Lecture Topics Biology Defining life and lifes characteris:cs (1 - - PowerPoint PPT Presentation

Lecture Topics ‐ Biology

• Defining life and life’s characteris:cs (1 lecture)
• The Top‐Down approach to understanding the origins of

life (2 lectures)

– The limits of life – Extreme environments

• The origin of life (3 lectures)

– The top‐down and boFom‐up approaches – “replicator‐first” versus “metabolism‐first” – The characteris:cs of early life: The Lost City hydrothermal vent environments as a possible model

• The origin of eukaryotes (2 lectures)

– Endosymbiosis theory – The possible role of virus’s in the origin of eukaryotes

• Summary

NW Rota Brimstone (pH 2 with S°)

Depth 540 m

41st Saas‐Fee course from Planets to Life 3‐9 April 2011

Lecture 1: The ‘Biology’ of Astrobiology – An overview (John Baross)

• Can we define life and is that important in our

search for life elsewhere?

• Is “life as we know it” the only form of life

possible, and/or the best of all possible designs for life?

• What are the limits of Earth life – can it evolve to

grow outside the limits of Earth environments?

• What do the characteris:cs and requirements of

Earth life tell us about poten:ally habitable planetary bodies –

And the origin and early evolu:on of life

The origin and early evolu0on of life: Background lectures

• “Top‐Down” approach: What we can learn from

extant organisms

– Possible environmental seangs for the origin of life – Ancient metabolisms and their origin – The origin of a replicator: “The RNA world” – The Last Common Universal Ancestor (LUCA) – The origin of eukaryotes (the importance of symbiosis)

• “BoFom‐Up” approach: What we can learn from
• rganic chemistry, Earth history, geology and

geochemistry?

Lecture 1 ‐ outline

• Can we define life?
• Canonical characteris:cs of Earth life – would

they apply to life‐forms different from Earth life?

• Diversity and the three domains of life

Can we define life and is this an important issue?

There are multiple definitions that can be separated into several categories

• 1. Darwinists (many examples)
• 2. Metabolists
• 3. Energists/Thermodynamists (e.g. Schrödinger,

1944)

• 4. Biosphereists (Shapiro and Feinberg, 1990)
• 5. Complexists
• 6. Others

Evolutionists definitions of life –” Descent with modification” (mutation and natural selection) (a few)

• Life is a self-sustained chemical system capable of

undergoing Darwinian evolution (Joyce, 1994)

• Life is a self-replicating, evolving system based on
• rganic chemistry (Pace, 2002)
• System capable of evolution by natural selection

(Sagan, 1970)

• Material system that undergoes Darwinian evolution

(C. McKay)

• The minimal living system must be self-duplicating

and mutable, and it must have the capacity for hetero-catalysis for bringing about chemical changes in the environment that support the self-duplication function (Hartman)

The “metabolists” defini:on

Generally, a series of chemical reac:ons that produce energy and increasing complexity of

• rganic compounds (replica:on and evolu:on

are not part of this defini:on) This idea has become more important as a model for the origin of life than as a defini:on Metabolism is the sum of all chemical reac1ons in a living organisms

• 1. Catabolism – breakdown of complex organic

molecules into simpler compounds and releases energy

• 2. Anabolism – building of complex organic molecules

from simpler ones and requires energy

The Biospheric Defini:on of Life Feinberg & Shapiro, 1980

• Life is fundamentally the ac:vity
• f a biosphere. A biosphere is a

highly ordered system of maFer and energy characterized by complex cycles that maintain or gradually increase the order of the system through an exchange

• f energy with the environment

– This defini:on would include as life, “plasma life” in the interiors of stars including white‐dwarf stars and interstellar gas clouds

Image of Serius A and Serius B taken by the Hubble Telescope. Serius B, which is a white dwarf, can be seen as a faint pinprick of light at the lower lei of the much brighter Serius A (Wikipedia)

Definition of life: Cleland and Chyba (2002; 2007) discuss the philosophical dilemmas on the nature of definitions (“Definitions specify meanings by dissecting concepts that we already possess”)

