louis pasteur in one advance louis pasteur discredited the concept of spontaneous generation. he...

In one advance Louis PasteurLouis Pasteur discredited the concept of spontaneous generation. discredited the concept of spontaneous generation.

He offered proof that even bacteria and other microorganisms arise from parents resembling themselves. microorganisms arise from parents resembling themselves. He thereby highlighted an intriguing question:How did the first generation of each species come into existence?

When the earth formed some 4.6 billion years ago, it was a lifeless, inhospitable place. A billion years later it was teeming with organisms resembling blue-green algae. How did they get there?

How, in short, did life begin?How, in short, did life begin?

http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html Leslie E. Orgel

… in the mid-19th century two important scientific advances set the stage for modern discussions of the origin of life.

http://www.geocities.com/CapeCanaveral/Lab/2948/orgel.html

The theory therefore implied that all current life-forms could have evolved from a single, simple progenitorall current life-forms could have evolved from a single, simple progenitor - an organism now referred to as life's last common ancestorlife's last common ancestor.

… individuals bearing traits that provide the best adaptation to the … environment meet with the greatest reproductive success. …… some of the differences between individuals in a population are heritable. In other words, environmental pressures select adaptive traits for perpetuation. Repeated generation after generation, natural selection natural selection could thus lead to the evolution of complex organisms from simple ones.could thus lead to the evolution of complex organisms from simple ones.

The second advance, the theory of natural selectionthe theory of natural selection, suggested an answer. According to this proposal, set forth by Charles Darwin and Alfred Russell Wallace,

For much of the 20th century, origin-of-life research has aimed to flesh out Darwin's private hypothesis - to elucidate how, without supernatural intervention, spontaneous interaction of the relatively simple molecules dissolved in the lakes or oceans of the prebiotic world could have yielded life's last common ancestorlife's last common ancestor.

… it had to possess genetic informationit had to possess genetic information - heritable instructions … and the means to replicateand the means to replicate and carry out those instructions. Otherwise it would have left no descendants. Also, … its genetic material had to allow for some random variationits genetic material had to allow for some random variation in the heritable characteristics of the offspring so that new traits could be selected …

Darwin …posited in the final paragraph of The Origin of Species that "the Creator" originally breathed life "into a few forms or into one." Then evolution took over: "From so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."

In private correspondence … he suggested life could have arisen through chemistry, life could have arisen through chemistry, "in some warm little pond, with all sorts of ammonia and"in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc. present." phosphoric salts, light, heat, electricity, etc. present."


… One can safely inferinfer that intricate features present in all modern varieties of life intricate features present in all modern varieties of life also appeared in thatalso appeared in that common ancestorcommon ancestor. …. …

… all living things consist of similar organic (carbon-rich) compounds. … the proteins … are fashioned from one set of 20 standard amino acidsone set of 20 standard amino acids. …… carry their genetic information in nucleic acids - RNA and DNA - and use essentially the same genetic codeessentially the same genetic code. This code specifies the amino acid sequences of all the proteins …

… … we can infer that our last common ancestor stored genetic information in we can infer that our last common ancestor stored genetic information in nucleic acids that specified the composition of all needed proteins.nucleic acids that specified the composition of all needed proteins.… … relied on proteins to direct … the reactions required for self-perpetuation.relied on proteins to direct … the reactions required for self-perpetuation.

Hence, the central problem of origin-of-life research can be refined to ask, By what series of chemical reactions By what series of chemical reactions did this interdependent system of nucleic acids and proteins did this interdependent system of nucleic acids and proteins come into being? come into being?


… a paradoxa paradox. Nowadays nucleic acids are synthesized only with the help of proteins, and proteins are synthesized only if their … nucleotide sequence is present.

Moreover, it was easy to envision ways that DNA could evolve from RNA and then, being more stable, take over RNA's role as the guardian of heredity. We suspected that RNA came before proteins … we had difficulty composing any scenario in which proteins could replicate in the absence of nucleic acids.

C&R Fig 26.11 C&R Fig 26.13

a world in which RNA catalyzed all the reactions necessary a world in which RNA catalyzed all the reactions necessary forfor a precursor ofa precursor of life's last common ancestorlife's last common ancestor to survive and replicateto survive and replicate. . … ribonucleotides in RNA are more readily synthesized than are the deoxyribonucleotides in DNA.

In the late 1960s Carl R. Woese … Francis Crick … and I … independently … proposed that RNA might well have come first and established what is now called the RNA worldRNA world -


{similarities}

{differences}

… there is good reason to think the RNA world did exist and that RNA invented protein synthesis.

Fortunately, even before the RNA-world hypothesis was proposed, investigators had gained useful insights into that chemistry.

