Professional Documents
Culture Documents
6 | Genes to Galaxies
Mr Frank Papadopoulos Dr J. E.W. L. Smith
& Mrs June Papadopoulos Mr Tim M Smyth
Mr George Papadopoulos Mr Duncan Sutherland
Mr John Paterson The Australian Association of Phi Beta Kappa
Mr Harry J Pemble The Outsiders Club of ISS2007
Mr Peter C Perry The Super Secret Club of ISS2005
Dr Christopher J E Phillips Mr Gavin M Thomson
Mr Enrico Piccioli Dr Jennifer J Turner
Ms Yvonne Pitsikas Mr John H Valder
Mr Geoffrey D Pople Ms Alex Viglienzone
Mr Allan F Rainbird Ms Jennifer H F Wanless
Mr John W L Rawson Dr David R V Wood
Dr David Z Robinson Ms Anne Woods
Miss Gracie Robinson Mr Thomas M F Yim on behalf of Jerome Yim
Dr P E Rolan Dr Xian Zhou
Professor Roger Short Fr Mervyn J F Ziesing
School of Physics
Building
Image:
Dr Phil Dooley
ISS 2009 | 7
Supporters of ISS2009
The Science Foundation for Physics warmly thanks the supporters of the
2009 ISS: Genes to Galaxies
The Messel Endowment
Department of Education and Training, NSW Government (DET)
Department of Innovation, Industry, Science and Research, Australian Government (DIISR)
The Kirby Foundation
Adolph Basser Trust
Faculty of Science, The University of Sydney
Chancellor’s Committee, The University of Sydney
The Smithsonian Institute
Mr Robert Arnott
Mr Greg Clark
Mr Trevor Danos
Mr Ron Enestrom
Associate Professor Robert Hewitt & Mrs Helen Hewitt
Mr John Hooke CBE
Associate Professor Brian James & Dr Ferg Brand through Dr Wie Xu
Dame Leonie Kramer
Mr Bruce McAdam & Mrs Janice McAdam
Mr Robert Rich
Mr Albert Wong
other individuals through the Foundation’s Annual Appeal
Australian students were selected with the support of the NSW Department of Education and
Training, and Science Teachers Associations in Victoria, Tasmania, South Australia, the Northern
Territory, the ACT and Western Australia. The following institutions assisted in the selection and
travel of the overseas students:
The Affiliated High School of Peking University, China
Rivers Collegiate, Canada
Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan
Ministry of Education, Malaysia
The Royal Society of New Zealand
Ministry of Education, Singapore
Ministry of Education, Thailand
The Association for Science Education, UK
The Royal Institution of Great Britain
The National Endowment for Science, Technology and the Arts (NESTA), UK
Department of Energy, USA
Raman Research Institute, India
8 | Genes to Galaxies
Preface
The Science Foundation for Physics within the The presence of some 144 gifted young people
University of Sydney is delighted to present from many countries creates an environment in
the 35th Professor Harry Messel International which each scholar can experience the values of
Science School (ISS) for high school students, different cultures and learn new ways of doing
from 12-25 July 2009. things. The Science Foundation stands for the
Pursuit of Excellence, and is pleased to have an
This anniversary year is the UN-designated
opportunity to acknowledge and reward excel-
International Year of Astronomy and celebrates
lence in these young people.
both 400 years since Galileo first turned his
telescope to the heavens and the 150th anni- The International Science School can only be
versary of the publication of Charles Darwin’s held because of the generous financial contri-
treatise ‘On the Origin of Species’. Therefore butions into The Messel Endowment and to
the theme for ISS2009 is Genes to Galaxies, the ISS from our supporters, and because of
acknowledging the immense contribution the time and energy donated by the lecturers.
made to science by these two great minds. The Like the Science Foundation itself, the sup-
second week of the ISS also coincides with porters, donors and lecturers are committed
the 40th anniversary of the first landing on to promoting science education at the very
the moon by Apollo 11 astronauts. It brings highest level of excellence. On behalf of the
together our themes of evolution and space Foundation, I express my grateful thanks to all
exploration, with speculation of possible intel- these benefactors.
ligent life beyond the Earth.
To our scholars this year, I wish you a most
The primary aim of all the Science Schools is to enriching fortnight here at the University of
acknowledge the excellence of the scholars who Sydney and trust that you, like those before
have been selected on the basis of their aca- you, will enjoy a remarkable and memorable
demic abilities, passion for science and leader- experience, make many life-long friends and
ship qualities. A new initiative for this ISS is the feel empowered to pursue your passion for
introduction of a module on Leadership and science.
Ethics in Science, produced with the support
of the Smithsonian Institute and introduced
during the opening lecture by the Chief Justice With very warm wishes
of Australia, the Honourable Robert French,
himself an ISS alumnus.
ISS 2009 | 9
History of the ISS
The Professor Harry Messel International The Great Lecturers
Science School has a long and distinguished
history. The 144 students attending ISS2009: One of the features of the International Science
Genes to Galaxies are the 35th group to gather Schools is the lecture series. Past ISS lectur-
at the University of Sydney for the Science ers include James Watson, who won a Nobel
School – in all, well over 4000 have attended a Prize for discovering the structure of DNA,
Science School since they began in 1958. and Jerome Friedman, also a Nobel laureate
for work on particle physics. Sir Hermann
Initially the Schools were annual events, and Bondi (physicist and astronomer at Cambridge
the first four Schools, held between 1958 and University), Margaret Burbidge (astronomer
1961, were for teachers. In 1962 Professor and champion for women in science), Carl
Harry Messel, the founder of the ISS, changed Sagan (famous astronomer and science broad-
the focus to honour excellence in senior high caster) and Lord Robert May (President of the
school students and to encourage them to con- Royal Society in the UK) have all given talks at
sider careers in science. the ISS.
And of course, who could forget the brilliant
A Truly International science demonstrations of Professor Julius
Science School “Why is it so?” Sumner Miller, which were
One student from New Zealand attended the such a popular feature of the ISS that they
very first Science School in 1962, and overseas spawned a television show! These days, Dr Karl
students have been a feature of the ISS ever Kruszelnicki (the University’s Julius Sumner
since. In 1967, ten students travelled from Miller Fellow) entertains and enthuses the ISS
the USA to attend the School; the following Scholars with his famous Great Moments in
year they were joined by five from the United Science.
Kingdom and five from Japan. Between 1960 and 1979 the ISS lectures were
South-East Asia joined the ISS in 1985 when shown on television – in fact, many people re-
students attended from Singapore, Malaysia, call waking up early on Sundays to make sure
Thailand and the Philippines – however, that they didn’t miss the telecast! One member of
was the only time the Philippines has partici- the School of Physics here at the University of
pated. China has sent five students to every ISS Sydney is adamant that the lectures shown on
since 1999, except for 2003 when the SARS TV were a key part of her decision to become
epidemic restricted travel in the region and an astronomer.
they reluctantly withdrew. In 2007 we were un- Today, the ISS is no longer a feature of the
fortunate not to be joined by Malaysia but we television schedule, but we have moved on to
did welcome India for the first time. embrace new technology. In 2003 part of the
This year we are very pleased that for the lecture series was broadcast on the internet as
first time we will be joined by students from a trial run, and in 2007 the entire series was
Canada, in fact from the home town of Harry made available as both video webcast and au-
Messel, the originator of this program. Thus dio podcast. In 2009 this book of lectures will
ISS2009 has students attending from ten be made available on-line, together with pod-
countries in total: Canada, China, India, Japan, casts of the lectures, thus available to anyone
Malaysia, New Zealand, Singapore, Thailand, with internet access on Earth, and beyond.
the UK and the USA, and of course, every state
and territory of Australia.
10 | Genes to Galaxies
Science School 1958-2007
For High School Teachers
ISS 2009 | 11
Authors
12 | Genes to Galaxies
Associate Professor Charles H. Lineweaver is
the coordinator of the Australian National University’s
Planetary Science Institute and holds a joint appoint-
ment as an Associate Professor in the Research School of
Astronomy and Astrophysics and the Research School of
Earth Sciences.
Authors | 13
The search for
the earliest life
on Earth
Malcolm Walter
T he record of life on Earth takes
two forms: fossils and other evi-
dence in the geological record,
and what is encoded in the ge-
nomes of living organisms.
From about 3 Ga onwards we have lots of rocks The universal tree also suggests that the most
to examine for evidence of life, so we can be primitive organisms with living close relatives
more confident about our interpretations. were hyperthermophiles, that is, they lived at
high temperatures, more than 80˚C. So in the
Events in the history of life are dated mostly
ancient rock record we should be looking for
using the fact that some isotopes of elements
the deposits of former hot springs to see what
are unstable and break down at known rates to
lived in them. We know how to find such
form other isotopes and elements. The usual
deposits – they are often ores of gold, silver,
method of dating very ancient rocks uses ura-
copper, lead and zinc.
nium and lead isotopes bound in crystals of
zircon, zirconium silicate.
16 | Genes to Galaxies
Earth - The first billion years
Like the other planets, the Earth formed from
a great cloud of dust and gas. Under the influ-
ence of gravity the cloud clumped into rocky
and icy lumps that grew bigger and bigger. The
volatile molecules were driven to the cooler
further parts of the solar system as the Sun be-
gan to generate heat, forming the “gas giants”,
Jupiter, Saturn, Uranus and Neptune, the com-
ets, and other objects such as Pluto. The small
rocky planets, composed of less volatile mate- Figure 3: Shark Bay stromatolites in the
rial, Mercury, Venus, Earth and Mars, formed shallow subtidal environment.
close to the Sun. By 4.56 Ga they were about Malcolm Walter
their present size. However, for the next billion
years the growth process, “accretion”, contin- 1. Stromatolites. These are macroscopic sedi-
ued and was very violent. Soon after 4.56 Ga mentary structures resulting from the activities
an object the size of Mars smashed into the of “mats” of microbes living on the seafloor
Earth with such energy as to melt and vapor- and in lakes. They still form in some modern
ise the surface of the planet, throwing a vast environments such as Shark Bay in Western
amount of material into orbit, which cooled to Australia (Figure 3), so we are able to observe
form the Moon. Frequent impacts from giant how they form and use this information to help
asteroids continued until about 3.9 Ga. Some interpret the ancient forms.
of these would have vaporised the developing In 3.43 Ga rocks in the Pilbara region, a wide
oceans, generating a “steam atmosphere”. Life range of different forms of stromatolites (Figure
might have started in this violent period but 4) formed all the way from a rocky coastline to
have been extinguished. We do not know. offshore in several tens of metres of water. In
Imagine an Earth with thousands of volcanos, 3.5 Ga rocks there are stromatolites at the vents
no continents but perhaps numerous islands of former hot springs.
that would later clump together to become 2. Microfossils. These are fossilised microbes
continents, and a hot ocean. Somewhere life (Figure 5). Despite the fact that microbes have
got started and managed to survive, proliferate no hard parts they are sometimes fossilised
and take over to generate the surface environ- when they become embedded in precipitated
ment we now depend on for our existence. silica which then hardens to form a rock called
Faint evidence of the presence of life is found chert. They can be found by using an optical
in highly altered 3.9 Ga rocks from Greenland. microscope to examine slices of chert so thin
There are no conventional fossils, just sugges- that light can pass through them.
tive patterns of carbon isotopes.
3. Carbon isotopes. Carbon has two stable
A snapshot at 3.5 Ga isotopes, 12C and 13C. Some biochemical proc-
esses such as photosynthesis preferentially use
We know from studying the rocks of the compounds of “light” carbon, 12C. This results
Pilbara region and the Barberton Mountainland in the cellular matter being enriched in 12C,
that life was well established by 3.5 Ga. Despite leaving the water in which the organisms grew
occasional controversies, the evidence can be enriched in 13C. If calcium carbonate then
described as compelling because multiple lines precipitates out of the water to form limestone,
of evidence reinforce and support each other. and the microbes die and are fossilised in the
18 | Genes to Galaxies
How did life start?
There is a simple answer to that question:
no-one knows. However, there are ways to ap-
proach the problem, and a great deal has been
learned in the last 50 years. A famous experi-
ment was conducted in 1952 by Stanley Miller
(then a university student in Chicago) and his
supervisor Harold Urey. They filled a glass flask
with a mixture of gases considered to represent
the composition of the atmosphere on the early
Earth – methane, ammonia, hydrogen, carbon
monoxide and water. To represent lightning
they created electrical sparks through the mix-
ture of gases. The result was a brown liquid
that when analysed was found to contain ami-
no acids. These are the building blocks of pro-
tein molecules that are essential components
Figure 6: Spindle-shaped microfossil at of the cells of all living organisms. So they had
least 3.0 billion years old from the Pilbara demonstrated one possible step in the origin
region of Western Australia. About 40 µm of life. Since then it has been discovered that
in maximum dimension. there are many other ways that quite complex
Photograph courtesy of Kenichiro Sugitani and carbon compounds (“organic compounds”) can
reproduced with permission.
form by natural chemical processes. This even
happens in gas clouds in the universe (about
sediments. Oil contains abundant biomarkers. 100 different carbon compounds have been
After organisms die, decay and are buried in identified in such clouds), and so would have
sediment some chemical components of their been part of the cloud that condensed to form
cells survive. Some of these organic compounds the solar system.
are characteristic of particular types of organ-
isms, so when found in rocks they are markers It is a long way from organic compounds to life
for the former presence of these organisms. and much is yet to be learned. For example,
Compounds characteristic of cyanobacteria, no-one has yet been able to synthesise a pro-
and others characteristic of eukaryotes have tein molecule, let alone the genetic molecules
been found in 2.7-2.8 Ga rocks in the Pilbara RNA and DNA. But there are comprehensive
region and in South Africa. There is some hypotheses about how life might have started
controversy about this work as it is difficult to and many of the necessary steps have been
prove that these molecules are not later con- shown to be feasible. Perhaps viruses played a
taminants, but most of the evidence indicates role before there were cells. A potentially very
that they are as old as the rocks in which they informative approach is to determine what
are found. essential components of cells are found in the
most primitive forms of life known, and ex-
So we know that by 2.5 Ga, and probably trapolate back to predict what the earliest cells
much earlier, all three domains of life were were probably like.
flourishing on Earth. That means that most
of the biochemical processes that characterise
modern life had evolved by that time. All sub-
sequent evolution has utilised those basic proc-
esses first established by microbes.
Water on Mars
It has been known since the NASA Mariner
missions in the 1960s that something liquid
flowed on the surface of Mars early in its his-
tory. That is demonstrated by an abundance
of now-dry river valleys (Fig. 2). Liquid water
Figure 1: An image of Mars showing the now is not stable on the surface of Mars be-
northern polar cap. The white patches are cause of very low temperatures combined with
water-ice clouds. low atmospheric pressures (Fig. 3). As a result,
Image courtesy of NASA/nasaimages.org water ice sublimes directly to vapour without
passing through a liquid phase. Even at the
have discovered that early in its history it was current very low temperatures there is still an
warm and wet, like the Earth, although now it active “hydrological cycle”. One of the Viking
is a frozen desert (Fig. 1). landers in 1976 observed water frost on rocks
and the Phoenix lander in 2008 observed snow
All life on Earth requires liquid water, and so falling.
the assumption is made that that will also be
true of life elsewhere. Similarly, all life on Earth A range of observations have demonstrated that
is constructed from compounds of carbon, and the polar caps of Mars are a mixture of carbon
this too is assumed to be true of life elsewhere. dioxide ice and water ice. Recent studies using
This is just a normal conservative scientific ap-
proach, of making predictions on the basis of
current knowledge. It does not rule out other
possibilities, but indicates where the focus
should lie.
22 | Genes to Galaxies
Figure 3: A phase
diagram comparing
the surface
environments on
Earth and Mars,
showing why pure
liquid water can not
exist on the surface
on Mars.
