thought that an asteroid hitting the earth or a deep-sea methane release had caused the extinction, which obliterated more than two-thirds of reptile and amphibian families.

However, analysis of a unique set of molecules found in rocks taken from the Dolomites in Italy has enabled scientists to build up a picture of what actually happened. The molecules are the remains of polysaccharides, large sugar-based structures common in plants and soil, and they tell the story of the extinction.

The molecules date from the same time as a major volcanic eruption that caused the greatest ever outpouring of basalt lava over vast swathes of land in present day Siberia.

The researchers believe that the volcanic gases from the eruption, which would have depleted earth's protective ozone layer and acidified the land and sea, killed rooted vegetation. This meant that soil was no longer retained and it washed into the surrounding oceans.

The chemistry of the rocks reveals that although the sugar molecules were found in marine sediments, they derived from land, supporting the theory that massive soil erosion caused them to end up in the sea.

Soil materials in the oceans would have blocked out light and soaked up oxygen. Analysis of rock chemistry suggests that after the soil crisis on land, the marine ecosystem succumbed to the stresses of environmental change and oceanic life faltered, completing a global catastrophe."

Extinction Events

2005-08-31T20:56:00.000-07:00

ODPTC 5 Biggest Extinction Events

2005-08-31T20:50:00.000-07:00

Science & Technology at Scientific American.com: The Woodstock of Evolution -- The World Summit on Evolution, held in the Galapagos Islands, revealed a science rich in history and tradition, data and theory, as well as controversy and debate: "Interestingly, despite the impact of the five biggest mass extinctions (Ordovician 439 Ma, Devonian 367 Ma, Permian 245 Ma, Triassic 208 Ma, Cretaceous 65 Ma), many organism groups passed through all of these extinction episodes safely, such as the cockroach. 'What is amazing is not only the extent of loss, but how fast life bounces back,' Fortey concluded."

Importance of Mass Extinction Events

2005-08-26T20:59:00.000-07:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): Richard Fortey from the British Museum of Natural History discussed the evidence of evolution in the Phanerozoic (from 542 Ma, million years ago, till the present). Fortey emphasizing the importance of mass extinction events in resetting the direction of evolution, the importance of evolutionary arms races in driving morphological innovation, the relationship of climate change and changing geography to evolutionary change, and the extent to which evolution can be described as directional. With half a billion years of a solid fossil record, Fortey said we can track the evolutionary periods of creativity and crises.

EVOLUTION: ON THE EVOLUTION OF HUMANS AND CHIMPANZEES

2005-07-31T23:59:00.000-07:00

EVOLUTION: ON THE EVOLUTION OF HUMANS AND CHIMPANZEES: "What does the chimpanzee genome sequence tell us about the role of natural selection in human evolution? Purifying selection is clearly evidenced by the fact that mutations that alter the amino acid sequence, which in many cases presumably have a deleterious effect, have gone to fixation at a much lower rate than those that do not. Traditionally, this is expressed in terms of the ratio of non-synonymous (dN) to synonymous (dS) substitutions, dN/dS, where dS is here used as an index of the rate of unconstrained, neutral evolution. When dN/dS is less than 1, the usual interpretation is that negative selection has taken place on non-synonymous substitutions. When dN/dS is greater than 1, positive selection is likely to have accelerated the rate of fixation of non-synonymous substitutions. Note that purifying selection is the conservative force in molecular evolution, whereas positive selection is the diversifying force that drives molecular adaptation. dN/dS is estimated to be ~0.25, on average, for the human chimp comparison. In other words, about 75% of all amino acid replacements seem to be removed by purifying selection."