Two kinds of definitions:

1. Words or terms whose existence depends solely upon human interests and concerns, such as “bachelor” or “fortnight” are readily defined 2. “Natural kind” terms such as “life”, “water” and “heat” cannot be defined by describing properties because there is more to their meanings than the features we identify (e.g. water is defined as H2O and not by characteristics such as “cooling”, “tasteless”, “odorless” etc) 3. Defining life from properties of life has problems because there are “non-living” analogues. (e.g. replication - clays and other minerals replicate; ability to evolve - mineral growth involves changes “mutations” that replicate; energy and fire, etc)

Definition of life: continued

What we don’t know is how all of the components that make up a living en:ty become life. Cleland and Chyba (2007) approach this dilemma by poin:ng out that “to answer the ques0on ‘What is life?’ we require not a defini0on but a general theory of the nature

• f living systems.” This theory does not yet

exist.

Moreover…….

A defini:on of life would have to include any living en:ty even if it were radically different from Earth life. This implies that a defini:on of life is not a list

• f canonical characteris:cs possessed by earth

life, such as being carbon based, self‐ replica:ng and having the ability to undergo Darwinian evolu:on.

However…..

A case can be made that the ability to replicate and undergo Darwinian evolu:on are essen:al characteris:cs of all life even if significantly different from earth life, but they would not be part of a defini:on of life but instead essen0al mechanisms to produce progeny and to create diversity and complexity

But – what about…..

Q, requiring neither maFer nor energy Calamarain, a life form built from pure energy

Life: A chemical system capable of Darwinian evolu0on

This defini:on holds a model of what is possible, vs. what is conceivable. If we were to encounter Calamarain or Q on a real, not conceptual Star Trek, we would be forced to change our defini:on to include them as living

• systems. We do not change now because we don’t believe that the weirder

life conceived in the Star Trek scrip:ng room is possible outside of that room (from Steve Benner)

We exclude other kinds of life because we do not believe that it could have arisen naturally, even though we believe it can exist and certainly will exist in the future (from Steve Benner)

Nanites and Data are examples of ar:ficial life. We don’t doubt that androids can be created, including androids who (note the pronoun) desire to be human. Ar:ficial life form A biosignature, not biology

Back to the ques1on: Do we need to define life in order to detect it?

• Life may not be definable but there are

characteris:cs of life that might be canonical of all life and they would leave “biosignatures”

– Carbon‐based – Self‐replica:ng – Uses chemical and light energy – Undergoes Darwinian evolu:on – Requires water and more than 20 elements

All studies on the origin of life rely on these characteris:cs as the basic star:ng points

Which of these canonical characteris:cs of Earth life has the greatest likelihood of being different in extraterrestrial carbon‐based life? (note my bias for carbon‐based life)

We don’t know ‐ our search for life elsewhere remains primarily earth‐centric

Many believe that life can be recognized even is radically different from life as we know it “Life can be recognized by what it does: living

• rganisms create hallmark molecules and

create chemical disequilibrium” Ken Nealson (University of Southern California)

The Earth‐centric approach to our search for life on other planetary bodies

• Follow the water, follow the energy, etc
• Look for Biosignatures:
• 1. organic compounds that follow the rules of carbon

chemistry found only in organisms (living or fossils)

• 2. ra:os of CHONPS etc that are indica:ve of life

(Redfield Ra:os), chemical disequilibrium, etc

• 3. isotopic frac:ona:on of C, S, N as indica:on of

metabolism

• Look for intact “cells” enclosed in a membrane

The earth‐centric approach to life elsewhere is very

• ien expressed in the popular media, for

example….