Image courtesy of
NASA/nasaimages.org
gamma ray spectroscopy and ground penetrat- is known because there are volcanoes that
ing radar observations from satellites have have been active in the last few million years.
shown that water ice is very widespread on the Olympus Mons is an example (Fig. 4).
planet, but most is covered by sediment. There
At the equator in Summer, water could be
is evidence of glaciers.
liquid within a hundred metres of the ground
So there is no shortage of water. There will surface. There is evidence that even now occa-
be liquid water at depth in the crust of Mars sionally water comes to the surface, perhaps af-
because the interior of the planet is hot. That ter an earthquake or a meteorite strike. NASA’s
orbiter Mars Global Surveyor discovered large
numbers of small gullies on the walls of me-
teorite craters (Frontis piece). The gullies are
fresh and have not been eroded by the wind,
and new ones appeared over the lifetime of
the mission (Fig. 5). Although it is not known
with certainty, the most plausible explanation
is that the gullies were eroded by brief outflows
of liquid water from underground aquifers.
More recently, possible droplets of water were
photographed on the legs of the Phoenix lander
in 2008 (Fig. 6).
Allen Hills in Antarctica in 1984 and was the that they could escape the gravity of Mars. The
first to be catalogued that year, hence the name. force of the blast melted parts of the rocks and
Amongst the thousands of meteorites that as they flew up through the atmosphere gases
have been found, 34 are known to have come were trapped in the melt. The rocks cooled in
from Mars. We know that because they have a space, permanently trapping the gases.
distinctive chemical and mineralogical compo-
Back on Earth, in a laboratory in Houston, the
sition different from any other rocks found on
rock was broken open and examined with an
the Earth or the Moon, and different from all
electron microscope. Structures resembling
other meteorites. Trapped within tiny bubbles
fossil microbes were found on the broken
in one of these meteorites are gases that match
surfaces (Fig. 8). That discovery led to more
the composition of the atmosphere of Mars.
detailed analyses to determine whether the
It happened like this: an asteroid hit Mars and meteorite contained any other evidence of life.
blasted surface rocks off at such a high velocity Organic compounds called polycyclic aromatic
Figure 6: The globules shown boxed on a leg of the Phoenix lander in 2008 are
interpreted by some scientists as water that can remain liquid because it is extremely
salty.
Image courtesy of NASA/nasaimages.org
24 | Genes to Galaxies
Figure 7:
Meteorite
ALH84001
which was once
considered to
contain evidence of
life on Mars.
Image courtesy of
NASA/nasaimages.org
hydrocarbons (“PAH’s”) were found, along with This demonstrates that Mars is still an active
distinctive patterns of carbon isotopes. This planet. It is not possible at present to determine
and other evidence formed the basis for the whether the methane is biological or geological
claim that the meteorite contained evidence of in origin. On Earth that distinction is made by
the former presence of life on Mars. measuring the carbon isotopic composition of
the methane. Biological processes strongly se-
Since 1996 many scientists have studied
lect the lighter isotope, 12C, whereas geological
ALH84001 using a wide range of sophisticated
processes do not. It is not yet possible to meas-
techniques. The conclusion is that all of the
ure the isotopic composition on Mars but there
observed features can be explained by non-
are plans to do so on a forthcoming mission.
biological chemical processes, and none is
evidence for life. This is typical of how science
works: hypotheses are offered and then many Exploration to date
are refuted. There have been more than 40 attempted mis-
sions to Mars, the first in 1960. In the early
Methane in the Martian years there were many failures but the success
atmosphere rate now is very high. Only two successful mis-
sions have had the specific goal of searching for
Telescopes on Earth can be used to analyse the life, NASA’s Viking 1 & 2 in 1976. Both were
atmosphere of Mars because different gases stationary landers with onboard laboratories
have characteristic infrared spectra. In 2003, to analyse for organic compounds and to test
patches of atmosphere rich in methane were for gases produced by living organisms. One
discovered. Three large patches, or “plumes”, experiment gave ambiguous results but it is
are now known. This is significant because now accepted that no life was detected. In
methane is unstable on Mars and would break retrospect that result is not surprising. It is now
down rapidly. So there must be active sources known that the surface of Mars is highly oxi-
spewing the methane out of the crust. This also dising, so any organic compounds that might
happens on Earth where there are two types of have been present would have been destroyed.
sources: volcanoes and microbes. In addition, Mars lacks both a substantial
magnetosphere and an ozone shield, so both I think it is very likely that there was microbial
cosmic and ultraviolet radiation reach the sur- life on Mars and probably still is. But I think
face and would kill any organisms present. we will have to wait until astronauts go to Mars
later this century to finally determine whether
So is there life on Mars? or not there is or was life there.
We have learned over the last 50 years that And the obvious question is, why bother? The
the conditions essential for life as we know it answer is that the question of whether we are
existed widely on Mars early in its history, and alone in the universe is one of the most pro-
still exist in subterranean environments and found questions we face. If there are microbes
occasionally on the surface. But so far the only on Mars, and if we can demonstrate that they
hint that there is life is the presence of methane had a separate origin from life on Earth, then
in the atmosphere. we will be able to predict that life is abundant
throughout the universe. Somewhere out there
Within 20 years we will have much more in- will be other industrial societies, probably far
formation from robotic vehicles and we may be more advanced than ours.
able to gather enough information to suggest
the presence of life. A final demonstration may
require the return of samples, and such a mis-
sion is being planned for 2020. That mission
will be both enormously complex and enor-
mously expensive.
26 | Genes to Galaxies
The search for life on Mars | 27
Paleolithic
nutrition:what
did our ancestors
eat?
Janette Brand Miller
Neil Mann
Loren Cordain
P aleolithic nutrition is the study of
diets consumed by our early ‘stone
age’ ancestors, members of our spe-
cies who lived from around 750,000
years ago up until 10,000 years ago (Figure 1).
During this period, hominids relied on stone
technology to sustain their scavenging, hunting
and gathering lifestyle (Figure 2). Paleolithic
diets are a subject of interest for various reasons.
Apart from the intrinsic value of knowing more
about our past, many health experts have sug-
gested that the ‘native diet’ during human evolu-
tion is the healthiest diet, the one that meets
all our nutritional needs and to which we are
genetically adapted. Just as veterinarians try to
give zoo animals a diet closest to that which they
consumed in the wild, many nutritionists believe
that the diet eaten for the greater part of one mil-
lion years of human evolution is the ideal diet.
Conversely, they believe that modern illnesses
such as type 2 diabetes and coronary heart dis-
ease are a consequence of eating a diet to which
we are not genetically adapted (Figure 3). The
last 10,000 years ago (a mere ‘tick’ on the evolu-
tionary clock) have brought near inconceivable
changes to diet and physical activity.
Paleolithic Nutrition First stone tools appear in the fossil
record ~2.4 MYA
Figure 1 Figure 2
African Climate
Discordance Hypothesis
20 MYA and 7 MYA
The discordance
between modern diets
and paleolithic diets
contributes to many
diet related health
problems of modern
man
Figure 3 Figure 4
Figure 5 Figure 6
30 | Genes to Galaxies
Climate dictates food sources existence. Even during the warm inter-glacials,
parts of the world remained cold (e.g. Arctic
For most of geological time, the world’s climate and sub-arctic regions) and continued to have
was warmer and more homogeneous than it little vegetation. The human inhabitants of
is today (Figure 4). Our pre-human ancestors those regions maintained a hunting/fishing
who lived in Africa >7 million years ago en- existence right up to recent times. Indeed, the
joyed a warm, moist environment and gathered Inuit and other native Canadians are a modern
ripe fruits, leaves and berries from the tropical day example of a group whose historic diet was
forests (Figure 4 and 5). But gradually the plan- high in animal food and low in plant matter.
et cooled. About 2.5 million years ago, a severe
Ice Age sent global temperatures plummeting During the early and mid 20th century, anthro-
and prompted the conversion of moist African pologists studied the planet’s few remaining
woodland into much drier open savanna. As hunter-gatherer societies. To their surprise,
the grasslands expanded, the tree cover shrank they found them generally free of the signs
and one or more species of forest dwelling and symptoms of the so-called diseases of
chimpanzee evolved into bipedal hominids civilization. Although their nutritional patterns
(Figure 6). Homo habilis who lived 2 million probably would not have been identical to
years BP supplemented a largely vegetarian diet hominids living during the Paleolithic period,
with meat left over from predators’ kills (i.e. they represent the best ‘window’ we have into
they scavenged). But Homo erectus who lived the range and quantity of wild and unculti-
1.5 million years BP is known to have actively vated foods making up humanity’s ‘native’ diet.
hunted. Many scientists believe that hunting Consequently, the characterization and descrip-
was the pressure that selected for the larger and tion of hunter-gatherer diets has important
larger brain of our species, Homo sapiens sapiens implications in designing therapeutic diets that
(the phrase “man the hunter” originated with reduce the risk for chronic diseases in modern,
this idea)(Figure 7 and 8). western cultures.
As one Ice Age followed another, hunting and These ethnographic and anthropological stud-
fishing became a dominant way of life in both ies tell us that there was no single, uniform
warm and cold environments. During Ice Ages, diet which typified the nutritional patterns
large amounts of water become locked into of all pre-agricultural humans. Humans were
the polar ice caps, making the whole planet masters of flexibility, with the ability to live in a
drier because less water falls as rain and snow. rain forest or near the polar ice caps. Yet, based
Plant growth slows, rainforests shrink and upon limited information, many anthropolo-
grasslands dominate the landscape. Herbivores gists incorrectly concluded that the universal
came into their own and grazing animals pattern of subsistence was one in which plant
multiplied in their millions. From 50,000 foods contributed the majority of food energy.
years ago, we know that Neanderthals were However, more recent and comprehensive
cold-climate hunters of large game. Indeed, ethnographic compilations (Cordain et al,
over winter they subsisted primarily on game. 2000a) as well as quantitative dietary analyses
One large mammoth kill would have nourished in foraging populations, have been unable to
a family group of 50 individuals for at least confirm the conclusions of these earlier studies.
3 months. Similarly, Cro-Magnon man who In fact, the later studies demonstrated that ani-
replaced the Neanderthals about 35,000 years mal foods, rather than plant foods, comprised
ago, lived through the coldest of the Ice Ages the majority of energy in the typical hunter-
on a high meat diet. The Hall of Bulls in the gatherer diet.
famous Lascaux Caves in southern France is a Unfortunately, in the context of western diets,
testament to the importance of animals to the increasing meat consumption (particularly
people who lived 17,000 years ago (Figure 9). red and processed meat) is linked to a greater
Similarly, we know that the ancestors of the risk of cardiovascular disease. In countries like
Aborigines who inhabited Australia 40-50,000 the USA, meats contribute much of the fat,
years ago led a hunting and shellfish gathering
Figure 7 Figure 8
Figure 9 Figure 10
50 45
45 42 On average, plant 9
On average,
40 35 35 foods contributed hunted animal
35 25-35% of energy foods contributed
Frequency
Frequency
30
30 26-35% of energy
25 23 Only 13% obtained
20 more than half their 5 47
% Dependence % Dependence
Figure 11 Figure 12
32 | Genes to Galaxies
and more importantly, about one third of the by plants versus animal foods). Our analysis
saturated fat, the kind mostly clearly linked (Figures 11-14) of Gray’s Ethnographic Atlas
to adverse outcomes. Thus, a high meat diet, data (Gray, 1999) showed that the dominant
regardless of its fat quantity and type, is gener- foods in most hunter-gatherer diets were de-
ally perceived to be unhealthy and to promote rived from animal food sources. We found that
cardiovascular and other chronic diseases. nearly 3 in 4 of the world’s hunter gatherer
Yet Australian red meat derived from grazing populations obtained at least half of their food
animals is generally lean, low in saturated fat energy from hunted and fished animal foods,
and contains significant amounts of healthy whereas fewer than 1 in 7 obtained more than
long chain omega-3 fats. Our research provides half their calories from gathered plant foods.
evidence that the animal foods that dominated Not a single hunter-gatherer society was com-
hunter-gatherer diets were also low in saturated pletely vegetarian. The statistical mean among
fat and high in good fats. This nutritional pat- all 229 hunter-gatherer societies in Gray’s atlas
tern would not have promoted atherosclerosis indicated that 68% of calories came from ani-
(hardening of the arteries) or chronic disease. mal foods and 32% from gathered plant foods
(Figure 15).
Confusion over pre-
agricultural diets Quantitative studies of
Early theories on the natural, or native hu-
hunter gatherer diets
man diet assumed that Paleolithic people were The major limitation of ethnographic data is
skilled hunters of big game whose diets were that much of the information is subjective in
primarily carnivorous in nature. However, by nature. Murdock’s scoring for the five basic
early 1970s, this “Man the Hunter” explana- subsistence economies in the Ethnographic Atlas
tion was being contested by Richard Lee and were approximations, rather than precisely
other anthropologists on the basis of evidence measured food intake data. Fortunately, more
suggesting that contemporary hunter-gatherer exact, quantitative dietary studies were car-
peoples consumed more gathered plants than ried out on a small number of hunter-gatherer
hunted animal food (Lee, 1968) (Figure 10). societies. Table 1 lists these studies and shows
For example, Lee’s studies of the African !Kung the plant to animal subsistence ratios. The
people demonstrated that gathered plant foods mean score for animal food subsistence is 65%,
comprised 67% of their average daily energy while that for plant food subsistence is 35%.
intake while hunted animal foods encompassed These values are similar to our analysis of the
the remaining third. Lee further compiled data entire (n = 229) sample of hunter-gatherer
from 58 hunter-gatherer societies who were societies (Figure 15). If we exclude the two
listed in the Ethnographic Atlas (Murdock, polar hunter-gatherer populations (who have
1967), showing that hunted animal food made no choice but to eat animal food because of
up only 35 per cent of food intake, irrespective the inaccessibility of plant foods) from Table 1,
of latitude. the mean score for animal subsistence is ~60%
and that for plant food subsistence is ~40%.
Over the next 30 or so years, Richard Lee’s
Consequently, there is remarkably close agree-
analysis was widely misinterpreted to mean
ment between the quantitative data in Table 1
that gathered plant foods typically provided
and the ethnographic data.
the major food energy in worldwide hunter-
gatherer diets, while hunted animal foods made
up the balance. But this general perception Other evidence for meat eating
is incorrect because fished animal foods must Isotope studies of fossil bones can tell us more
be summed with hunted animal foods in the information about the type of foods that our
analysis of the ethnographic data to more cor- ancestors ate. Isotopic analysis of the skeletons
rectly evaluate dietary plant to animal energy of Neanderthals (Richards et al, 2000a) and
ratios (i.e. the percentage of energy contributed Paleolithic humans (Richards et al, 2000b)
Frequency
40 contributed >66%
Frequency
of energy 35
35 of energy
30
1
30
25 23
20
15
Mode = (46-55%) 10 6
5 5
5
Median = (26-35%) 5 2 Mode = (66-75%)
0 0
0 Median = (86-100%)
05 6 15 16 25 26 35 36 45 46 55 56 65 66 75 76 85 86 100 05 6 15 16 25 26 35 36 45 46 55 56 65 66 75 76 85 86 100
% Dependence % Dependence
Figure 13 Figure 14
32 % 38 %
Plant Animal
Food 62 %
68 % Plant Food
Animal Food
Food Refined Vegetable Oils Refined Sugars
Alcohol
(except honey)
Figure 15 Figure 16
CHO CHO
CHO 49% 55% or more
22-40 %
Figure 17 Figure 18
34 | Genes to Galaxies
Table 1: Quantitatively determined proportions of plant and animal food in hunter-
gatherer diets.
suggests that the dominance of animal foods are essential cellular lipids that are found only
in the human diet was not simply a recent in animal foods. The implication is that by eat-
phenomenon limited to contemporary hunter- ing abundant pre-formed sources of these fatty
gatherers, but rather one with a long history. acids, our bodies gradually lost the ability to
These studies provide objective evidence that synthesise them ‘in house’.
the diets of hominids living in Europe during
Finally, our species (again like cats) has a
the Paleolithic were indistinguishable from that
limited capacity to synthesize the amino
of carnivores such as arctic foxes and wolves.
acid taurine from its precursor amino acids.