If this conclusion is correct, the main task … explaining how the RNA world came into being. The answer to this … requires knowing something about … the prebiotic soupthe prebiotic soup: the aqueous solution of organic molecules in which life originated.

Oparin and Haldane proposed … that the atmosphere of the young earth, like that of the outer planets, was reducing: it contained very little oxygen and was rich in hydrogen (H2) … methane (CH4) and ammonia (NH3).

By the 1930s Alexander I. Oparin in Russia and J.B.S. Haldane in England had pointed out that the organic compounds needed for life could not have formed on the earth if the atmosphere was as rich in oxygen (oxidizing) as it is today.

J.B.S. Haldane was approached by a distinguished theologian to ask what inferences could drawn about the nature of the Creator from the study of His Creation. Haldane replied with his usual terseness: "That He has an inordinate fondness for beetles.“ - approximately one-fifth of all known species are beetles--350,000 and growing.


The Original Origin-of-Life ExperimentThe Original Origin-of-Life Experiment In the early 1950s Stanley L. Miller … did the first experiment designed to clarify the chemical reactions that occurred on the primitive earth.

In the flask at the bottom, he created an "ocean" of water, which he heated, forcing water vapor to circulate …The flask at the top contained an "atmosphere" consisting of methane (CH4), ammonia (NH3), hydrogen (H2) and the circulating water vapor. Next he exposed the gases to a continuous electrical discharge ("lightning"), causing the gases to interact. … products … passed through a condenser and dissolved in the mock ocean. The experiment yielded many amino acidsmany amino acids …

Years after this experiment, a meteoritea meteorite that struck near Murchison, Australia, was shown to contain a number of the samethe same amino acidsamino acids that Miller identified …


This meteorite, that fell near Murchison, Australia on 28 September 1969, turned out to contain a variety of organic molecules including both purines and pyrimidines as well as the amino acids listed here. The amino acids and their relative proportions were quite similar to the products formed in Miller's experiments. The question is: were these molecules simply terrestrial contaminants that got into the meteorite after it fell to earth.

Probably not:

•Some of the samples were collected on the same day it fell and subsequently handled with great care to avoid contamination.

•The samples lacked certain amino acids that are found in all earthly proteins.

•Only L amino acids occur in earthly proteins, but the amino acids in the meteorite contain both D and L forms (although L forms were slightly more prevalent).

Discovery of amino acids from Didwana-Rajod meteorite and its implication on origin of life.Tewari et al. 2002. J. GEOLOGICAL SOCIETY OF INDIA 60:107-110.Abstract:Aromatic amino acids Phenylalanine, Tyrosine and Tryptophan have been identified for the first time from the Didwana-Rajod meteorite which fell on Earth (most probably from asteroid belt between Mars and Jupiter in our Solar system) in 1991 near Didwana in Nagaur district of Rajasthan.

1999 Kuiper Prize Lecture: Cometary origin of the biosphere.Delsemme AHICARUS 146: (2) 313-325 AUG 2000

Abstract:

Most of the biosphere was brought on the primitive Earth by an intense bombardment of comets. This included the atmosphere, the seawater and those volatile carbon compounds needed for the emergence of life. …

Margulis & Sagan (1995)

“Of the six kinds of atoms crucial to life on earth - carbon, nitrogen, oxygen, sulfur and phosphorus - all have been detected in space. Hydrogen is the most common element in DNA, RNA, proteins, fats … is also the most common element in the universe.Ammonia (NH3) was discovered in interstellar space in 1968. H3C2N, cyanoacetylene, was detected in 1970. Alcohol (CH3CH2OH) abounds in the constellation Orian. Other compounds found both in space and in living things include water, acetylene, formaldehyde, cyanide, methanol, and formic acid. “ {from spectraphotometry}

{Not the O2 - Gaia}

… recent investigations indicate the earth's atmosphere was never as reducing as Urey and Miller presumed.… it seems prudent to consider other mechanisms for the accumulation of the constituents of proteins and nucleic acids in the prebiotic soupthe prebiotic soup.

For instance, the amino acidsamino acids and nitrogen-containing bases needed for life on the earth might have been delivered by interstellar dust, meteoritesmeteorites and comets. …

Initial indications of abiotic formation of hydrocarbons in the Rainbow ultramafic hydrothermal system, Mid-Atlantic Ridge.Holm NG, Charlou JL. 2001. Earth and Planetary Science Letters 191:1-8.

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… some of the organic materials required for life … may have arisen in deep-sea ventsdeep-sea vents, the submarine fissures in the earth's crust through which intensely hot gases are cycled.

End of the Leslie E. Orgel essay.


Ever since the pioneering work of Aleksandr Oparin and John Haldane the prebiotic soup theorythe prebiotic soup theory has dominated thinking about how life emerged on Earth. According to the modern version of this theory, organic compounds accumulated in the primordial oceans and underwent polymerization, producing increasingly complex macromolecules that eventually evolved the ability to catalyze their own replication.