Hominids

2005-07-31T20:59:00.000-07:00

How many Biological Species of Hominids

2005-07-31T20:50:00.000-07:00

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): U.C. Berkeley paleoanthropologist Timothy White said, 'A glance at the extant fossil record looks like Gould was right. There are at least two dozen fossil species in six million years of hominid evolution. However, says White, the bush is not so bushy. 'Name diversity does not equal biological diversity.' The problem lies in the difference between 'lumpers' and 'splitters' in species classification. The academic pressures to publish extraordinary new discoveries dictates that if you want to get your fossil find published in Science or Nature, and you want the cover illustration, you cannot conclude that your fossil is yet another Australopithicus africanus, for example. For such purposes, it's better come up with an interpretation indicating that this new find you are revealing for the first time to the world is the most spectacular discovery of the last century and that it promises to overturn hominid phylogeny and send everyone back to the drawing board to reconfigure the human evolutionary tree. Training a more skeptical eye on many of these fossils, however, shows that many, if not most of these fossils belong in already well-established categories. White concludes that the specimen labeled Kenyanthropus platyops, for example, is very fragmented and is most likely just another Australopithicus africanus.

Redating Of The Latest Neandertals In Europe

2005-07-31T20:40:00.000-07:00

Redating Of The Latest Neandertals In Europe: "An international team of researchers has redated the two Neandertals from Vindija Cave, the results of which have been published in the Jan. 2-6 early edition of the journal Proceedings of the National Academy of Sciences (PNAS).

The resultant ages are between 32,000 and 33,000 years ago, and perhaps slightly older. In 1998, the fossils had been radiocarbon dated to 28,000-29,000 years ago.
Since that time, the increasing application of direct radiocarbon dating to late Neandertal and early modern human fossils in Europe has greatly altered perceptions of the chronological relationships between Neandertals and modern humans during the time that the latter spread westward across Europe.

In particular, it has shown that many of the purportedly early modern human fossils are much more recent, while confirming the early ages of important fossil samples in central and eastern Europe. This work has been combined recently with refinements in the sample purification techniques for the radiocarbon dating bone and teeth, to provide more accurate, and usually older, dates for important fossil specimens.

These new fossil ages still document a substantial chronological overlap between Neandertals and modern humans in Europe, but primarily the work highlights the currently tenuous nature of scenarios of modern human dispersals in Europe based on small numbers of direct radiocarbon dates, using various sample preparation protocols, on diagnostic human fossils in this time range."

The original news release can be found here.

Homo floresensis

2005-07-31T20:14:00.000-07:00

Science & Technology at Scientific American.com: The Woodstock of Evolution -- The World Summit on Evolution, held in the Galapagos Islands, revealed a science rich in history and tradition, data and theory, as well as controversy and debate: "Found in Liang Bua cave, the type specimen of Homo floresiensis was dated at 18,000 years old, meaning that they had to be modern humans because all other hominid species had long ago gone extinct. But with a cranial capacity of only 300 cubic centimeters--about the same size as that of Lucy and modern chimpanzees--this means that they were able to fashion complex tools (and possibly boats) with tiny brains; the implication is that brain architecture, not size, is what counts for creating higher intelligence. A second published specimen put to rest the pathology hypothesis that Homo floresensis was a microcephalic human. The best evidence, says White, points to insular dwarfing, a rapid punctuation event out of Homo sapiens that led to a shrinkage of these isolated people. Such dwarfing effects can be seen on this and other islands, where large mammals get smaller (like the dwarf elephant), and small reptiles get larger (like the Komodo Dragon). The chances of any living members of this species still existing in the hinterlands of Flores are extremely remote, but some observers have noted that the indigenous peoples of Flores recount a myth of small hairy humans who descend from the highlands to steal food and supplies."

Evolutionary Explanations For Aging Plateau

2005-07-31T01:00:00.000-07:00

The End Of Aging? New Study Examines Evolutionary Explanations For 'Biological Immortality': "'For decades, demographers and gerontologists noticed that late life human data did not fit [expected] models: there was a shortage of deaths,' write Michael R. Rose, Casandra L. Rauser, and Laurence D. Mueller. 'More specifically, the exponential increase in age-specific death rate seemed to slow down considerably, if not cease.'