Indeed, hominids may have experienced genet-
Vegetarian diets are known to result in lower
ic adaptations to animal-based diets early on in
blood concentrations of taurine. This implies
their evolution, analogous to those of obligate
that the need to synthesize taurine may have
carnivores such as cats (felines).
been unnecessary because dietary sources of
Carnivorous diets reduce the evolutionary pre-formed taurine had relaxed the selective
selective pressures that act to maintain ana- pressure to maintain the metabolic machinery.
tomical and physiological features needed to
There are additional signs that we were grow-
process and metabolize large amounts of plant
ing dependent on animal food sources. One of
matter. Like cats, humans have experienced
our essential micronutrients is Vitamin B12 and
a reduction in gut size and metabolic activity,
found only in animal foods. Similarly, the rich-
along with a concurrent expansion of brain
est sources of iron, iodine, folic acid and vita-
size (Figure 7). This occurred at the very same
min A are animal foods. The most common nu-
time that more and more energetically dense
trient deficiencies today are associated with low
animal food was incorporated. The brain is a
meat consumption. Iron deficiency anaemia
very energy-demanding organ, responsible for
is prevalent in both rich and poor countries,
about one quarter of our basal metabolic rate.
while iodine deficiency affects up to 2 billion
Further, similar to obligate carnivores, humans
people world wide, resulting in goitre, cretin-
have a limited ability to manufacture the long
ism and enough mental retardation to reduce
chain, highly polyunsaturated fatty acids that
a population’s average IQ. (Incidentally, iodine
characterize our complex brain and nervous
deficiency is rising sharply in Australia because
system. Long chain polyunsaturated fatty acids
dairy manufacturers no longer use iodophors as
Vegetables
3-5 Servings Fruit
2-4 Servings
Figure 19 Figure 20
cleansing agents in dairy factories). Folic acid Foraging humans are similar to other animals
deficiency causes a birth defect in which the in natural settings in that they attempt to
brain and spinal cord do not develop normally, maximize the energy ‘capture’ rate, i.e. the
a condition known as ‘neural tube defect’. ratio between the energy obtained from a food
Although dark green leafy vegetables are a good source compared to the energy expenditure
source of folic acid, the very richest source is needed to acquire it while hunting, fishing
animal liver, a commodity regularly consumed or gathering (this is known as the Optimal
by our hunter-gatherer ancestors. Finally, hu- Foraging Theory). Table 2 shows the energy
mans have a finite capacity to convert the yel- return rates for a variety of plant and animal
low/orange coloured carotenoids in plant foods foods that were known components of hunter-
into vitamin A. Today, vitamin A deficiency gatherer diets. Clearly, animal foods yield the
blindness is the most common cause of vision highest energy return rates, and larger animals
loss in the world and again, the richest sources generally produce greater energy returns than
of vitamin A are liver and animal flesh. So smaller animals. Although the potential food
gradually, but surely, we evolved a metabolism mass would be similar between a single deer
that depended on at least moderate intake of weighing 45 kg and 1,600 mice weighing 30 g
animal foods. each, foraging humans would have to expend
significantly more energy capturing the 1,600
Hunter-gatherer mice than a single deer. Hence, the killing of
foraging strategies larger animals increases the energy capture/
energy expenditure ratio not only because it
Our analyses of both the ethnographic data and reduces energy expenditure, but because it in-
the quantitative dietary data (Table 1) show creases the total energy captured.
that animal foods were our preferred energy
source, even when plant food sources were Due to the relative constancy of the protein
available year round such as in the tropics. content of an animal’s muscle mass, the energy
Only when it was difficult to procure animal density of an edible carcass is almost entirely
food sources, or when energy-dense, easily dependent upon its body fat content. Varying
procured plant foods were available (eg the amounts of body fat determine the protein to
mongongo nut for the South African !Kung fat energy ratio in an edible carcass. Because
people), did plant foods prevail as a major en- smaller animal species have proportionately
ergy component in hunter-gatherer diets. less body fat than larger species, their carcasses
contain more protein as a percentage of their
available food energy. Hunter-gatherers tended
36 | Genes to Galaxies
Table 2: Energy return rates upon encounter from foraged foods.
to shun very small animals or fat-depleted ani- important factor in shaping their food procure-
mals because of their excessive protein content. ment strategies. Lean meat, therefore, could
Historical accounts documented the adverse not be eaten in unlimited quantities, but rather
health effects that occurred when people were had to be accompanied by sufficient fat, or by
forced to rely solely on fat-depleted, wild ani- carbohydrate derived from plant food sources.
mals (Speth & Spielmann, 1983). Excessive This simple physiological fact could explain
protein consumption without additional sourc- our innate drive to consume fatty and sweet
es of fat or carbohydrate caused a condition de- foods.
scribed as “rabbit starvation” in early American
explorers. They suffered nausea, diarrhea and Modern vs traditional
even death if very lean small animals were the food choices
only source of food. Clinically, this syndrome
is probably caused by the finite ability of the Before the development of agriculture and
liver to up-regulate the rate-limiting enzymes animal husbandry, dietary choices would have
that synthesise urea, culminating in very high been limited to minimally processed, wild plant
levels of ammonium ions and acidic amino and animal foods. With the initial domestica-
acids in the blood. For the foraging human, the tion of plants and animals, the original nutrient
avoidance of excessive dietary protein was an characteristics of foods changed, subtly at first
38 | Genes to Galaxies
Salt The total quantity of salt included in the cholesterol levels include lauric acid (C12:0),
typical diet of westernized nations amounts myristic acid (C14:0), palmitic acid (C16:0),
to nearly 10 g/day. About 75% is derived from and some trans fatty acids (Grundy, 1997),
salt added to processed foods by manufactur- whereas monounsaturated (MUFA) and poly-
ers; 15% comes from discretionary sources (ie, unsaturated (PUFA) fatty acids reduce choles-
cooking and table salt use), and the remainder terol levels. Stearic acid (C18:0), the major fatty
occurs naturally in basic foodstuffs. The system- acid in chocolate and lean red meat is neutral.
atic mining, manufacture, and transportation Omega-3 long chain PUFA, found in fish and
of salt have their origin in the last 10,000 years. seafood in general and Australian grass fed beef
The earliest salt use is thought to have taken and lamb, have wide ranging protective capaci-
place in China about 6000 BC. Paleolithic ties including the ability to reduce blood lipids.
hunter-gatherers living in coastal areas probably Consequently, it is possible to consume high
dipped food in seawater or used dried salt in a fat diets that do not produce an adverse blood
manner similar to nearly all Polynesian socie- lipid profile or cardiovascular disease.
ties at the time of European contact. But most
In their classic study of Greenland Eskimos
recently studied inland hunter-gatherers add no
who had a near absence of cardiovascular dis-
or little salt to their food.
ease, Bang and Dyerberg (1980) contrasted the
dietary and blood lipid profiles of the Eskimos
Diet and chronic disease to Danes (Table 3). Despite a much greater ani-
in hunter-gatherers mal food intake than the Danes, the Eskimos
Dietary fat maintained a more healthful blood lipid profile.
The reduced cholesterol levels in the Eskimos
In our analysis of hunter-gatherer diets
are likely accounted for by the higher dietary
(Cordain et al, 2000), we found that most
intake of ‘good’ fats. The protein intake of the
groups exceeded the dietary recommendation
Eskimos was more than twice as high as the
to eat 30% or less of energy as fat (Figures 17
Danes, and this pattern (elevated protein at the
and 18). In fact, over half of them consumed
expense of carbohydrate) is characteristic of
amounts not too dissimilar to current western
hunter-gatherers (Cordain et al, 2000a).
and Mediterranean dietary intakes. Despite
this, the available evidence suggests that hunt- Dietary protein
er-gatherers were generally free of the signs and Our analyses of contemporary hunter-gatherer
symptoms of cardiovascular disease. Research diets show that the average protein intake was
shows that indigenous populations that derive as high as 35% energy (Figure 16). This is
the majority of their diet from animal products more than twice the level consumed by cur-
have surprisingly low levels of cholesterol and rent western populations (~15% energy). High
other fats in the blood. Moreover, death certifi- protein intake in western diets is perceived
cates, autopsies and clinical studies indicate a to be linked to high calcium excretion in the
low incidence of coronary heart disease among urine and faster progression of kidney disease.
the Inuit and other polar populations, consum- Yet, paradoxically, high protein diets have
ing high intakes of animal foods. However, in been shown to improve metabolic control in
western diets, higher animal food consumption type 2 diabetes patients. In her classic study of
is frequently associated with increased mortal- Australian Aborigines temporarily reverting to
ity from chronic disease. The low incidence a hunter-gatherer lifestyle, Kerin O’Dea showed
of cardiovascular disease among indigenous that animal foods contributed ~65% of the total
populations subsisting largely on animal foods energy, producing an overall macro-nutrient
represents a paradox. distribution of 54% protein, 33% carbohydrate
There is now strong evidence that the absolute and 13% fat energy. Following a 7-week period
amount of dietary fat is less important in re- living as hunter-gatherers in their traditional
ducing the risk for cardiovascular disease than country in north-western Australia, 10 diabetic,
the type of fat. Fatty acids that increase blood overweight Aborigines experienced either a
40 | Genes to Galaxies
slowly digested and produce low glycemic and and omega-3 fatty acids, would have served
insulin responses. Observational studies sug- to inhibit the development of cardiovascular
gest that foods with a high glycemic load and disease. Other dietary characteristics including
low fiber content increase the risk for type 2 high intakes of antioxidants, fibre, vitamins and
diabetes (Barclay et al, 2008). phytochemicals along with a low salt intake
may have operated synergistically with lifestyle
Other environmental factors
characteristics (more exercise, less stress and
It is likely that hunter-gatherers consumed very no smoking) to further deter the development
high intakes of antioxidants and phytonutrients of disease. The modern healthy food pyramid
and undertook more intense physical exercise with its foundation based on cereals rich in car-
or work patterns (Cordain et al, 1998). These bohydrate supplemented with small amounts
characteristics would have provided pre-agri- of animal foods (Figure 19) differs greatly from
cultural people with further protection from the human evolutionary pyramid (Figure 20).
chronic diseases such as diabetes. Biochemical Yet it is still possible to consume a healthy
studies of hunter-gatherers have shown high diet based on evolutionary principles in which
plasma concentrations of folate and vitamin the quality of fat, protein and carbohydrate
B12. Adequate intake of these two vitamins are more critical that their quantity or energy
along with vitamin B6 reduce homocysteine, an distribution. Indeed, the insights gained from
important risk factor for cardiovascular disease. Paleolithic nutrition are likely to influence fu-
Hunter-gatherers rarely if ever added salt to ture dietary guidelines around the world.
their foods, and studies of salt-free Yanomamo
Indians have shown these indigenous people Although concerted attempts were made to acknowledge the
source of all images, in some cases this could not be ascertained.
to maintain low blood pressures that do not
Please contact the author if an infringement has taken place.
increase with age. Finally, except for certain
American Indian societies (starting about 5,000
years ago), regular smoking of tobacco was un- Further reading
known in hunter-gatherers. Any or all of these Barclay A, Petocz P, McMillan-Price J, Flood
dietary and environmental elements would VM, Prvan T, Mitchell P, Brand-Miller JC.
have operated together with the macronutrient Glycemic index, glycemic load and chronic
characteristics of hunter-gather diets to reduce disease risk – a meta-analysis of observational
signs and symptoms of the chronic diseases studies. Am J Clin Nutr 2008; 87: 627-37.
that plague western societies.
Cordain L, Watkins BA & Mann NJ (2001):
Fatty acid composition and energy density of
Conclusions foods available to African hominids: evolution-
The diet of our ancestors was characterized ary implications for human brain development.
by higher intake of meat and lower intake World Rev. Nutr. Diet. 90, 000-000.
of plant foods than is generally recognized.
Cordain L, Brand Miller J, Eaton SB, Mann N,
Modern human beings display physiological
Holt SHA & Speth JD (2000a): Plant-animal
features which suggest an increasingly carnivo-
subsistence ratios and macronutrient energy
rous diet during human evolution. Our large
estimations in worldwide hunter-gatherer diets.
brains increased in size at the expense of the
Am. J. Clin. Nutr. 71, 682-692.
gastronintestinal tract and dictated high intake
of nutrient-rich foods. The high reliance on Cordain L, Brand Miller J, Eaton SB & Mann
animal foods may not have elicited an adverse N (2000b): Macronutrient estimations in
blood lipid profile because of the benefits of hunter-gatherer diets. Am. J. Clin. Nutr. 72,
high dietary protein and low level of dietary 1589-1590.
carbohydrate. Although fat intake would have Cordain L, Gotshall RW, Eaton SB & Eaton SB
been similar to or higher than that found in (1998): Physical activity, energy expenditure
western diets, there were important qualitative and fitness: an evolutionary perspective. Int. J.
differences. The high levels of MUFA and PUFA Sports Med. 19, 328-335.
42 | Genes to Galaxies
Paleolithic nutrition: what did our ancestors eat? | 43
A Walk Around the Neighbourhood:
Understanding
the Nature and
Structure of
the Milky Way
N. M. McClure-Griffiths
W e live in a hefty spiral-
patterned galaxy called
the Milky Way. Though
we can all see the Galaxy
on a nightly basis, we know surprisingly little
about our home. Some very important ques-
tions about the shape and structure of the
Milky Way remain unanswered: Exactly how
big is the galaxy? Where is the Sun in relation
to the Galactic Centre? If we could look at the
Milky Way from above what would it look like
and how many spiral arms would it have? How
does the Milky Way evolve and how do we in-
teract with our neighbours? I will take us on a
walk around the Milky Way revealing what we
do know about the structure of the galaxy and
how it lives its life. I will finish with some of
the things we hope to learn in the next decade
as new telescopes become available and help us
solve the mysteries of our home.
One of the first things you might do upon
moving into a new house is take a walk
around the neighbourhood. What’s around
the corner? Where’s the nearest shop? How far
to the school? Even though we’ve been living
in our home galaxy, the Milky Way, since the the Southern Hemisphere, the Milky Way is
beginning of time we don’t really know much the most striking feature in the sky. Figure 1
about the neighbourhood. We can’t go out is a wonderful example of how the Milky Way
and explore the neighbourhood because the looks in the night sky both in the Northern
neighbourhood is far too big. Just going to the and Southern Hemispheres. Our name for this
star next door would take about 30,000 years. band of stars comes from the Latin name for
Instead, most of what we know about the it: “via lactea”, meaning milky road or milky
Milky Way neighbourhood comes from astron- way. We often refer to the Milky Way by its
omy and its mostly ground-based telescopes. In Greek derived name “The Galaxy”, which also
this chapter I will try to give you a brief tour of means “milky”.
the Milky Way, hopefully answering questions
Studying the Milky Way is simultaneously
about what the Milky Way looks like, how it
made easy by its close proximity and difficult
lives its life, and how it interacts with some of
because we are deeply embedded within the
its nearest neighbours.
Galaxy. Even with years of study we are still
struggling to understand the basic properties
The Milky Way as a galaxy and structure of the Galaxy. We do know that
Stars are grouped throughout the universe the Milky Way is a rather hefty galaxy, made up
in islands called galaxies. Galaxies take on a of something like 200 to 300 billion stars and
variety of different shapes, but many look like weighing in at about 600 billion times the mass
large pinwheels. The closest galaxy is the one of the Sun or a little over 1 x 1042 kg. Mass
in which we live, the Milky Way. Most of us are estimates for the Milky Way are based on meas-
probably familiar with the Milky Way as a great uring the rotational speed of the Galaxy as far
band of white-ish stars stretching from horizon out as possible and using basic laws of gravity
to horizon. On a dark night, particularly in (Kepler’s Laws) to estimate the mass enclosed
in the orbit.