The prebiotic soup scenario thus suggests that the first living entities appeared, and evolved through the RNA world to DNA/protein biochemistry, when Earth was cool rather than boiling hot. Because of the reduced luminosity of the young Sun, Earth may indeed have been completely covered with ice during its early history. The first self-replicating molecular entities may have developed under these conditions from the prebiotic organic ingredients.

Jeffrey L. Bada and Antonio LazcanoScience Jun 14 2002:1982-1983.

The Surveyor 3 spacecraft's microorganisms were recovered from inside its camera that was brought back to Earth under sterile conditions …

50-100 organisms (common bacteria - Streptococcus mitis), survived launch, space vacuum, 3 years of radiation exposure, deep-freeze at an average temperature of only 20 degrees above absolute zero, and no nutrient, water or energy source.

No other life forms were found in soil samples retrieved by the Apollo missions or by two Soviet unmanned sampling missions, although amino acids - not necessarily of biological origin - were found in soil retrieved by the Apollo astronauts.

http://science.nasa.gov/newhome/headlines/ast28may99_1.htm

Apollo 12 Commander Pete Conrad inspects Surveyor 3's camera assembly on April 20, 1967

http://science.nasa.gov/default.htm

http://science.nasa.gov/newhome/headlines/ast28may99_1.htm

Culture plate from Surveyor 3 camera foam. The US Communicable Disease Center confirmed it as

Streptococcus mitis a common harmless bacteria from the nose, mouth and throat in humans.The Streptococcus genus consists of Gram-positive bacteria which appear as chains under microscopic observation. Members of Streptococcus can be aerobic, anaerobic, or microaerophilic. … the largest group of bacteria isolated from the oral cavity … almost 50% of the organisms isolated from plaque & gingival sulcus. …streptococci are part of the normal flora and symbiotically limit the growth of competing harmful bacteria in the mouth.… the normal human houses about a trillion bacteria on the skin, 10 billion in the mouth, and 100 trillion in the gastrointestinal tract. … far in excess of the number of eukaryotic cells in … the human host. … there is more of "them" than "you'' in you.there is more of "them" than "you'' in you.

The normal flora occupy available colonization sites which makes it more difficult for other microorganisms (nonindigenous species) to become established.{note risk of yeast infections after antibacterial antibiotics}

Fig 26-15. Whittaker’s five-kingdom system.

The five-kingdom system recognized the two fundamentally different types of cells, prokaryotic and eukaryotic …

Fig 27-2. The three domains of life.

This phylogenetic tree represents the hypothesis that the two major prokaryotic groups diverged very early and that Archaea is more closely related to Eukarya than to Bacteria.

My evolutionary concerns center on the bacteria and the archeaarchea, whose evolutions cover most of the planet's 4.5-billion-year history.

http://www.bact.wisc.edu/microtextbook/ClassAndPhylo/molPhylogeny.html

http://www.life.uiuc.edu/Micro/woese.html

Carl R. WoeseProfessor of Microbiology B.A. (Math & Physics), Amherst College, 1950 Ph.D. (Biophysics), Yale University, 1953 Postdoc. (Biophysics), Yale University, 1953-1960 Biophysicist, General Electric Research Laboratory, 1960-1963

Using ribosomal RNA sequence as an evolutionary measure, my laboratory has reconstructed the phylogeny of both groups, and thereby provided a phylogenetically valid system of classification for prokaryotes. The discovery of the archaea was in fact a product of these studies.

http://www.life.uiuc.edu/Micro/woese.html

The archaeaarchaea are unique organisms. While prokaryotes in the cytological sense, they are actually more closely related to eukaryotes than to the bacteria. …

{maybe; it’s not obvious from the table on the preceding slide, & …}

The group contains both the methanogens and numerous organisms that grow at extremely high temperatures (in some cases above 100° C). As such, they provide potential insights into mechanisms of thermophilia and methanogenesis.

Carl R. Woese

http://www.bact.wisc.edu/microtextbook/ClassAndPhylo/molPhylogeny.htmlB. … hot springs in Yellowstone National Park. Large areas are covered by a biofilm of yellow and brown coloured prokaryotes, including Sulfolobus species. http://helios.bto.ed.ac.uk/bto/microbes/thermo.htm#crest

Copyright 2001 The Guardian (London)

June 7, 2001

Australian scientists are to vaccinate sheep and cattle against … - flatulence.