The sudden plateau in mortality rates after a certain age has long been observed with other organisms, but its presence in human populations has been dismissed as a result of the advent of nursing homes and modern medicine. However, close examination of demographic data supports a distinct third phase of life history known as "late life," characterized by the cessation of age-related deterioration.

"Late life is a unique and distinct phase of life very different from aging," write the authors. "Each phase evolves according to very different rules. Evolutionary biology has a new set of problems to solve."

The authors posit that late life arises after the forces of natural selection affecting both fertility and mortality cease to have an impact."

Rose, Michael R., Casandra L. Rauser, Laurence D. Mueller. "Late Life: A New Frontier for Physiology." Physiological and Biochemical Zoology 78:6.

Hominid Migrations

2005-06-30T20:59:00.000-07:00

mtDNA and Migration Routes

2005-06-30T20:50:00.000-07:00

Science & Technology at Scientific American.com: The Woodstock of Evolution -- The World Summit on Evolution, held in the Galapagos Islands, revealed a science rich in history and tradition, data and theory, as well as controversy and debate: "University of Cambridge professor Peter Forster, an expert in archaeogenetics outlined our migrational history over the past 200,000 years as follows: Between 190,000-130,000 years ago, a single female known formally as the 'mitochondrial coalescent' but dubbed 'mitochondrial Eve,' gave rise to every living human today. Between 80,000 and 60,000 years ago, a large population from the center of Africa migrated to all areas of Africa, as well as the area of present-day Saudi Arabia. This migration may have taken two routes, a northern one up the Nile and around the Red Sea, and a southern one across the narrow straight which, during the last ice age would have only been five kilometers across (Forster thinks the latter the most likely route). Between 60,000 and 30,000 years ago there was a great migration to Southeast Asia, Northern Asia, and Europe. Between 30,000 and 20,000 years ago, people spread throughout the rest of the world, including Australia, and between 20,000 and 15,000 years ago they migrated into North America, making their way into South America between 15,000 and 2,000 years ago. The final migration over the past 2,000 years saw the settlement of the Pacific islands."

Paleogeology and Paleoclimate

2005-05-31T20:59:00.000-07:00

eocene oligocene glaciation

2005-05-31T20:50:00.000-07:00

PALEOCLIMATE: ON TRANSIENT GLACIATION: "there was little global cooling associated with the late Eocene glaciations, suggesting that, as in the earliest Oligocene event[5], most of the shift in delta-18O was due to an increase in ice volume and that cooling may have been limited to high latitudes (or that ice-sheet accumulation there was limited by moisture rather than temperature). As in the earliest Oligocene, the isotopic data seem to require the presence of ice sheets on Antarctica at least as thick as those today, and substantial ice sheets in North America (most likely Greenland). This latter result runs contrary to conventional wisdom, which holds that the Northern Hemisphere glaciation began tens of millions of years later."

Biochemical Energetics

2005-04-30T20:59:00.000-07:00

For a reaction A + B –> C + D, A and B are the reactants and C and D are the products. Energetically favorable reactions proceed spontaneously from reactants to products. In such a case the energy state of reactants is lower than the energy state of products, meaning that the reaction proceeds in a downhill direction in terms of chemical energy. However, to reach this downhill state, the reactants must pass over a 'speed bump', an energetic barrier.

Catalysts lower the energetic barrier between substrates and products yet catalysts emerge unchanged from the reaction. Biological catalysts are called enzymes – these are usually proteins, but may be molecules of RNA (ribozymes). Enzymes increase the rate of reactions by virtue of a transient binding of substrate (A and/or B) to the active site of the enzyme. This binding of substrate to enzyme occurs at the active site where it is stabilized by numerous weak interactions (hydrogen bonds, electrostatic interactions, hydrophobic contacts, and van der Waals forces). The enzyme-substrate complex dissociates into enzyme (in original state) and products (C,D).