Figure 1: Images of the Milky Way in the night sky taken from both the Northern and
Southern Hemispheres. The Milky Way stretches from horizon to horizon as a band of
“milky” white stars and the occasional dust cloud that blocks out the starlight from
behind the clouds. Also visible here are the Large and Small Magellanic Clouds as light
purple spots near the centre of the right-hand image. These are some of our nearest
galaxy neighbours.
Image credit: Axel Mellinger / http://home.arcor-online.de/axel.mellinger/
46 | Genes to Galaxies
Figure 2: Artist’s
impression of the
Milky Way as it
might appear if
we could fly out
of it and look
back down. The
model used here
is assembled from
many pieces of
information about
the spiral structure
and bar structure
of the Galaxy. The
position of the Sun
is marked and most
of the spiral arms
are named.
NASA/JPL-Caltech/R.
Hurt (SSC-Caltech)
Taking measure of the Milky Way diameter is source of great uncertainty for the entire history
in many ways even more tricky. Most of what of Milky Way studies. The most recent meas-
we know about the structure of the Galaxy urement, painstakingly made with one of the
more than a few thousand light-years1 from the world’s largest optical telescopes, Keck, give a
Sun comes from measurements made of radio value of 26000 LY with an error range of 2000
and infrared radiation, which pierce through LY (Ghez et al 2008). Other reliable measure-
the fog of the Galaxy’s interstellar gas and dust. ments suggest values as low as 24,700 LY or as
Because the Milky Way is viewed as a relatively high as 27,600 LY. Most other properties of the
thin band of stars on the sky we have long Galaxy’s structure, including the full extent of
known that it must be a disk-like structure. In the disk and its height depend on the Galactic
fact, the Milky Way has dimensions somewhat Centre distance so it is crucial to measure it as
like a compact disc. The stars lie in a disk of accurately as possible.
diameter about 100,000 light-years (LY) with a
We also know that the Milky Way is shaped
thickness of only about 1000 LY. Surrounding
like a pinwheel in what is known as a barred
the disk is a spherical ball of mostly gas and a
spiral-type galaxy. Each one of the arms of the
few stars called the halo. This halo is important
pinwheel is made up of very bright, massive
to the evolution of the Milky Way as a whole
stars. While the space between spiral arms
and we’ll come back to it later.
also has many stars, these are generally smaller
The Sun lies about 26,000 LY from the centre and less bright. The result, if we could see
of the Galaxy, but this number has been the the Milky Way from above, might look like
the artist’s impression shown in Figure 2. The
1 A light-year is the distance light travels in one year or number and position of these arms has been
9.5 x 1012 km.
48 | Genes to Galaxies
another. So how do these weather systems It is only in these dense areas that enough mat-
develop? We’ll discuss that in the next section ter can accumulate in a small enough area for
when thinking about how the Milky Way lives gravity to pull it together in a tight ball so that
its life. nuclear fusion can ignite the gas as a star. The
topic of how exactly stars form is an interest-
How Does the Milky ing one and one that dominates a great deal of
Way Live its Life? astrophysical research, but we’ll leave that topic
for another day. Right now, we’ll focus just on
The formation and evolution of galaxies like how gas cools and condenses to form molecu-
the Milky Way is a topic of current study. How lar clouds, what disrupts gas in the Milky Way
do the bits and pieces of cold gas left floating and whether that gas flows in or out of the
around the Universe come together to form a Galaxy.
galaxy? What influences how galaxies live their
lives? Although we don’t have clear answers Disrupting Interstellar Gas
about how the Milky Way formed, there has The basic cycle of life and death in the inter-
been enormous progress in the past few years stellar medium is shown in Figure 3. Most of
on studying how the Milky Way lives its life. It interstellar space is filled with diffuse (density
is the interstellar gas that largely controls the li- of 1 atom per cubic centimetre), warm (tem-
fecycle of the Milky Way. After all, it is from the peratures of ~5000 K) atomic hydrogen. This
gas that stars form and it is to the gas that the gas is disrupted by a variety of forces and inter-
stars return when they die. We know that most stellar processes.
stars are formed in clouds of molecular gas,
The first process we discuss disrupts the gas
which are the densest areas of interstellar space.
on scales of tens to thousands of light-years.
Figure 3: Cartoon diagram of the evolution of gas in the interstellar medium. This
diagram shows how gas moves through its various stages, such as diffuse interstellar
medium to molecular clouds and on to stars and what processes effect how the gas
makes these transitions. Blue arrows represent processes where gas must cool and red
arrows represent processes that can heat the gas.
J Dawson (Naygoya University/CSIRO)
50 | Genes to Galaxies
Figure 5: Gigantic supershell GSH
277+00+36 imaged shown in diffuse
atomic hydrogen emission. The bright
areas are where gas has been swept up by
hundreds of stellar winds and supernovae
leaving a largely evacuated cavity (dark
black) in the centre. The cavity has a
diameter of nearly 2000 light-years.
N McClure-Griffiths, CSIRO/ATNF
52 | Genes to Galaxies
some very simple calculations that show that a collision course with the Milky Way. Smith’s
the rate at which new stars are formed in the Cloud is 11,000 light-years long and 2,500
Milky Way should have exhausted all of the light-years wide. At present it is only 8,000
interstellar gas and star formation should have light-years from the Milky Way disk and mov-
ceased long ago. And yet, we know that this is ing towards the disk at more than 240 km/s,
not true as we observe gas in the present-day aimed to strike the Milky Way’s disk at an
Galaxy and continuing star formation. This angle of about 45 degrees. The cloud contains
gas supply problem is not solved but there are enough hydrogen to make a million stars like
some indications that there is a slow trickle of the Sun; so it is clear that objects like these
gas from extragalactic space and the Galactic have a role to play in keeping the Galaxy well
halo itself that makes it way on to the disk to fed (Lockman et al. 2008).
feed our gas hungry Galaxy. You may be wondering where hydrogen
The gas flowing into the Galaxy takes several clouds like Smith’s Cloud come from. For
forms. One form are so-called “high velocity clouds as massive as this there are two main
clouds”, which litter the Galaxy’s halo and get hypotheses: first, that they are left over from
their name because they are moving quickly the formation of the Milky Way and second,
with respect to the Galaxy. These clouds of cool that they have been pulled off nearby galaxies
hydrogen were discovered in the 1960’s and it that interact with the Milky Way (see Wakker
was immediately realised that they might be a & van Woerden 1997). The first hypothesis
potential source of gas influx. Despite that, it works with the idea that the Milky Way came
has taken many years to find clear examples together from many smaller building blocks,
of high velocity clouds interacting with the put together something like Lego. The building
Milky Way. One of the nicest recent examples is blocks are gravitationally attracted to a central
shown in Figure 7, which is of a large cloud of mass and as they fall in they start spinning,
cold hydrogen called Smith’s Cloud that is on which gives our Galaxy its rotation. Invariably
Figure 7:
Hydrogen gas in
the high velocity
cloud, Smith’s
Cloud. The
comet-like shape
indicates the
cloud’s direction
of motion, which is
inclined at about
45 degrees to the
disk of the Milky
Way. The cloud is
travelling at more
than 240 km/s and
will collide with the
Galaxy in about 40
million years.
Courtesy: Bill Saxton/
NRAO/AUI/NSF
not all of the building blocks come together at as it does, gradually condense much like rain-
once and some are left to trickle into the Milky drops, before it falls back onto the Galactic disk
Way over time. Some high velocity clouds are (Shapiro & Field 1976). The direct evidence
almost certainly of this origin. for this activity is very difficult to come by, but
nonetheless we assume that it must be happen-
The second origin for high velocity clouds is
ing at least to some degree in the Milky Way.
that large chunks of gas are stripped off other
galaxies as they pass near the Milky Way. This All of these methods: gas leftover from the for-
is also known to occur. One excellent example mation of the Milky Way, gas stripped off near-
is the Magellanic Stream, shown in Figure 8 by galaxies, and cooling halo gas can provide
on an image of the Southern sky in hydrogen some gas influx for the Milky Way. However, if
gas. The Magellanic Stream is the long verti- we add up all of the cool gas we observe in the
cal stripe of gas running from blue through to halo of the Milky Way we find that there still is
orange down the centre of the image. This gas not enough to fully feed the star formation of
is stripped off the Large and Small Magellanic the Milky Way over its history (Putman 2006).
Clouds, which are small galaxies neighbouring Clearly either the influx rate was much higher
(about 150,000 light-years away) the Milky in the past, which is unlikely, or we are miss-
Way. Each galaxy has a mass of 1/10 (or less) ing some gas. Current research is underway to
the mass of the Milky Way so as they pass near discover the “missing” gas.
the Milky Way our Galaxy steals material from
them, which streams behind their direction of What are the big remaining
motion like the tail of a comet. This stripped mysteries and prospects
material slowly makes its way onto the disk of
for future discovery?
the Galaxy to feed its star formation habit.
The structure and nature of the Milky Way
Another form of gas influx is from matter con-
are far from completely understood. There are
densed directly from the halo. As we discussed
a number of big mysteries that remain about
above, chimneys can expel hot gas from the
the Galaxy’s structure and how it operates. For
disk up into the Galaxy’s halo. Most of this gas
example, we still don’t have a very good idea
doesn’t escape the Galaxy’s gravitational field so
about how many spiral arms there in the Milky
it remains in the halo floating around for mil-
Way and exactly where they are. The map
lions of years. Over time the gas may cool and
54 | Genes to Galaxies
presented in Figure 2 is our current best guess, References:
but most Milky Way researchers would argue
that a lot of work needs to be done to con- Benjamin et al. First GLIMPSE Results on
vince ourselves that this is a valid guess. Even the Stellar Structure of the Galaxy. The
relatively simple things like the distance to Astrophysical Journal (2005) vol. 630 pp. L149
the centre of the Galaxy are still being refined Churchwell et al. The Bubbling Galactic Disk.
with recent changes of up to 10%. More dif- The Astrophysical Journal (2006) vol. 649 pp.
ficult questions like, where exactly is the edge 759
of the Milky Way disk are very much up in
English et al. The Galactic Worm GW 123.4-
the air. On the topic of the nature of the Milky
1.5: A Mushroom-shaped H I Cloud. The
Way there are many things that we still don’t
Astrophysical Journal Letters (2000) vol. 533
understand. Some of these we have identified
pp. L25-L28
here, such as: how do molecular clouds form
from diffuse atomic gas? Where are all of the Ghez et al. Measuring Distance and Properties
chimneys that are needed to hold up the halo? of the Milky Way’s Central Supermassive Black
Where is the missing mass of the Galactic halo Hole with Stellar Orbits. The Astrophysical
that is needed to continue to fuel star forma- Journal (2008) vol. 689, pp.1044-1062
tion in the Milky Way? And lying at the heart
Lockman et al. The Smith Cloud: A High-
of many questions about the life of the Milky
Velocity Cloud Colliding with the Milky Way.
Way is the role of magnetic fields, which we
The Astrophysical Journal (2008) vol. 679 pp.
have not discussed at all here. The Milky Way
L21
is threaded with a magnetic field, much like the
Earth is threaded with a magnetic field. We be- McClure-Griffiths et al. A Distant Extended
lieve that the magnetic fields of the Milky Way Spiral Arm in the Fourth Quadrant of the
control how gas moves around, how molecular Milky Way. The Astrophysical Journal Letters
clouds form, even how stars form, but we (2004) vol. 607 pp. L127
know very little about this elusive component.
McClure-Griffiths et al. Loops, Drips, and Walls
The future is bright for a better understanding in the Galactic Chimney GSH 277+00+36. The
of the Milky Way. The next fifteen years will see Astrophysical Journal (2003) vol. 594 pp. 833
a variety of new telescopes, each one very well
Putman. Potential Condensed Fuel for the
suited to answering some of the big questions
Milky Way. The Astrophysical Journal (2006)
about the Milky Way. In just a few years time
vol. 645 pp. 1164-1168
we will see the Atacama Large Millimetre Array
start operating in Chile, adding answers to the Shapiro et al. Consequences of a New Hot
key questions of how molecular clouds form Component of the Interstellar Medium.
and how stars from these clouds. In Australia Astrophysical Journal (1976) vol. 205 pp. 762
we hope to host Square Kilometre Array by Wakker et al. High-Velocity Clouds. Annual
2020, which will be able to get at those elusive Review of Astronomy and Astrophysics (1997)
magnetic fields amongst many other things. vol. 35 pp. 217-266
Space based telescopes will measure distances
to tens of thousands of stars giving us a much
better idea of the Milky Way spiral structure.
And finally Extremely Large optical telescopes
will be built in the next decade with the hope
of being able to explore in other galaxies the
processes that we can see in the Milky Way.
The next fifteen years will hopefully bring
about a revolution in our understanding of the
Milky Way!
A virus
defence
pathway
and a
technology
Peter Waterhouse
T he development and use of vac-
cines against viruses such as
polio, smallpox, and measles
have to be among the great ac-
complishments of medical science. The history
of how it all started from Edward Jenner’s dis-
covery (that milkmaids and dairymen infected
with the mild cowpox virus were protected
against smallpox) is widely known. However, it
is not so generally appreciated that plants can
also be protected from a severe virus by prior
infection with a mild strain of a closely related
virus. This “cross protection” in plants was
recognized as early as the 1920s, but plants do
not possess an antibody-based immune system,
so the mechanism underlying this defence
remained a mystery for many decades. A few
years prior to the turn of the millennium, our
understanding began to dawn and after a flurry
of research the existence of an unsuspected,
but immensely powerful, mechanism, in both
plants and animals, has been revealed. This
mechanism can be triggered and directed to not
only provide protection against viruses but also
to silence any gene, and has led to a technology
called RNA interference (RNAi) which is being the sequence for the production of a protein of
used for applications ranging from improved the inferred amino-acid sequence. This DNA to
agricultural traits to fighting cancer. RNA to Protein is called the central dogma. As
I hope will become clear, it is also important to
In this first of my two chapters, I will describe
note that the DNA is in a double stranded form
how the gene silencing pathway was discov-
(with the two strands binding together like a
ered, and how it works, and then give some
zipped-up zip), but the messenger RNA is sin-
examples of how it has been exploited. In
gle stranded (like one side of an unzipped zip).
the second chapter, I will describe how this
And the zipping rule of dsDNA is very simple,
mechanism turned out to be a sophisticated
for two strands to bind together they must have
multidimensional pathway which not only
“complementary” sequences. Each nucleotide
protects cells against viruses but also tightly
can be one of four types called (in abbreviated
controls the regulation of genes required for
form) A, C, G or T, and A will only bind to T
normal development in almost all forms of
and C will only bind to G. So, for example,
multi-cellular life.
if a short strand of DNA has the nucleotide
sequence =>ACGTAT it will only zip up nicely
Genes and Transgenes with a strand having the sequence TGCATA<=
Genes are encoded in the nucleotide sequences (the arrows are to show that strands have polar-
of double stranded (ds) DNA molecules, which ity and when two strands zip up they actually
are folded up to form chromosomes in the nu- point in opposite directions).
cleus of eukaryotic cells. Each gene is made up The other take-home message I want to convey
of three adjacent sections: the “promoter”, the is that our understanding of how a gene is
“coding region”, and the “ terminator”, (Figure composed of three sections allows us to make
1). The promoter sequence defines where an transgenes. As you will see in the next section,
enzyme (called a polymerase) binds to the DNA we make a transgene that is inserted into a
and starts to copy the sequence of one strand of plant so that it makes the coat protein of a virus
the DNA into molecules of single stranded (ss) but not the whole virus. We do this simply by
RNA. This copying proceeds across the coding taking a dsDNA copy of a plant gene, replacing
region and stops when it reaches the termina- the coding region of the plant gene with the
tor sequence. The RNA production is in the coding region of the virus coat protein gene,
nucleus but once made, each RNA molecule and then inserting this [plant promoter- virus
(called messenger RNA) is transported to the coat protein coding region – plant terminator]
main compartment of the cell (the cytoplasm) piece of dsDNA into a chromosome of a plant
where it is used as the template for another (Figure 2).
enzyme complex (the ribosome) to decipher
58 | Genes to Galaxies
Promoter Coding Region Terminator
Plant gene
+
Virus gene coding region*
Plant transgene
*The gene has been converted to dsDNA from the ssRNA version in the virus.