More than 635,000 sheep and 410,000 cattle are to be treated to reduce methanogenic archaea -primitive organisms that colonise their rumens and help digest one of the most indigestible of substances, grass. The organisms have only one drawback: methane, or natural gas. A sheep can belch and fart 19 litres a day …A cow can burp up to 280 litres a day. Methane is a strong greenhouse gas - 21 times more potent than carbon dioxide. An estimated 400m tonnes of methane a year wafts upwards from sheep and cattle the world over, adding to the inexorable warming of the air.

So the Australians decided to do something. …… we expect the vaccine will reduce methane emissions by 20% …

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3 Domains3 Domains(see Fig 27.2)

http://whyfiles.org/022critters/archaea.html

1998. The pretty picture we've shown you turns out to be a simplification of reality. Now that the complete genomes of more than a dozen microbes are known, it seems that Eukarya - the higher organisms - may not have sprouted off the Archaea, as Woese supposed. Genetic information from organisms on the three branches of life seem contradictory at this point. As Woese said… "Each picture is different, so there's tremendous confusion." The problem could be rooted in the ability of organisms like bacteria to transfer groups of genes among themselves, or even to engulf other organisms and incorporate their genes. That kind of transfer would make a tree metaphor, with everything tracing back to a common ancestor, less appropriate than a network metaphor, with myriad connections between what we've been calling branches on the tree of life.

Woese's Proposed Classification of Lifeforms(see C&R Fig 26.1 & 26.16)

Abstract:The three-domain proposal of Woese ef al. … divides all living organisms into three primary groups or domains named Archaea (or archaebacteria), Bacteria (or eubacteria), and Eucarya (or eukaryotes), with Eucarya being relatives (or descendants) of Archaea.

Life's third domain (Archaea): An established fact or an endangered paradigm? A new proposal for classification of organisms based on protein sequences and cell structure.Gupta RS. 1998. Theoretical Population Biology 54:91-104.

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lAlthough this proposal is currently widely accepted, sequence features and phylogenies derived from many highly conserved proteins are inconsistent with it and point to a close and specific relationship between archaebacteria and gram-positive bacteria, whereas gram-negative bacteria are indicated to be phylogenetically distinct. …I propose that the primary division within prokaryotes is between Monoderm prokaryotes (surrounded by a single membrane) and Diderm prokaryotes (i.e., all true gram-negative bacteria containing both an inner cytoplasmic membrane and an outer membrane). …Protein phylogenies and signature sequences also show that Protein phylogenies and signature sequences also show that all eukaryotic cellsall eukaryotic cells have received significant gene contributions have received significant gene contributions from both from both an archaebacteriuman archaebacterium and and a gram negative eubacteriuma gram negative eubacterium.. …

(see C&R Table 27.2).

Properties of BacteriaBacteria, ArchaeaArchaea & EukaryaEukarya

Nuclear envelope No No Yes

Organelles in membrane No No Yes

Peptidoglycan in cell wall Yes - some No No

Membrane lipids Unbranched Some branched Unbranched

Initiator amino acid Formyl-methionine Methionine Methionine

non-coding Introns No Some Yes

Mitochondria/chloroplasts No No Yes

Chromosomes 1 circular 1 circular >1 linear

Protein synthesis inhibited by diphtheria toxin No No Yes

Meiosis and mitosis No No Yes

Ribosome size 70s 70s 80s

Response to streptomycin Inhibited Inhibited Not inhibited

Response to penicillins Inhibited Not inhibited Not inhibited

Response to linezolid (Zyvox) Inhibited Not inhibited Not inhibited

We have been emphasizing the Unity of Lifethe Unity of Life, but the Diversity of Lifethe Diversity of Life is essential to antibiotic strategies.

http://helios.bto.ed.ac.uk/bto/microbes/penicill.htm#crest… natural penicillins obtained from culture filtrates of Penicillium spp. are active only against Gram-positive bacteria (which have a thick layer of peptidoglycan in the wall)

Biological warfareBiological warfare

For a detailed description of the modes of action see:http://www.ultranet.com/~jkimball/BiologyPages/A/Antibiotics.html#aminoglycosides

Purple bacteria: photoautotrophic,use light to split H2S & CO2

release S2 & carbs

Rhizobium: anaerobic chemoheterotroph, use plant carbs to split N2 & release usable nitrogensee pg 721

Chemoheterotrophs: ex: gut ‘flora’ - E. colieat your lunch & excrete

Cyanobacteria: photoautotrophic‘bluegreen algae’,use light to fix CO2 & N2

Gram +chemoheterotrophsendosporesex: anthrax

Gram +mycoplasmas,smallest cells; lack cell wall(not really gram +)

Gram +actinomycetes,branching colonies in soilex: Streptomycetes

Chlamydias:obligate intracellularparasites - STD can’t make ATP

Spirochetes:chemoheterotrophs,syphilis & Lyme disease

louis pasteur in one advance louis pasteur discredited the concept of spontaneous generation. he...

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