Informational Macromolecules

2005-03-31T20:59:00.000-08:00

The Genetic Code

2005-03-31T20:58:00.000-08:00

Fun with Numbers

2005-03-31T20:50:00.000-08:00

Permutations are the possible rearrangements of things when order is important. Combinations apply when order is not important. The principle behind the math of permutations is quite simple, though actual numbers grow exponentially.

Taking the letters caug, for example, yields the following permutations
caug augc ugca gcau
cuag uagc agcu gcua
gauc aucg ucga cgau
guac uacg acgu cgua
aguc guca ucag cagu
ucga cgau gauc aucg

That is, 24 permutations arise from the ordered rearrangement of 4 letters. This number is much more easily worked out by the formula:
4! = 4.3.2.1 = 24

So, if we started with 7a's 8c's 6u's and 5g's, we would have 26! = 26.25.24....1 = 4.032914611266056e+26, which approximates to 11^26 permutations.

e= Euler's number = base of natural logarithms = 2.71828 18284 59045 23536 02874 7135...)

In more general terms, n! = n.(n-1).(n-2)...1

Of course, we might have started with different combinations of 'caug' totalling 26, for example 8a's 7c's 6u's and 5g's, and for each combination we would have 26! = 11^26.

Here, the total number of combinations of 4 letters assembled into total groups of 26 is 14,950 = 26! divided by 22!

This brings the grand total number of permutations to 14,950 x 11^26. This simplifies to about 1.7 x 10^29 -- that is 1.7 followed by 29 zeros.
permutation-combination calculator

Why these letters? The letters are the symbols for the bases in RNA = CAUG = cytosine, adenine, uracil, and guanine. The minimal genome is calculated to be about 260 genes – thousands of bases, so exponentially more permutations.

Idists employ such numbers in their effort to demonstrate that the genetic code for a particular protein – determined by the order of bases in the nucleic acid chain – could not arise by chance. Proids ignore, or are ignorant of, several important features of the genome and proteome when they employ such numbers, and talk of monkeys typing Shakespeare.

Basic Biochemistry

2005-02-28T18:47:00.000-08:00

Introduction to Biochemistry
Biochemistry includes the study of ions, inorganic molecules, and organic molecules involved in biological processes – for example enzymes, structural molecules, transport molecules, and metabolic pathways. Molecular genetics deals specifically with the information macromolecules involved in genetic inheritance.

Basic Physical Chemistry

2005-01-31T18:59:00.000-08:00

An atom consists of a positively charged nucleus (protons, neutrons) surrounded by a single negatively charged electron (hydrogen) or ‘shells’ of electrons. A molecule consists of two or more atoms joined by chemical bonding. Bonds vary in type and the strength of bonding depends upon the participation atoms and upon other interactions between molecules (inter-molecular), or within a molecule (intra-molecular).

In order of increasing strength of bonding:

Intermolecular Van Der Waals bonds are weak and operate over short distances.

Non-covalent bonds result from electrostatic attraction of charged groups in molecules.

Hydrophobic attraction involves an orientation of un-charged molecules toward un-charged components of the medium and away from charged components, such as water.

A hydrogen bond results from an attractive intermolecular force between two partial electric charges of opposite polarity. Although stronger than most other intermolecular forces, a hydrogen bond is much weaker than either a covalent or ionic bond.

In covalent bonds, atoms share an electron or electrons.

In ionic bonding an atom donates an electron to another atom.

Fallacies of Logic

2004-12-31T20:59:00.000-08:00

Below are examples of the fallacious arguments to which creationists, idists, and proids resort in their attempt to prove their point. Because idism appeals to the pseudo-intellectual fundamentalist Christian, most examples will be pulled from idists and proids.

This is not to say that evolutionists do not make the occassional logical blooper. Perhaps the commonest is the circular argument. It should be noted that explanations can also appear circular, but this is not such a problem because explanations are not arguments.