Figure 2: Making a plant transgene
Aphids
- vectors of
plant viruses
Healthy and
Virus-Infected
Potato
Virus particles
60 | Genes to Galaxies
or the antisense transgene, or neither (Figure
5). This convinced us that dsRNA was the trig-
ger that was somehow protecting the plants
against the virus.
Target RNA
62 | Genes to Galaxies
stretch of 21 nucleotides that is exactly comple- There have been some amazing applications of
mentary to the guide sequence, the Argonaute RNAi in plants, such as coffee plants that pro-
acts like a pair of scissors and cuts the “target” duce decaffeinated beans and opium poppies
RNA in the middle of the recognised sequence. that produce desirable pharmaceutical com-
Because the dsRNA being introduced into the pounds, and I would like to finish this chapter
cell is usually several hundred nucleotides with three further examples that hopefully give
long, it is Diced up into many different 21nt an idea of how useful and versatile the technol-
fragments, and each one is loaded into a dif- ogy can be.
ferent Argonaute molecule. This means that a
One of the important aspects of crop produc-
single target ssRNA molecule may be cleaved in
tion is flowering time. For instance, if a cereal
several different places by the loaded Argonaute
crop flowers too early, it may have not yet
population. Chopping the target RNA into
made sufficient energy stores to fuel its maxi-
pieces prevents it from being translated into
mum grain production. Similarly, if it flowers
protein, thus silencing the gene.
too late in the season there may be insufficient
time to produce a good yield. So, being able to
A few examples control flowering time in plants could be a very
RNAi has been used or has shown potential for useful tool in horticulture and agriculture. In
many purposes including human therapeutics Arabidopsis, there is a gene called FLC which
(Table 1) and functional genomics. The entire represses flowering and we have used RNAi to
nucleotide sequences of the genomes of a switch it off and bring on flowering (Figure 9).
number of species (including human, fruit fly, This clearly shows that the technology has the
nematode, and Arabidopsis) have been deter- potential to regulate flowering time in crops.
mined. From these sequences we can predict An application of RNAi in plants that is much
the coding regions of all of the genes within closer to agricultural use is the silencing of
each genome. However for a significant propor- genes involved with seed-oil production. Some
tion of these genes, we have little or no idea seed-oils are much better for human health
about their functions. So, large scale projects than others, and some oils are more stable at
are currently underway using RNAi to silence high temperatures than others. It all depends
each of these genes, one by one, in nematodes on the fatty acid composition of the oil. For
and in Arabidopsis so that the changes in form example palm oil is very high in palmitic acid
or behaviour that result from silencing the which makes it stable at high temperatures but
genes can give clues about their roles. also unhealthy for human consumption, as it
raises LDL cholesterol levels. Olive oil, on the
Table 1
Therapeutic potential of RNAi
in Humans Virus Immunity Flowering Time Pharmaceuticals
Neurological
Obesity
disorder
Various forms of High blood
Cancer Cholesterol
Spinal muscular
Depression
atrophy B uerose
Blue os Healthy
Oils
Growth hormone
HIV
deficiency Healthy
Health Oils
Ol
Diabetes Hepatitis B
Figure 9: Custom-made changes using
Malaria Hepatitis C
RNAi
64 | Genes to Galaxies
Gene Silencing I: A virus defence pathway and a technology | 65
Reproduced with kind permission HarperCollins Publishers Australia
(c) Karl S. Kruszelnicki Pty Ltd 2009
www.abc.net.au/science/k2
The
X-Chromosome
eXplained
Back in the Olden Days, before research into cloning and stem cells,
most people didn’t know much about genetics or DNA. However,
they had a vague impression that there was something called the ‘X
chromosome’, so named because it looked like the letter ‘X’. Well,
this is not the case, but as an aside, the X chromosome did help
give the world Communism.
Shape of DNA
Every cell in your body (except for the red blood cells) carries DNA.
(Red blood cells are so dedicated to their job of carrying oxygen
efficiently, that everything irrelevant has been stripped off including
the DNA. Red blood cells are not made by other red blood cells
they are made by stem cells in the bone marrow in the long flat
bones of your body.)
The human DNA is a very skinny and very long molecule. The
DNA in each molecule is a few billionths of a metre wide, but if you
stretched it all out it would be a few metres long. It looks like a
ladder with two side rails and about three billion rungs joining the
side rails to each other.
66 | Genes to Galaxies
The X-Chromosome eXplained | 67
This ladder is twisted into a right handed spiral as part of an
efficient way of folding something a few metres long into a space
smaller than one millionth of a metre wide. The twisted ladder is
about 2.3 nm (nanometres or billionths of a metre) wide. The
scientific name for this molecular structure is a ‘double helix’.
The ‘rungs’ are 0.34 nm apart. There are four different types of
rungs, called A, T, C and G. The ladder is twisted and one complete
‘turn’ of the spiral is 3.4 nm, so 10 rungs will fit into one turn. The
scientific name for the rungs is ‘nucleotides’ or ‘base pairs’.
Genetic Code
One of the great scientific discoveries of the 20th
century was that the rungs were actually a ‘code’ to make
amino acids. The famous ‘Genetic Code’ is amazingly
simple and yet incredibly deep. If you put enough amino
acids together, you have a protein. If you put enough
proteins together, you have a living creature (OK, you
need a few other things as well).
Three rungs (nucleotides/base pairs) in a row have
enough information to tell the ‘machinery’ in the cell to
make an amino acid. Look at the first rung. There are four
possibilities: A, T, C or G (the four different types of
rung). There are the same four possibilities for the
second rung, and for the third rung. So the total number
of different combinations is 4 x 4 x 4 = 64 (running from
AAA to TCG to GGG).
However there are only about 20 common amino acids
in life on Earth. So there is some redundancy, i.e. several
combinations of A, T, C and G will give the same amino
acid. For example, the combinations CGC, CGA, CGG, AGA
and AGG will all tell the ‘machinery’ in the cell to make
the amino acid arginine. However, at the other extreme,
two of the amino acids have only a single combination
each, e.g. methionine and tryptophan.
68 | Genes to Galaxies
Job of DNA
Our DNA is, among other things, an architect’s blueprint that will
make and then maintain a human being.
Most of the time, the DNA exists as a myriad of long slender
filaments, floating all tangled up in the nucleus of the cell but not at
all neatly condensed. This gives them a huge surface area, which
makes it easy for the ‘machinery’ in the cell to ‘read’ the DNA to
make proteins. These proteins could be insulin from your pancreas,
enzymes from the cells in your gut to dissolve your food or muscle
in your muscle cells to move your arms, legs and eyelids.
Chromosomes
Whenever a cell is about to split into two more cells, the DNA will
condense for a brief time into little clumps. A skinny strand of DNA
gets wound into a coil, and this coil gets wound again, and so on
a process called ‘DNA supercoiling’. As part of this process,
proteins are wrapped by the coiling DNA and also wrap around the
DNA. These clumps that appear when a cell divides are the famous
chromosomes. They have a central point and four arms, making
them look a little like the letter ‘X’.
By the way, the number of chromosomes varies with the species
just eight in the fruit fly, 46 in human beings and hares, 48 in
gorillas and chimpanzees, 104 in goldfish and a massive 380 in
butterflies.
Chromosomes were first seen in cells by the Swiss botanist Karl
Wilhelm von Nageli in 1842. Chromosomes are really hard to see,
but if you soak the cells with the right dyes you can then see these
coloured bodies hence the name ‘chromo’ meaning ‘colour’ and
‘some’ meaning ‘body’.
The original technique to visualise chromosomes was to ‘poison’
the cell with a drug called colchicine, which locks the cell in at a
certain stage of division. The scientists then stained the cell with
dyes to make the chromosomes obvious, took a photograph (via a
microscope) of the chromosomes, developed the photograph, cut
out the chromosomes with scissors, arranged them in pairs and
Shapes of Chromosomes
Chromosomes come in two main shapes.
The so-called Linear Shape is the ‘classic’ X-shape.
But it doesn’t really look like an ‘X’. Instead of four
separate arms all coming from a single point, there are
usually two sets of parallel legs. Usually, there are two
shorter arms (called ‘p’ from the French word petit
meaning ‘small’) and two longer arms (called ‘q’, because
‘q’ is the next letter in the alphabet after ‘p’). Like the Y-
chromosome, this is another case of a name being
chosen because it’s the next letter in the alphabet.
The other chromosome shape is the circle. This is
often found in smaller creatures, such as bacteria.
Mystery of Chromosomes
It took a long time to learn about our chromosomes. In fact, until
1955, we thought that human beings had 48 chromosomes the
real number is 46.
They were a huge mystery until very recently, the most
mysterious of them all being the 45th chromosome. Part of the
mystery surrounding this particular chromosome was its involvement
in diseases carried by females. Although these diseases, which
included haemophilia and red green colour blindness, didn’t affect
females, they affected males very strange.
For a long time, this mystery remained unsolved. In algebra, the
symbol ‘X’ stands for the unknown quantity, as in the X Factor and
this is how the X chromosome was given its name. (If it was named
after its shape, then all the chromosomes would be called ‘X’.)
70 | Genes to Galaxies
And the Y chromosome? Well, it was pretty mysterious too. ‘Y’
is the next letter in the alphabet after ‘X’, which is how the
Y chromosome got its name. It’s as simple as ABC.
Communism
So what’s the link with Communism? Admittedly, it is a little tenuous
but it is related to the X chromosome.
It seems that Queen Victoria had a spontaneous mutation in her
X chromosome that could cause the bleeding disease, haemophilia.
This led (via some very convoluted logic) to Communism.
72 | Genes to Galaxies
was a German not a very popular nationality in Russia at the time
of World War I.
All this led to enormous unrest and, ultimately, to the Bolshevik
uprising.
Part of the Czar’s inability to attend properly to his duties of
office may have been his preoccupation with the terrible
haemophilia of their only son, Alexei. Therefore, he failed in his regal
duty to govern Russia properly. And that’s how the X chromosome
played a mysterious part in giving the world Communism …
References
Angier, Natalie, ‘For motherly X chromosome, gender is only the beginning’,
The New York Times, 1 May 2007.
Steven, Richard F., ‘The History of haemophilia in the royal families of Europe’,
British Journal of Haematology, April 1999, pp 25–32.
76 | Genes to Galaxies
explained by a precise structural description of The founders of molecular biology, such as
these proteins and of the way they behave as Francis Crick and Jacques Monod, said that
nanomachines. We will consider one of many they had discovered the secret of life. Clearly,
possible examples. The potassium channel, many questions remain unsolved in biology,
located in the cell membrane, is involved in and much exciting work awaits future biolo-
the production of the nerve influx, i.e., the gists! The development of an organ as complex
way nerve cells communicate with other nerve as the brain is clearly not understood. And the
cells, and activate target cells such as muscle way to fight many diseases is unknown. But
cells. It was demonstrated more than fifty Crick and Monod were not wrong. Some fun-
years ago that the nerve influx results from the damental principles explaining the characteris-
occurrence of transient transmembrane cur- tics of present-day organisms have been under-
rents, due to the passage of ions across the cell stood – the existence of genetic information, of
membrane. It was later shown that the passage a genetic code. The advances in understanding
of ions was permitted by the existence of pro- organisms have been so dramatic that it is now
tein channels. The structure of these channels reasonable to conceive of synthesizing a living,
has been characterized, and it has been fully totally artificial organism, as some synthetic
explained how the channels are able to fulfil biologists now do.
their three functions: to open transiently when
the transmembrane voltage is altered by the II Molecular explanations must be
propagation of the nerve influx, to close after a complemented, and extended
short time, and to be specific for one particular
ion (Jiang et al. 2003). To provide this explana- There are different ways to complement the
tion, the static structure revealed by X-ray dif- current molecular description of organisms.
fraction studies is used to provide a scenario of The first is to follow the same path as during
the internal movements of the macromolecule, the last decades. Recently, totally new phe-
how its different parts move one relative to the nomena have been discovered. They do not
other. This dynamic description explains how abolish the previous observations, but they add
these proteins are able to work as superb na- a layer of complexity. Whereas the regulation of
nomachines to fulfil their functions. gene expression was attributed to proteins, the
so-called transcription factors, microRNAs are
The heuristic power of structural determina- increasingly seen to play a part in gene regula-
tion, its capacity to provide satisfactory expla- tion. Similarly, regulation of gene expression
nations of the behaviour of macromolecules, by the control of proteins surrounding DNA,
is not decreasing: the opposite is true. The the histones and more generally the chroma-
huge progress made in these methods, the tin, appears more and more important. These
development of new methods providing a more epigenetic marks can be transmitted through
dynamic description of the internal movements cell division, and in some cases as in plants,
of these nanomachines, and the possibility of through generations. They can be modified by
using the information gathered to design new the environment, and they give organisms a
therapeutic agents make it highly improbable capacity to stably adapt to new environments
that the role of structural information in the by modifications that do not alter genetic in-
explanations of biologists will diminish. The formation. In addition, the numerous studies
description at higher levels of organization will done on the different molecular networks in
probably expand (see later), but these new lev- cells – gene regulatory and signalling networks
els will not replace the molecular level. What – unveil interactions and regulations never
was learned from the description of macromol- seen before.
ecules will remain at the core of our knowledge
of organisms. The macromolecular level is not Even more significant are the technological
one among many other levels: it is the level at developments that complement the structural
which information is encoded in the genome. determination, and make it more precise and
This gives it a preeminent role. more dynamic. The first consists in studying
78 | Genes to Galaxies
hypotheses more precise. These changes in the reason, but not the only one, was the difficulty
way of doing research, what is called episte- of the task, and the lack of an appropriate
mology, are probably more important than the methodology. Another reason was mutual
increase in knowledge or the development of ignorance, resulting from the different univer-
new technologies in the design of what will be sity training of functional and evolutionary
biology in the mid and late 21st century. biologists.