Illustra(on from the New York Tribune, February 8, 1920 en(tled “Scien(sts, Agreeing Mar(ans Are Super‐Race, Believe That Planet May Be Signaling to Us” (detail) Cap:on: “Scien:sts agree that the people of Mars differ from us in many

• ways. The Mar:ans are believed to have very large noses and ears and immense lung

development because of rarified atmosphere. Their legs are poorly developed, because maFer on Mars weighs less than here and sturdy legs are not needed to bear their weight. Birds and buFerflies are very large and beau:ful. One of many examples of Earth‐ centric views about life on other planets and moons

Evidence for intelligence and religion on Mars

“The astounding March 11 discovery made at the Ross‐Waterhaus Observatory in Johannesburg, South Africa comes just weeks aier University

• f Arizona scien:sts announced their findings that a huge flood swamped the Red Planet in ancient :mes. At least one expert (no name)

believes this proves that the NOAH story is true ‐ only it didn’t happen on Earth. The tale of Noah’s found in the book of Genesis may have been brought to Earth by Mar:an visitors in prehistoric :mes”

What about the possibility of “Weird life” that is different from Earth life – could we detect it?

“Weird” life

• What is “weird” life and why are we

interested?

• Degrees of “weirdness” ‐ from slight

modifica:ons of Earth’s carbon‐based life to seriously “weird” non‐carbon based life

• Life that exists out of the bounds of habitat

condi:ons on Earth ‐ the limits of C‐based life is currently unknown

Some degrees of “Weird” life

• Slightly weird

– Same biochemistry but different amino acids and nucleo:des – Novel metabolisms; different gene:c code

• Slightly more weird

– Same biochemistry but u:lize novel energy sources other than light or chemical energy

• More weird

– Different biochemistry, non‐protein catalysis, for example – Carbon‐based but func:on in non‐aqueous solvents – Silicon‐based life

• Seriously weird such as non‐cellular life

Would we be able to recognize a living en0ty that was radically different from Earth life?

Is it possible for humans to make en::es that fulfill all of the criteria for life? For example, the “digital

• rganisms” produced from a program named

‘AVIDA’. They mutate, evolve and increase in complexity (Dllab.caltech.edu/avida). Craig Venter of the Venter Ins:tute is working on synthesizing life (as we know it) using advanced molecular methods (Nature 2010)

Nature 2010

A genome synthesized from scratch has been assembled, modified, and implanted into a DNA‐free bacterial shell to make a self‐ replica:ng bacterium, Mycoplasma mycoides (a bacterium with a small genome) Does this work have any significance in understanding the origin of life? Astrobiology?

"The Venter Ins:tute work may

help to link chemistry to natural

• history. The sequences of the

genomes of ex:nct ancestral Mycoplasma species might be inferred from the sequences of various modern mycoplasmae, including M. capricolum, M. genitalium and M. mycoides — the three bacteria that Venter and his colleagues' synthesis started with. The new synthe0c technology allows resurrec0on

• f such ancient bacteria,

whose behavior should inform us about planetary and ecological environments 100 million years ago." Steven Benner, Founda:on for Applied Molecular Evolu:on, Florida (Nature 20 May 2010)

"Now that the Venter Ins:tute has

demonstrated how to reassemble a microbial genome, it may be possible to answer one of the great remaining ques:ons of biology: how did life begin? Using the tools of synthe0c biology, perhaps DNA and proteins can be discarded — RNA itself can act both as a gene0c molecule and as a catalyst. If a synthe0c RNA can be designed to catalyze its own reproduc0on within an ar0ficial membrane, we really will have created life in the laboratory, perhaps resembling the first forms of life on Earth nearly four billion years ago."

David Deamer, professor

• f Biomolecular

Engineering, University of California, Santa Cruz (Nature 20 May, 2010)

Possible implica:ons from Venter’s research

• A method to inves0gate the actual limits of

carbon‐based life (growth at higher or lower temperatures, growth without water and in

• rganic solvents, u:lize energy sources other

than light or chemical, etc)

• Construct a “minimal cell”
• Construct RNA life
• Hypothesis tes:ng

Back to the requirements for C‐based life ‐ acquiring and maintaining life – Astrobiology implica:ons

• Acquiring life

– de novo origin – Transported from elsewhere

• Maintaining life

– Liquid water – Energy sources (chemical or light) – Chemistry (more than 30 elements)

• Life uses the most abundant

elements in the universe (CHONPS) + Fe

• Life uses light or chemical energy

sources (H2 was probably the first energy source used by the earliest microbial ecosystems ‐ e.g. methanogenesis and photosynthesis)

