1: Introduction

Living world is very distinct from the rest of the world.

If it was not “created” it must have been introduced from outer space: the panspermia notion.

In the very beginning

Oparin, Aleksandr Ivanovich (1894-1980)

(A friend of Lysenko, a power figure in USSR that was a plant breeder who considered genetics to be an obstacle to agriculture development. Put his opponents in prison.)

First attempt to give a scientific description of how life started that is not creationist nor via panspermia was by the Russian scientists Alexander Oparin in 1920.

The primitive oceans were a “soup” of various biochemicals that were created by UV, lightings, etc (in a non-oxidizing enviroment).

Oparin “theory”

According to Woese, this is a “vague” and “is frankly a “Just So Story””.

Oparin “theory”

• There is no fundamental difference between a living organism and lifeless matter. Life must have arisen from simple molecules.

Oparin “theory”

•Taking into account the recent discovery of methane in the atmospheres of Jupiter

and the other giant planets, Oparin postulated that the infant Earth had

possessed a strongly reducing atmosphere, containing methane,

ammonia, hydrogen, and water vapor .•In his opinion, these were the raw

materials for the evolution of life.

•1 .There had to be a supply of organic molecules produced by a non-biological

process •2 .They had to be assembled into

polymers like proteins and nucleic acids .•3 .Those polymers had to be assembled

into a self-replicating system .

The “soup” in details (I)

•The first organisms to develop had all the nutrients they needed: they were extreme heterotrophs.

•When the nutrients were exhausted, they somehow developed the ability to use light as an energy source, and had became autotrophs.

The “soup” in details (II)

An empty fridge serves as a driving force for evolution

Oparin suggested that cells came first, then enzymes, and genes later. Found that when lipids are inserted to water, they form cell like structures. He suggested that these structures accumulated metabolites, and that cell division was without replication but rather – a random process.

• In many textbooks, this was taken a step forward, suggesting that these early organisms were anaerobic heterotrophic procaryotes, such as some streptococcus…

• One primitive cell (called urcaryote) gained the ability for endocytosis, ingested other procaryotes and the fused organism eventually became the eucaryotic cell.

The “soup” in details (III)

Stanley Miller (1930-

Miller’s experiments fail in an oxidizing atmosphere containing CO2 or SO2.

His experiments work with electrical charge, UV, or ionization radiation.

When one add hydrogen sulphide (SH2), there are sulphur containing AA in the output: methionine and cystein.

Nucleic acids were not produced

Joan Oro (1923-2004)

Synthesized adenine in prebiotic conditions (maybe) from hydrogen cyanide.

He suggested that organic molecules arrived to our early biosphere by comets.

The problem is that the synthesis requires very specific conditions – not necessarily realistic to prebiotic era.

Tom Cech (1947-

Discovered that RNA can also be enzymes. These RNA enzyme are known as ribozymes. Received the Nobel prize in chemistry 1989 for his discoveries.

His discovery strongly supports the RNA world hypothesis.

DNA world / RNA world

The RNA world hypothesis proposes that a world filled with life based on ribonucleic acid (RNA) predates the current world of life based on deoxyribonucleic acid (DNA).

RNA is everywhere…

Important RNA property

•The ability to self-duplicate, or duplicate other RNA molecules .

•Relatively short RNA molecules that can duplicate others have been artificially produced in the lab .

•The ability to catalyze simple chemical reactions which would enhance the

creation of molecules.

•RNA can bind to form a double helical structure.

RNA default

•RNA is less stable than DNA

•Storing large amounts of information in RNA is not easy

•large RNA molecules are inherently fragile

Meet LUCA:The Last Universal Common Ancestor

Also called LUA (last universal ancestor)

What was: LUCA

•It had properties shared by all independently living organisms on Earth

–The genetic code is based on DNA .–The genetic code is expressed via RNA

intermediates.–The genetic code is expressed into proteins.–synthesis of lipids or carbohydrates are the result of

protein enzymes.–ATP is used as an energy intermediate .–The cell is surrounded by a cellular membrane

composed of a lipid bilayer .–The cell multiplies by duplicating all its contents

followed by cellular division

1: Introduction

1: Introduction

•Life was classified as

plants and animals

•When Bacteria were discoveredthey were initially classified as plants.

•Ernst Haeckel (1866) placed all unicellular organisms in a kingdom called Protista, separated from Plantae and Animalia.

In the very beginning

1: Introduction

1: Introduction

Thus, life were classified to 5 kingdoms:

When electron microscopes were developed, it was found that Protista in fact include both cells with and without nucleus. Also, fungi were found to differ from plants, since they are heterotrophs (they do not synthesize their food).

LIFE

FungiPlants Animals ProtistsProcaryotes

1: Introduction

Later, plants, animals, protists and fungi were collectively called the Eucarya domain, and the procaryotes were shifted from a kingdom to be a Bacteria domain.

Domains EucaryaBacteria

FungiPlants Animals ProtistsKingdoms

Even later, a new Domain was discovered…

1: Introduction

•The translation apparatus is universal and probably already existed in the “beginning”.

rRNA was sequenced from a great number of organisms to study phylogeny

1: Introduction

Carl R. Woese and rRNA phylogeny1: Introduction

A distance matrix was computed for each two organisms. In a very influential paper, they showed that methanogenic bacteria are as distant from bacteria as they are from eucaryota (1977).

1: Introduction

One sentence about methanogenic “bacteria”

“There exists a third kingdom which, to date, is represented solely by the methanogenic bacteria, a relatively unknown class of anaerobes that possess a unique metabolism based on the reduction of carbon dioxide to methane”.

These "bacteria" appear to be no more related to typical bacteria than they are to eucaryotic cytoplasms.“

1: Introduction

From sequence analysis only, it was thus established that life is divided into 3:BacteriaArchaeaEucarya

1: Introduction

1: Introduction

The rRNA phylogenetic tree

Model of Martin and RusselPhil. Trans. R. Soc. Lond. B

(2003) 358, 59–85

Iron monosulphide precipitates

Domains EucaryaBacteria

FungiPlants Animals ProtistsKingdoms

This is also completely wrong !!!

Eukaryote diversity

The tree of eukaryotes

•Our understanding of eukaryotic relationships has been transformed by the

use of molecular data to reconstruct phylogenies (Sogin et al., 1986). Prior to

that, the diversity of microbial eukaryotes was vastly underestimated, and the

relationships between them and multicellular eukaryotes were difficult to

resolve (Taylor, 1978) .

The tree of eukaryotes

•The current view of eukaryotic phylogeny is of a small number of large

‘supergroups’, each comprising a spectacular diversity of structures,

nutritional modes, and behaviours. Some of these supergroup hypotheses are well

supported, while others remain the subject of vigorous debate. Furthermore the

relationships between supergroups are poorly understood .

[Sciences vol. 300, no. 5626 pp.1703]

[Sciences vol. 300, no. 5626 pp.1703]

Red algae

Foraminifera

Foraminifera

Dinoflagellate

Tetrahymena

Ciliate

PlasmodiumApicomplexa

Brown algae

TrypanosomaGiardiaParabasalida

Amoeba

Main point of eukaryote tree

•Multicellularity developed independently in different lineages.

•The ability to photosynthesized, also occurred independently in different

lineages.

•Algae do not have a common ancestor.

•Fungi are our close cousins.

•Plant and Fungi are not related.