The situation is rapidly changing, for differ-
III The encounter ent and converging reasons. The first is the
between functional and progress of transdisciplinarity within biology.
evolutionary biology The trigger was the development of genom-
ics and post-genomics, which required the
In a famous article published in 1961, the great
skills of computer scientists, mathematicians,
evolutionist Ernst Mayr noticed that there were
physicists, and engineers. This new group of
two highly different categories of biologists:
“biologists” had not been trained to find the
those interested in the way cells and organisms
separation between the two branches of biol-
function, in the elucidation of the complex
ogy “natural”. When they started to work in
mechanisms behind this perfect functioning,
biology, they rapidly moved from functional
and those more interested in the raison d’être
to evolutionary questions, without having the
of these complex functions and the adapta-
feeling of committing a transgression.
tion they provide to organisms harbouring
them. The first category includes physiologists, This is particularly evident in systems biol-
molecular and cell biologists, biochemists; the ogy, where researchers seek to describe the
second, evolutionists, but also ecologists and organization of macromolecules in complex
zoologists. Geneticists are at the boundary networks in cells and organisms, and the be-
between the two groups: they can be molecular haviour of these networks. Leaders in the field,
geneticists or population geneticists. Ernst such as Uri Alon and Stanislas Leibler, rapidly
Mayr underlined the differences between the moved from a description of these systems to
two approaches, and their complementarity questions about their origin, and the adaptive
(Mayr 1961). But this complementarity was value they provide. Some of the scenarios imag-
one of principle, not of facts. Functional biolo- ined for their origin and/or adaptive value were
gists worked as if the complex structures they sometimes naive, or supported by inadequate
studied had no history, were not the product observations (Keller 2005). These researchers
of evolution; and evolutionary biologists paid clearly demonstrated the value, but also the
no attention to the mechanisms behind adapta- difficulty, of bringing together the two forms of
tion, considering that organisms had multiple biology.
possibilities to adapt, and that the description
The second reason for the encounter between
of the mechanisms by which they specifically
these two branches of biology is also a natu-
adapted would add nothing to our understand-
ral consequence of the development of gene
ing of the evolutionary process. The gap be-
sequencing programmes. A sequence is not
tween the two forms of biology was the niche
informative per se. One of the only ways to
in which the supporters of Intelligent Design
extract information from a sequence is to com-
found their arguments: they stated that there
pare it with other sequences. This comparison
are no natural explanations for the emergence
can be used to discover the function of hitherto
of these splendid functional devices in organ-
unknown genes, and the question is therefore
isms: they may only have been designed by a
limited to functional biology. But, in general,
superior intelligence.
comparison of sequences, or of the organiza-
During the last century there were some at- tion of genes in the genome, immediately leads
tempts to fill the gap between the two forms to questions about the evolution of the systems
of biology. But these efforts did not lead to the under comparison. These questions can be
development of research programmes. One limited to a description of what happened, for
80 | Genes to Galaxies
of pathogens to treatments, such as antibiot- biology will probably be more open to diver-
ics, has been fully explored: the mechanisms sity, to a plurality of models, to what happens
involved have been described in the smallest in nature and not in the test tube or in the
detail, as has the propagation of resistance. laboratory.
The study of diseases like cancer is also benefit- Fundamental progress was made during the
ting from these combined efforts of functional 20th century in the description of macromo-
and evolutionary biologists. Instead of being lecular mechanisms. The complex evolutionary
considered as the simple result of the addition history of these mechanisms, and the diversity
of somatic mutations, the formation of tumours it generated, have yet to be described. This
and metastases is now seen as a long evolution- shift in interest is clearly visible when one
ary process in which cancer cells progressively considers the question of life. As I mentioned
adapt to new niches within the organism. previously, the founders of molecular biology
More generally, the study of diseases is giving were convinced that they had discovered the
increasing scope to evolutionary considera- secret of life. And they were not wrong! But
tions. To explain pathology affecting human what remains to be described is the complex
beings, one must take into account the recent process which generated life and its different
evolutionary history that has generated modern forms. From a question of principles, the ques-
humans, and the ecological niche in which this tion of life has been transformed into a histori-
evolutionary history took place. cal question. To reproduce extant forms of life
artificially is an objective which is no longer
By comparing the models and results of both
beyond the reach of synthetic biologists. But
branches of biology, scientists will be able to
to understand how life emerged is a different
elaborate a less naive vision of what happened
question, which is far from being solved. How
during evolution. Such a naive vision is obvious
the complex systems in organisms progressively
in the case of the evolutionary origin of modern
emerged, and how they were gradually coupled
humans, perhaps because so much is at stake!
during the long prehistory of life will require
For the moment, one has the choice between
the work of many biologists. I hope that many
the naive models of evolutionists trying to
of you who attend these lectures will partici-
describe how our ancestors left the branches
pate in this exciting adventure!
of the trees and stood up in the savanna, and
those of geneticists and molecular biologists
outlining the crucial change in one gene, the Bibliography:
“language gene” (Vargha-Khadem et al. 2005) Angus Buckling, R. Craig Maclean, Michael A.
or the “jaw gene” (Stedman et al. 2004). Brockhurst and Nick Colegrave (2009) “The
Human evolution was far more complex, Beagle in a bottle”; Nature 457: 824-829
more tortuous, and so much remains to be
discovered! François Jacob (1982) The possible and the
actual (Seattle: University of Washington Press)
Youxing Jiang et al. (2003) “X-ray structure of
Conclusion a voltage-dependent K+ channel”; Nature 423:
The closer relations progressively established 33-41
between functional and evolutionary biology
Evelyn Fox Keller (2005) “Revisiting ‘scale free’
will deeply affect the way biology is studied.
networks”; BioEssays 27: 1060-1068
Consider, for instance, the importance of
Michael J. Kerner et al. (2005) “Proteome-wide
model organisms in 20th century biology: the
analysis of chaperonin-dependent protein fold-
fruit fly (Drosophila), bacteria (Escherichia coli
ing in Escherichia coli”; Cell 122: 209-220
and its bacteriophages), the nematode, mice.
Most efforts by biologists were focused on these Thomas D. Kocher (2004) “Adaptive evolu-
systems. They were not useless, they permitted tion and explosive speciation: the cichlid fish
the characterization of the most fundamental model”; Nature Reviews/Genetics 5: 288-298
mechanisms operating in organisms. The new
82 | Genes to Galaxies
The frontiers of current biological research | 83
Why is it important to read
On the Origin
of Species in
2009?
Michel Morange
I n the previous lecture, I showed how
the theory of evolution has an increas-
ingly important role in present-day
biology. Not only is evolutionary biol-
ogy an important subdiscipline of biology, but
evolutionary questioning is progressively being
introduced into the different parts of functional
biology. What was the origin of these complex
molecular devices? Can we reconstitute the
processes by which they were progressively
elaborated during evolution?
My aim now will be different. It is to return
to the main author of the theory of evolution,
Charles Darwin. I will try to convince you
that in 2009 it is still important to read On the
Origin of Species by Means of Natural Selection, or
the Preservation of Favoured Races in the Struggle
for Life (hereafter OS; Darwin 1859), more im-
portant than reading all the commentaries that
have been written on Darwin. It is important,
despite the fact that the theory of evolution is
no longer what it was for Darwin. Reading OS
remains crucial because it is a lesson in honest
and excellent science.
I will successively remind you of some of Darwin also lacked any explanation for two
the major facts concerning Darwin, but also important facts constituting the basis of his
how the theory of evolution has dramatically theory. He had no mechanistic explanation for
changed since his time. Then, I will turn my the spontaneous variations that he observed
attention to OS, and give you a reader’s guide. in organisms, what he called “the plasticity of
I will argue that Darwin, and Darwin’s work, organisms”. This lack of explanation forced
remain highly important for us today. him to ascribe to the direct action of the exter-
nal environment a role not attributed to it by
I Some important characteristics modern-day evolutionists. In a similar way, he
of Darwin’s work, and the had no explanation for the capacity of these
variations to be transmitted to the offspring of
transformations of the
affected organisms. He proposed his theory of
evolutionary theory pangenesis in his second book. This attempt
As you all know, the work of Darwin is spread generated the production of other models,
through various books. After he returned from and progresses towards a satisfactory theory of
his trip around the world on the HMS Beagle, heredity, an objective reached with the redis-
Darwin progressively elaborated his theory of covery of Mendel’s Laws in 1900. But his own
evolution by means of natural selection. His model was clearly wrong, giving as it did a
project was to publish a huge treatise, compris- large role to the heredity of acquired character-
ing all the data that he had collected in favour istics, and contradicting the then young cellular
of his theory. This changed dramatically when theory.
he received in 1858 a manuscript from Alfred These weaknesses and omissions in the work of
Russel Wallace proposing a theory very similar Darwin were corrected by his successors, and
to his own. He decided to publish rapidly one I will briefly recall some of the major advances
book, OS, a kind of summary of the treatise he that have progressively shaped the modern
had been planning. The remaining material was theory of evolution.
presented in three other books: The Variations
of Animals and Plants under Domestication, In the 1880s, the German naturalist August
which contained his model of heredity known Weismann provided strong theoretical and
as the theory of pangenesis (1868), The Descent experimental arguments against the existence
of Man and Selection in Relation to Sex (1871), of the heredity of acquired characteristics. In
and The Expression of the Emotions in Man and the 1920s, there was a progressive emergence
Animals (1872). These four books represent of population genetics, i.e., quantitative models
the core of Darwin’s theory. But Darwin also of inheritance of the allelic forms of genes.
wrote many monographs on highly different They gave a precise, quantitative description of
subjects: on the reproduction of orchids, on fitness. These models demonstrated that varia-
the role of worms in the formation of soils, on tions, leading to a small increase in fitness, are
insectivorous plants, on barnacles, etc. Darwin nevertheless capable of invading the population
was a true naturalist, interested by the facts of under study in a limited number of genera-
Nature. This is clearly apparent when one reads tions. The encounter between genetics and the
the notebooks that he published after his long Darwinian theory of evolution, initiated by the
journey on the Beagle. rise of population genetics, was completed in
the 1930s with the wide movement of unifica-
Despite this diversity of interests, microorgan- tion called the Evolutionary Synthesis. Three
isms, bacteria, are totally absent from OS. The contributions to this synthesis are emblematic:
book was published too early, at a time when Theodosius Dobzhansky demonstrated that the
microbiology was progressively emerging observations made by geneticists on Drosophila
through the work of Louis Pasteur and Robert in their laboratories explained the variations
Koch. This is a pity when one knows the strong observed in nature in wild populations. Ernst
experimental support that microorganisms Mayr provided strong arguments in favour of
bring today to the theory of evolution. the formation of new species by geographic
86 | Genes to Galaxies
isolation – the so-called allopatric model. of mutation in conditions of stress, have also
George Simpson showed that palaeontologists’ contributed to the elaboration of this complex
observations on fossils were not incompatible ensemble of theories, models and mechanisms
with the models elaborated by population that constitutes the modern theory of evolu-
geneticists. Evolutionary Synthesis remains the tion. Epigenetic variations are also progres-
framework in which evolutionary biologists sively being allocated a role in this complex
work today. ensemble.
This does not mean, however, that evolutionary The present state of evolutionary theory dif-
biology has not been enriched by many new fers considerably from the theory elaborated
contributions since the 1930s. After the Second by Darwin, and first published 150 years ago,
World War, the interpretation of evolutionary even if the concept of natural selection still has
facts in terms of strategies, strategies of organ- an important place in present-day explanations.
isms and, later, strategies of genes, appeared I will provide two examples to illustrate these
and has progressively assumed increasing im- huge differences. Darwin accepted the exist-
portance, not only in explaining evolutionary ence of an inheritance of acquired characteris-
facts, but also a heuristic tool, permitting biolo- tics, whereas the modern theory of evolution
gists to imagine evolutionary scenarios. The totally rejects. Darwin did not experimentally
development of molecular biology also had a test his theory, whereas experimental evolution,
huge impact on evolutionary theory. Molecular “evolution in a bottle”, is playing an increasing-
data provided decisive arguments in favour of ly important part in the work of evolutionists.
a common origin for all organisms on Earth.
The historical contribution of Darwin was de-
Comparison of protein and gene sequences be-
cisive. But, for the reasons mentioned before,
came the dominant tool to elaborate phyloge-
it is probably a mistake to call this complex
netic trees. Molecular data were used to correct
ensemble of models and theories on evolution
previous phylogenetic trees – such as the rela-
“Darwinism”. First, because it is an anomaly
tions between humans and our cousins, gorillas
in the landscape of scientific disciplines. The
and chimpanzees. Molecular biology also ex-
contributions of Newton and Einstein to phys-
plained the origin of the variations that under-
ics were as important as those of Darwin to
pin evolution, and showed their diversity: from
biology. Yet Newton and Einstein have not
the point mutation of a nucleotide, leading to
given their names to the theories and models
the replacement of one amino acid by another
that emerged from their work. To identify a
in a polypeptide chain, to more drastic events
theory and a man (or a woman) is the rule for
such as insertions and deletions, gene duplica-
ideologies – like Marxism – not for scientific
tion, and even duplication and translocation of
theories. More seriously, to identify the modern
part of or a whole chromosome.
theory of evolution with the name and work
Molecular data also showed that most of these of Darwin leads to totally biased debates and
variations are neutral, and escape the filter questions. Was Darwin right or wrong? Is
of natural election, as first proposed by the the theory of Darwin still valid today? These
Japanese evolutionary biologist Motoo Kimura questions have no sense. Darwin was both
(Kimura 1983). More recently, the discovery right and wrong, and only a part of his theory
of developmental genes – such as the home- is valid today. It is a common rule in science:
otic genes – led to the formation of a new scientific knowledge permanently evolves, and
discipline, Evo-Devo: the evolution of organ- the contributions of scientists, even the most
isms is related to the variations in structure or important ones, are bricks in the ever-evolving
regulation of the family of genes involved in edifice of science.
the control of development. Evo-Devo is one
In contrast, the right question is rarely asked:
of these lines of research where the separation
is this complex ensemble of theories, models
between functional and evolutionary biology is
and practices, which is called “the theory of
progressively erased. Other discoveries, such as
evolution”, likely to be found to be wrong in
microorganisms’ capacity to control their rate
88 | Genes to Galaxies
that his theory encountered, Darwin guessed this is no longer the case today, when experi-
some of the directions where it would be mental evolution is assuming an increasing
possible to overcome them. I will just give a role in the work of biologists. Nevertheless, the
few of many examples. Darwin insists on the weakness of any historical explanation persists.
important role of unselected variations in the
A second difficulty of the Darwin’s theory stems
evolution of organisms, a clear anticipation of
from the complexity of the events under study.
the neutralist theory developed by the Japanese
The action of natural selection is the result of a
researcher Motoo Kimura in the 20th century.
complex interaction between all the organisms
Darwin suggests also that the rate of variations
present in a given ecosystem – if we adopt a
can be modulated by the environment. Such a
present-day expression – not, as is commonly
possibility was demonstrated at the end of the
said, the result of the direct interaction of an
20th century in microorganisms, and its sig-
organism with its environment. The full de-
nificance actively discussed. Nonetheless, one
scription of this complex interaction is highly
has to admit that it was impossible for Darwin
difficult for the naturalist, if not impossible.
to see the true significance of this possibility,
The same is true if one considers extinctions,
at a time when nothing was known about the
the extreme possible consequence of the
mechanisms generating these variations, and
“struggle for life”. Once again, it is impossible,
when it was even conceived as possible that
according to Darwin, to understand why a
the environment directly moulded organisms.
given species has disappeared in the past. This
Darwin also perceived the possibility that a var-
emphasis on the complexity of the relations
iation could be beneficial not to its owner, but
between organisms, and between organisms
also to the other members of the same species.
and their environment, is a characteristic of
But he was not able to develop the conceptual
Darwin’s thought. It has deep resonances with
tools – kin selection, group selection – that
the present-day use of the theory of complexity
would be necessary to justify such a possibility.
to unravel the functioning of organisms and
The book is also important because it exhibits ecosystems. The bad side of this emphasis is
the difficulties of Darwin’s theory. The first that the explanatory and predictive power of
originates in the fact that Darwin proposed Darwin’s theory is reduced to the point where it
a radically new principle of explanation, at vanishes altogether!
odds with those used in other disciplines.
Another challenge to the theory concerns the
Consider physics: scientists try to explain the
explanation of discontinuities in the evolution-
phenomena they observe by the existence of
ary process, the most obvious of which is the
laws, or of mechanisms. The theory of evolu-
formation of new species. Darwin’s theory is
tion by variation and natural selection is not a
based on the existence of a continuous spec-
law, and even if it is frequently described as a
trum of variations. For Darwin, naturally oc-
mechanism, it has nothing in common with the
curring variations are of small amplitude. The
mechanisms considered by physicists. Not only
transformation of organisms is a continuous
is the theory unusual, but its validity is limited
process. Nevertheless, evolution of organisms
to the domain of organisms, a scandal for many
is characterized by huge evolutionary leaps,
physicists! Since organisms are a part of the
discontinuities, one of which is the formation
natural world, how is it possible that they obey
of new species. How can discontinuity origi-
specific laws? These unusual characteristics of
nate from a continuous process? How can a
Darwinian theory partially explain the opposi-
new species emerge? This is a highly difficult
tion that it has encountered, and the reluctance
and recurrent question. The problem of specia-
with which it has been accepted.
tion occupied the minds of many evolutionary
This theory is also difficult per se. First, because biologists during the 20th century, and is still
it is a theory accounting for historical facts. doing so at the beginning of the 21st century.