• Life requires oxidants. CO2, S°, Fe(III)

are most important in dark ecosystems (O2 important the last two billion years)

• Life builds cataly:c and energy‐

transfer organic macromolecules around metals and metal‐sulfur clusters

• Life requires trace elements such as

boron, vanadium, tungsten, nickel, etc

Nitrogenase

From Nisbet and Sleep, Nature 2001

Chemistry and Earth Life

Key

The elements used by living

• rganisms either in structural

macromolecules (proteins, lipids), energy transformation, electron transfer chains, energy sources, and as oxidants or reductants

Needed for mineral catalysis and metal- S enzymes

Metal cofactor usage in the six major categories of enzymes as defined by the Enzyme

• Commission. Enzymes catalyzing oxida:on/reduc:on reac:ons exhibit the broadest

range of metal cofactors. Enzymes that catalyse the liga:on of subunit molecules only use magnesium ion cofctors. Metalloenzymes may reflect a transi1on from prebio1c chemistry catalyzed by metal ions or minerals to modern metabolism catalyzed by proteins (Stüeken et al., in prep.)

Metal‐cluster proteins are remnants of both prebio:c and early‐life use of minerals to catalyze chemical reac:ons (more on this later)

Also, Earth life has a “common ancestor”

• The “common ancestor” concept has its origin in

what is referred to as the “unity of biochemistry”, that is, all extant organisms share the same biochemical and molecular characteris:cs:

– Same nucleo:de bases – Same 20 amino acids – Same gene:c code – Lipids with straight chains of methyl branched chains – Metabolic energe:cs use phosphate anhydrides, thioesters

.

The “unity of biochemistry” is reflected in the evolu:onary rela:onship between all life ‐ referred to as the “Global Phylogene:c Tree”

Molecular phylogeny based on ribosomal RNA

The molecular revolu:on and the beginning of our understanding of the phylogeny of all extant life – from pure culture studies to revealing the phylogene:c diversity

• f microbial communi:es from environmental samples

Carl Woese ‐ University of Illinois

Universal Phylogenetic Tree

Characteris:c differences between the three domains of life: Archaea, Bacteria and Eukarya

Characteristics* Archaea Bacteria Eukarya

Cells with membrane-bound nucleus and other organelles No No Yes DNA circular1 Yes Yes No Ribosome size 70S 70S 80S Membrane lipids Ether linked Ester linked Ester linked Cell walls No PDG2 PDG No Histone proteins Yes No Yes Operons in DNA Yes Yes No Ribosome structure distinct distinct Archaeal-like Antibiotic sensitivity No Yes No Photosynthesis No Yes Yes Growth at temperatures >80°C Yes Yes No

*There are many physiological characteris:cs that are found only in bacteria and

• archaea. 1There are some excep:ons. 2PDG is pep:doglycan; Archaea do not have

PDG but do have at least 7 different cell surface layers (protein, lipid, etc)

polar head groups hydrophobic tails

H2C HC H2C O O O C C P O R O R O O O H2C HC H2C O O O CH2 CH2 P R R O O O

a) ester linkage ether linkage b) c)

(a) The structure of a bilayer lipid membrane; (b) the structure of the glyceryl esters that are major components of bacterial and eukaryotic cell membranes; (c) the structure of the glyceryl ethers that are major components of Archaeal cell membranes.

Other characteris:cs of the Bacteria and Archaea

• All methane producers (methanogens) are Archaea
• There are no photosynthe:c Archaea
• All oxygenic photosynthe:c bacteria belong to one group ‐

the cyanobacteria

• There is a high diversity of anoxygenic photosynthe:c

bacteria (most get their protons from H2S or organic compounds rather than water)

• Nitrogen fixa:on exists only in Bacteria and Archaea
• The bacteria and archaea u:lize several metabolic pathways

for “fixing CO2”, whereas eukaryo:c plants use one pathway.

• Only bacteria and archaea can grow anaerobically (without
• xygen) by breathing CO2, or nitrate, or sulfate or iron, etc