Direct experiments to test the theory were not
There are two additional difficulties with
realized at the time of Darwin, and the theory
Darwin’s theory. The first concerns the notion
could only provide scenarios. As we have seen,
90 | Genes to Galaxies
spirit of honesty, an emphasis on particular ex- Bibliography:
planatory schemes without rejection of others,
if there are no reasons to exclude them. Charles Darwin (1859) On the Origin of Species
by Means of Natural Selection, or the Preservation
It would be a mistake in this anniversary of Favoured Races in the Struggle for Life
year to praise Darwin, and his work, without (London: Murray)
mentioning its limits, hesitations, and errors.
Darwin made a decisive breakthrough in bio- Charles Darwin (1868) The Variations of
logical thinking. This breakthrough was so de- Animals and Plants under Domestication
cisive that he was alone, ahead of his contem- (London: Murray)
poraries, trying to fit his theory with the ob- Charles Darwin (1871) The Descent of Man and
servations made by naturalists over centuries. Selection in Relation to Sex (London: Murray)
The amplitude and the difficulty of this task
Charles Darwin (1872) The Expression of the
are most evident in what concerns the place of
Emotions in Man and Animals (London: Murray)
human beings in Nature. Darwin devoted two
of his major books to show how closely hu- Motoo Kimura (1983) The Neutral Theory of
mans are related to other organisms, that they Molecular Evolution (Cambridge: Cambridge
share with them many different behavioural, University Press)
anatomical and physiological characteristics.
The natural consequence was that Darwin was
convinced that the mechanism of evolution
by natural selection operated in the forma-
tion of human beings, and is still operating in
and among human populations. Nevertheless,
Darwin hesitated. With fewer racial prejudices
than most of his contemporaries, scandalized
by slavery, he emphasized the importance of
altruistic behaviours among humans. How to
reconcile these opposing views on the wide-
spread action of natural selection and on the
specific characteristics of human societies?
Darwin did not, and he refused to eliminate the
action of natural election from human societies.
How would it have been possible to do that
for the naturalist who included human history
in the natural history of organisms? Darwin
did not consider the disappearance of some
primitive human populations “unnatural”, or
the control of human reproduction useless. To
acknowledge this duality in Darwin’s writings
is simply to admit the difficulty of finding the
right place for radically new theories. Darwin
was not a saint, but a great scientist and an
honest man.
94 | Genes to Galaxies
Figure 2: A montage of galaxies, with our
nearest neighbour, the Andromeda Galaxy
appearing at upper-left, a large elliptical
at the upper-right, and several dwarf
galaxies in the lower panels. While the
elliptical and the dwarfs appear to similar,
they are hugely different in size. To see the
huge diversity of galaxies, visit Galaxy Zoo
(www.galaxyzoo.org).
Adam Block/ NOAO/AURA/NSF; Canada-France-
Hawaii Telescope & Coelum; NASA, ESA and
C. Conselice
Figure 3: The
results of the 2dF
Galaxy Redshift
Survey, which
measured the
distances to more
than 200,000
galaxies out to
a distance of
roughly two billion
light years. We
sit at the centre
of this picture,
and it is clear
that the galaxies
are laid out on a
Image courtesy of the 2dFGRS Team
fine structure of
clusters, filaments
and voids.
96 | Genes to Galaxies
Take a box that represents a large chunk of the
Universe, say 300 million light years on a size.
Fill this box with particles that represent the
distribution of matter in the Universe, with
more particle in regions which are more dense,
and less in the voids, and arrange the particles
to represent the almost smooth distribution of
mass in the early Universe. Then all we have to
do is to turn on the laws of physics, including
gravity and the universal expansion, and let
it evolve. Typically, state-of-the-art simulated
Universes require billions of particles and can
run for months on supercomputers.
The results of these numerical simulations
are no less than spectacular (Figure 4)! In
the initial stages, we can see the matter in the
Universe smoothly distributed throughout
the Cosmos, and as the Universe expands,
the density of matter steadily falls. However,
something interesting starts to happen and we
can see clumps and bumps appear in the mat-
ter distribution; it must be remembered that
these simulations represent a huge volume of
the Universe today and each of these lumps
contain masses which are billions times the
mass of the Sun. The expansion continues
and we can clearly see mass flowing into the
denser regions, with the knots increasing in
size. Intriguingly, a pattern emerges and the
clumps of matter are not isolated but are con-
nected through filaments and sheets, with these
bounding huge areas of low density.
Figure 4: Three ‘snapshots’ of the
numerical evolution of a cosmological In these pictures, the matter distribution we
volume, starting from the early Universe see represents the dark matter evolution, but as
(top) to the present day (bottom); the it is the dominant component of matter in the
box size is roughly one billion light years Universe (making up 90% of all matter) it is
across. As the Universe evolves, more this component that dictates the motion. As gas
structure becomes apparent as matter and stars will follow the dark matter, where we
flows into the denser regions. have high concentrations of dark mark matter
Nicholas Martin & Rodrigo Ibata (Observatoire de
we should expect high densities of stars and
Strasburg) gas, so the tightest knots in the simulations
represent the sites of galaxies, and where these
are grouped together, at the intersection of
evolution of matter in an expanding Universe;
the filaments and sheets, represent clusters of
basically they build their own Universes
galaxies.
within a computer, sit back and let gravity do
its magic. Examining the final stages of the Cosmic evolu-
tion, we can compare the distribution of galax-
What is required to build this ‘numerical simu-
ies in our synthetic Universe to that on the sky
lation’ of the Universe? In principle it’s quite
(Figure 3) and we see and the results are pretty
simple (but, of course, in practice it’s not).
98 | Genes to Galaxies
Figure 6: The black and white portions of this image are photographic images of
the central bulge of the Milky Way; if you go out on a clear night in the Southern
Hemisphere, you can see that this covers a huge area of sky. The brown smudge is the
Sagittarius Dwarf galaxy, which is actually on the far side of the Galaxy and crashing into
the disk. The dwarf is invisible to the naked eye and can be only imaged by identifying its
stars as being separate from those in the Milky Way. Rose Wyse/John Hopkins University
of the Milky Way. Over the last few decades, its growth. Initially, when all the knots of mat-
we have surveyed the sky to unprecedented ter are the same size, the collisions between
depths, and the conclusion is that the expected any two are quite violent, and the lumps crash
population of dwarf galaxies is just not there, together to form larger lumps. However, once
with only one tenth the number predicted the proto-galaxy has become established, be-
by the numerical simulations. This puzzle is coming the local dominant mass, the situation
not fully resolved, but many think that these changes. As small masses get too close, the tidal
dwarfs are actually out there, but in their form- gravitational force on them increases, with stars
ative stage, early bursts of star formation blew and dark matter being stripped from their outer
all the gas out and after the first generation of edges. The closer they get, the more material is
stars, there was no remaining material to form ripped off, until their orbit brings them as close
the next generation. With no stars, this leaves as possible before taking them away to larger
the dwarfs as invisible, dark matter lumps, distances. Soon, it is on its way in again, and
buzzing around but unseen; whether this is the again the process of tidal stripping begins anew,
case or not still waits to be solved. with more material being ripped off. The proc-
ess continues for several orbits until the little
If we examine the growth of a galaxy like our
galaxy has completely boiled away.
own Milky Way in detail, we can understand
how it has cannibalised smaller systems during
Figure 9: The
Field of Streams,
a small part of the
Sloan Digital Sky
Survey. In this field,
which covers a
quarter of the area
of the night sky,
the Sagittarius and
Monoceros Stream
are clearly visible,
as is a previously
unknown stream,
named the Orphan
Stream.
Vasily Belokurov, SDSS-
II Collaboration
Figure 10: A
computer simulation
of the future collision
between Andromeda
and the Milky Way
galaxies. At first,
as the galaxies
approach, little
happens, but once
the gravitational
pulls increase
sufficiently, the disks
of these two galaxies
are destroyed. The
final remnant, which
resembles a train
wreck, will settle
down to give a
featureless elliptical
galaxy.
Copyright © 2008 John
Dubinski
Gene
regulation
Peter Waterhouse
I n my first chapter, I described how the
existence of a virus protection mecha-
nism in plants was discovered, how it
operates, and how the mechanism has
been exploited in biotechnology applications.
In this second chapter, I continue the story
about this RNA degradation mechanism - of
which has some even more unexpected twists
to come.
Number of differ-
Species
ent microRNAs
Arabidopsis 187
Nematode 156
Drosophila 152
Mouse 547
Human 706
AG04 DNA
Epigenetic
changes
24nt
ds-RNA DCL3
DCL1
DCL2 DCL4
21nt
miRNA
AG01
22nt 21nt
AG01 AG01
mRNA cleavage
What Will
They Say?
Jill Tarter
P
lanning for the successful detection
of a signal from extraterrestrial intelli-
gence covers the territory from making
sure there is champagne on ice at the
observatory to trying to figure out how to hold
a global conference where all cultural, histori-
cal, religious, political, and creative traditions,
that are embodied by humans on planet Earth,
can be represented in a discussion of whether
and how we might reply. Science fiction and
the motion picture industry have provided lots
of scenarios depicting the aftermath of signal
detection, many are unrealistic, many are not
very satisfactory, almost all reflect the political
tensions around the globe at the time they were
created. What should we, the scientists who
are attempting to detect a signal, set out as our
protocol for behavior? At the SETI Institute,
we’ve spent some time thinking about these
questions; both before 1993 when we were
funded by NASA (a federal agency), and after,
as we raise private and corporate contributions
to continue the search efforts.
The protocol fluctuates over time, as we have
more experience with false-positive detections,
as our search efforts evolve, as humans around possibility of negative reaction to the message
the world becomes more aware of our explora- transmission. And there was a lot of reaction.
tory research, and as technology flattens the The most prominent critic of the Arecibo mes-
world and offers both solutions and challenges sage transmission was the British Astronomer
to global communication. This chapter will Royal, Sir Martin Ryle, who wrote to Drake and
give an overview of current plans, and future the newspapers complaining that it was “very
projects, all of which are based upon the con- hazardous to reveal our existence and location
viction that information about the detection of to the Galaxy; for all we know, any creatures
a signal and any information encoded within out there might be malevolent - or hungry.”
a signal are the property of all humankind. This criticism ignores the fact that it is already
Furthermore, it is important to state up front too late to conceal our presence; the Earth has
that in those places in this chapter where been ‘leaking’ signals into space for nearly a
opinions are presented, usually in the absence century, via our broadcast radio and TV signals.
of data, the opinionated statements strongly However, Prof. Ryle’s comments do mark the
reflect the biases and views of the author, a inception of a discourse on the merits of active
scientist who continues to be impressed by the transmission vs. passive SETI listening. In turn,
tyranny of light speed – it’s currently impos- this discourse raises the questions: if we ever
sible for us to get ‘There’ and it may be hard for decide that it is appropriate to transmit, either
‘Them’ to get here. ab initio or as a reply to a message received in
the future, then who should speak for Earth
Introduction: The and what should they say? These are big ques-
Arecibo Message tions, and of the type not routinely discussed
in the course of doing scientific research – but
In 1974, the large radio telescope in Arecibo, they come to the forefront very quickly when
Puerto Rico was upgraded with both a new the science is SETI. Is Ryle right, was Drake
surface of perforated aluminum panels and a putting the Earth (and you and me) in great
new radar transmitter working at a frequency peril by transmitting the Arecibo message?
of 2380 MHz. To mark the completion of
the upgrade project, Frank Drake, then the All Intelligent Civilizations
Director of the Observatory, decided to hold a
commissioning ceremony during which the ra-
Are Not Equal
dar transmitter was used to transmit a message Should active transmission be a part of SETI?
to space. The Arecibo telescope does not point SETI research is currently being carried out in
very far away from the zenith direction, and the several locations worldwide, occasionally even
ceremony and transmission were timed to coin- in Australia. I work at the largest of these re-
cide with the arrival of the Governor of Puerto search facilities, the SETI Institute, a non-profit
Rico. This meant that the direction towards corporation in Mountain View, California.
which the message was transmitted was a large We have grown steadily since we opened our
globular cluster of stars called M13 that hap- doors in 1984, and now typically have about
pened to be overhead at the appropriate mo- 150 people working at the Institute, but only a
ment, even though those stars were more than handful work with me in the Center for SETI
25,000 light years away, and any inhabitants of Research. The rest of my colleagues pursue
that region would not receive the message until astrobiology in the Carl Sagan Center for the
the year 26,974 AD! The message consisted of Study of Life in the Universe, or education and
1679 bits (1’s or 0’s represented by the switch- public outreach in our E/PO Center.
ing between two closely spaced frequencies)
In 1997, the SETI Institute convened a series
and was repeated twice, lasting only a few min-
of workshops that, among other things, seri-
utes. More about the content of that message
ously discussed the appropriate guidelines for
later, for now it is the act of sending a message
interstellar discourse. The results of those dis-
that is of interest. Perhaps Prof. Drake chose
cussions are part of a book, titled SETI 2020.
such a distant target because he anticipated the
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 117
The SETI 2020 workshop participants sug- Although it could happen tomorrow, detection
gested that ‘international consultation and ap- of a signal that raises the question of a reply
proval’ should be sought prior to undertaking will probably require a lot more searching than
a transmitting strategy, and they assumed that we’ve done to date. And no, I don’t think that
such approval would come from ‘appropriate they will arrive in shiny spaceships any time
international administrative bodies’. In much soon (and there’s no solid evidence that they’ve
earlier scientific discussions conducted under done so in the past either!) But you might be
the auspices of the International Academy of interested to know that at this very moment,
Astronautics and the International Institute of messages are deliberately being broadcast into
Space Law, scientists, diplomats, and lawyers space by dozens of entrepreneurs, who have
interested in SETI had drawn up an informal acquired access to decommissioned telecomm
protocol with the impressive title “Declarations transmitters around the globe. What messages
of Principles Concerning Activities Following are they sending? The transmissions are the
the Detection of Extraterrestrial Intelligence personal wisdom, philosophies, hopes, fears,
” which also presumed a measure of interna- and fantasies of those individuals that the vari-
tional approval. In that protocol, the text of ous marketing web sites have persuaded to part
Article 8 stated “No response to a signal or with some cold hard cash. I’m not kidding;
other evidence of extraterrestrial intelligence search the internet for yourself. But I wouldn’t
should be sent until appropriate international waste your money. There is little chance that
consultations have taken place. The procedures your message to the cosmos will be received.
for such consultations will be the subject of Those transmitted signals are relatively weak,
a separate agreement, declaration or arrange- and they are far too ephemeral to represent a
ment.” Most scientific teams conducting realistic active-SETI transmission program. It
SETI observations adopted this protocol as is the short-lived nature of these and previous
their own policy. In 2000 the United Nations transmission activities that convinces me that
Committee on the Peaceful Uses of Outer Space a realistic, active-SETI program is far in the
was informed of this protocol, and documents future, even if a global conversation should
were formally filed away, perhaps for action at conclude that it’s a good idea.
some future time. Today, we still have no global
Humans, at this stage of our evolution, aren’t
form of governance, there are no appropriate
very good at conceiving and fulfilling five-year
international administrative bodies that can
plans, and our success with 100 or 500-year
speak for all humans. Nevertheless, in ways
plans is pretty pathetic! If we Earthlings plan
not imagined even a decade ago, all humans
to conduct a systematic, active-SETI program,
may soon be able to speak for themselves using
it will be necessary to keep at it for many
social-networking technologies that are rapidly
thousand years, or more. That’s because a
becoming global in what appears to be a viral,
transmission program that lasts n years will
and unstoppable spread. Before too long, it
generate signals that travel through space, at a
will be possible to have a global conversation
rate of one light-year (~ 9.5 trillion kilometers)
with all cultures, traditions, ideologies, and
per year, growing weaker as they propagate
points of view participating. And note that it
and spread out, until they reach a potential
will be YOUR generation that is having this
recipient who is d light years away. The signals
conversation, not MINE. I can raise the issues
will be detectable by that recipient for only n
in this chapter and encourage you to prepare
years. That means that during the evolutionary
to answer them, but it is you and the rest of
history of the potential recipient, they must
the younger global inhabitants that will need to
be looking at Earth, with the right receiv-
feel your way forward towards an outcome that
ing tools, during the n-year window that the
represents all humans. It will take a while, and
signals present themselves. Unless n is a very
I think that technology will continue to assist
big number, the chances that the recipients are
the process in unforeseen ways (Twitter and its
looking Earthward when our signal arrives will
descendants might do this), but you probably
be very small (see Figure 1).
have time to be deliberate.
Therefore, I think that active-SETI programs future, civilization-ending impact from a giant
will have to wait until humans “grow up” asteroid might be to spread humans to at least
enough to be able to conceive and execute very one other planet. We’re looking hard at Mars
long term projects. as that destination. Just because we can do so,
should we do so? In truth, we’ve already made
Are other scientists dealing with these kinds of
similar decisions for planet Earth. We are rou-
questions? A close parallel in terms of moral,
tinely destroying rain forests and other habitats
ethical, and risk-appraisal discussions are the
in order to benefit some groups of humans
very active debates now taking place within
economically, at the expense of an uncounted
the small portion of the scientific community
number of species of life that we have yet to
involved in Planetary Protection. Among the
discover in those wild habitats. If we eliminate
astrobiologists at the SETI Institute, there are
unique and undiscovered forms of life on this
some researchers who worry about the poten-
planet, then there should be no reason not
tial for forward and backward contamination
to do the same on Mars. Or if we decide to
of life on Earth due to the planned robotic and
preserve Martian life forms because they are
human explorations of other bodies in our own
precious, then shouldn’t we preserve precious,
Solar System. Although we now contemplate
as yet unknown, life forms on Earth? These are
the possibility of microbial life in the briny
not questions that any of my colleagues and I
oceans beneath the frozen ice surfaces of the gi-
debated when we were in graduate school, but
ant moons of Jupiter (Europa, Ganymede, and
scientific exploration is taking us in new direc-
Callisto), and perhaps even Saturn’s tiny moon
tions, and as a result we need to expand the
Enceladus, the focus of concern over con-
boundaries of what it means to do science.
tamination is primarily Mars. Might microbes
brought back from Mars threaten life on Earth,
or might terrestrial organisms brought to Mars How Do You Speak To An Alien?
by human and robotic explorers contaminate Let’s return to the 1974 Arecibo message. A
that planet and threaten any native Martian life nice explanation of the components of the
forms? If life exists in liquid aquifers beneath Arecibo message appears on the Wikipedia web
the frigid desert surface of Mars, might it pose a site http://en.wikipedia.org/wiki/Arecibo_mes-
danger to life on Earth? sage. As previously mentioned, the message
Do humans have the right to ‘terraform’ Mars consisted of 1679 bits, and the transmission
in order to make that planet more habitable for was repeated twice. The repetition is impor-
us? One way to improve the chances for sur- tant, because it lets the recipient know that
vival of the human race, and protect it against a they got it all. The number of bits is important
because it helps to decode the message. 1679
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 119
is the product of two prime numbers 23 x 73. columns (see Figure 2) yields a definite pat-
Our concept of numbers and mathematics tern, even if not an obvious message, whereas a
encourages us to think that any extraterrestrial 73-column display looks pretty random.
technology will have a way of counting, and
So what did the Arecibo message say? In ad-
that numbers will be prime in their numbering
dition to assuming that we have mathemat-
system as well as in ours. On this planet we
ics in common with the recipients trying to
have now documented an isolated Amazonian
decipher this message, the message also made
community whose language and thought
use of the fact that anyone receiving the mes-
patterns do not include this sort of detailed
sage would have had to detect it with a radio
numerology, there are no words for the quan-
telescope and would realize that the message
tity of objects or specific numbers. But these
had been transmitted at a particular radio
people have not constructed transmitters or
frequency, or wavelength (wavelength = c/
receivers for interstellar communication. Our
frequency = 12.6 cm, where c is the speed of
bias is that mathematics will be universal for
light). The wavelength therefore is a shared
any technological civilization, but we should
unit of measurement, a common ruler. So the
try to remember that it is in fact a bias. Our
message starts out (if your custom is to read
stereoscopic, binocular vision system provides
from top to bottom) with a counting lesson,
us with depth perception, and the evolution
showing the graphical, binary representation
of our brain and our training allow us to in-
of the numbers 1 to 10. These numbers are
terpret two-dimensional representations, or
then used to give the atomic numbers of the
abstractions of information. This may not be a
biogenic elements H, C, N, O, P – the stuff our
universal capability of all technological civiliza-
DNA is made from! Next comes the formulas
tions either, but we find it hard to imagine any
for the base pairs of Adenine, Thymine (A-T),
other way of perceiving detailed information,
and Cytosine, Guanine (C-G) along with the
and so the Arecibo message incorporates this
dioxyribose-phosphate backbone of DNA, and
bias as well. What can you do with the product
a representation of its double helix structure,
of 23 and 73? You could take a linear string of
and an estimation of the number of nucleotides
1679 bits and rearrange it into 73 columns and
in the human genome (not yet sequenced
23 rows, or 73 rows and 23 columns to make
when this message was sent). The population
a two-dimensional picture, using two different
of humans on Earth (only 4 billion in 1974),
colors for the two different binary bits. In the
a human stick figure with a measurement bar
case of the Arecibo message, the choice of 23
indicating the human is 14 wavelengths tall.
A cartoon of our solar system, with the third
planet from the Sun offset towards the human,
indicates where the message came from. Finally
(or first if your custom is to read bottom up)
the spherical Arecibo telescope and the trans-
mitted message rays are depicted with a blatant
brag that it is 2430 wavelengths in diameter. A
pithy message, perhaps not easily understood;
also perhaps not what you might have chosen
to tell others about us. We’ve made a few more
attempts, not with transmitted signals, but with
greeting cards carried by spacecraft.
In 1972 and 1973, NASA launched the Pioneer
10 and 11 spacecraft to explore Jupiter and
Saturn. But they didn’t stop there; these space-
craft had sufficient energy to allow them to
Figure 2: 1974 Arecibo message arranged leave the solar system and travel towards the
in 2-dimensions, and decoded. stars (slowly – it will be millions of years before
either vehicle approaches a star). Once it was to realize that radio astronomical pulsars each
understood that these objects would travel into have unique periods for their pulses, and that
interstellar space, Carl Sagan convinced NASA with age pulsars spin down and their pulse
to include a plaque on each to send a message rates slow. The directions from the map center
to any distant technologies that might happen show the radial directions away from Earth
to discover them (see http://en.wikipedia.org/ in which the pulsars lie, the length of the line
wiki/Pioneer_plaque). These plaques include represents their distance, and the binary code
a handy ruler, though this time it isn’t based along each line gives the precise pulse period
on the frequency of a radio transmission, but (in time units of 1/frequency = 7 x 10-10 sec)
rather the frequency of the fundamental spin- at the epoch of spacecraft launch. There is a
flip transmission of the hydrogen atom (1420 15th leg, without a binary period, and that
MHz or a wavelength of 21 cm) which is the shows the distance and direction from Earth to
most abundant and simplest element in the the Galactic center. In the early 1970’s much of
universe. Figure 2 has a diagram of the space- the public and media seemed more concerned
craft with humans beside it for scale and their with the naked bodies on this plaque than with
height given in wavelengths. The human male the content of the message!
has his hand raised in greeting (or perhaps
In 1977 NASA reused this pulsar map, and
it means something else to those who might
the hydrogen line as part of the covers for
eventually find it). The solar system is shown
a two golden records containing the sights
with an indication of the spacecraft’s trajectory.
and sounds of Earth that were attached to
The 14-legged spider is actually a map that says
the Voyager 1 and 2 spacecraft (the offend-
where and when in the galaxy this craft was
ing naked humans occur only in the encoded
launched. The key to deciphering the map is
information on the record itself, see http://
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 121
en.wikipedia.org/wiki/Voyager_Golden_ life on Earth; it is hugely biased towards hu-
Record). The Voyagers also left the solar system mans, with little regard for the enormously im-
after completing a grand tour of the outer portant and diverse microbial community with
planets, and since they are traveling faster than which we share our world, or the other ani-
Pioneer 10 and 11, they are now the most mals, but then it is the humans who built the
distant objects made by humans, and their tra- spacecraft. The image set contains no poverty,
jectories will take them to the vicinity of nearby hunger, disease, war, pollution, deforestation,
stars in less than 100,000 years. Since a record overcrowding, or any other indication of a less
afforded much more opportunity for includ- than perfect world. We can expect that if the
ing information about us, a committee chaired Voyagers are ever found by another technologi-
by Carl Sagan was created to decide upon the cal civilization, and the contents of the record
content. The record contains greetings from are ever deciphered, they will probably realize
the children of Earth in 55 different languages, that we were putting our best foot forward.
as well as a message of peace from the then Quite apart from the technical difficulties, and
President of the United States, Jimmy Carter. the truth in advertising issues, the images that
90 minutes of music, believed by the commit- are included tell us humans a great deal, but
tee to be a fair representation of the musical they require a shared contextual background
history and traditions of Earth, are included for interpretation. We take that context for
for the discovers’ listening pleasure (should granted, indeed it is very difficult to ignore or
they have ears or other appropriate acoustical unlearn what it is we’ve evolved to interpret.
sensors), as are dozens of natural and human- Perhaps young children have the best capacity
created sounds of the planet. 115 drawings and for ignoring what they ‘know’ and seeing these
photographs are encoded as analog signals on images as others, who are not us, might do. As
the record (the record cover explains how to an example take one particular image of sprint-
recreate the images), and these can be viewed ers in the Olympics, rather than seeing the im-
at http://voyager.jpl.nasa.gov/spacecraft/scenee- age as depicting great athletic prowess, a child
arth.html. In true form, the committee created might ignore the notion of distance perspective
an edited, approved, and highly biased view of and see instead two species; the big and the
Figure 4: Successful detection of the carrier signal from the Voyager 1 spacecraft at a
distance of 106 AU
small. The big species is strange because it is this spacecraft repeatedly to insure that our
not quite bilaterally symmetric; each individual beamformers and control and detection soft-
has only 1 ½ lower limbs, and it isn’t always ware are all working like they should. Figure
the same side that is missing half a limb. And 4 presents a ‘waterfall plot’ showing a small
of course most children can delight in the fact piece of the spectrum surrounding the Voyager
that this home planet has invented anti-gravity, 1 signal as a function of time. Each point on
because none of the big species is touching the this plot represents a 1 second observation with
ground! As the committee members confessed, spectral channels that are each 1 Hz wide. The
this exercise was as much an effort intended for Green lines are intended to focus your eye in
humans as for extraterrestrials. Billions of years the right place. This signal is hard to detect
from now, when the Sun has evolved into a red with the naked eye, but Figure 5 illustrates
giant and the Earth has been consumed within that it is easily detected with the SETI special
its atmosphere, the Voyagers will preserve this purpose signal detection software – assuming
flattering encapsulation of the aspirations of everything is working properly. Some day we
those who built these craft. hope to detect such a signal from someone
else’s technology.
At the SETI Institute, we have another relation-
ship with Voyager 1 – we use it as our fiducial
or standard candle on the sky. Because it is so Earth Speaks
far away, the carrier signal that it emits to en- In 2009, the SETI Institute participated in the
able NASA to track its motion, and downlink Kids Science Challenge contest [http://www.
its data, arrives at the Earth as a very faint sig- kidsciencechallenge.com/], in which young
nal moving on the sky at nearly the same rate students were challenged to help us figure
as the distant stars. In fact that’s what we might out ways to make our search for ET better.
expect a signal from ET to look like, and we’ve The winner, Kamau Hamilton a 6th grade
built very sensitive signal detection equipment student from New York City, suggested that
to detect such emissions. As we have been extraterrestrials might not speak English, so
commissioning the Allen Telescope Array over that we should plan on communicating with
the past year, we’ve pointed our 42 dishes at the sounds of Earth. He was too young to have
SETI - Planning for Success: Who Will Speak to Earth? What Will They Say? | 123
known about the Voyager golden record, but he
independently came up with the same idea. We
invited Kamau to record sounds of Earth that
hadn’t existed in 1977, and we used his visit
to the SETI Institute to launch a web-based
project we’ve been thinking about for a long
time. This is a first tiny step towards holding
a global conversation to answer the questions:
who will speak for Earth and what should they
say? My colleague, Douglas Vakoch a social
scientist, has been wondering whether there
are any cultural universals (ideas, practices,
memes) that can be found in every human
group around the globe, now and perhaps
throughout time – things that really belong in
a message to ET if we want to define who we
are. Earth Speaks [http://earthspeaks.seti.org/]
is a web site on which we’ve posted Kamau’s
sounds of Earth. Now people around the world
are encouraged to contribute their own sounds,
peculiar to their locality, and their ideas of what
we should say or would like to say in a mes-
sage to an extraterrestrial to this web site. We
don’t have any plans to actually transmit these
messages, rather the content of these submis-
sions are being categorized and tagged with
key words and with region of origin as part of a
research project to uncover cultural universals.
The posts have been fun to read, one of my
early favorites ended with “… Also, don’t kid-
nap us and poke us. We hate that.”
Now that you have finished this article, you
can help us plan for success. Please go to the
Earth Speaks website and let us know what you
think should be contained in a message from
humans to extraterrestrial intelligence.
The research described in this paper was carried out at the Jet Propulsion Laboratory,
California Institute of Technology, under a contract with the National Aeronautics and
Space Administration.
Copyright 2009 California Institute of Technology.
Government sponsorship acknowledged.
U ntil that night, I had thought
that moments frozen in time
where your life flashes in
front of you only occurred
in the movies. I glanced down at my watch.
In California, it was 8:40 p.m. on January
3, 2004, and it seemed as if we had hit the
ground over an hour ago. In reality, our rover
Spirit had landed on Mars only five minutes
ago, but its radio beacon was nowhere to be
heard. We had no idea whether Spirit was safe-
ly on the ground, but unable to communicate
for reasons unknown, or whether the rover’s
tiny electronic heartbeat had been terminated
by an untimely demise.
I looked down at my display console in
the mission control center at the NASA Jet
Propulsion Laboratory. My boss, Rob Manning,
was sitting next to me. He called up a window
with a plot of Spirit’s signal strength as a func-
tion of time. I was frantically pointing to the
flat line indicating a zero signal at the current
time. Manning, an eternal optimist, and a virtu-
al legend within the NASA robotic space flight
community by virtue of having pulled off the
only previous Mars landing in recent history, 40 months prior was clouded with uncer-
calmly pointed to a blip on the graph repre- tainty about the future. Spectacular success
senting a point in time somewhere in the past. from the Independence Day landing of Mars
Pathfinder in 1997 was followed by the em-
Unfortunately, we had no idea whether the blip
barrassing crash of the Mars Polar Lander
indicating a positive radio signal was before or
shortly before its scheduled touchdown in
after the expected landing time. If it were after,
December 1999. Subsequently, NASA manage-
then we would have had positive evidence that
ment in Washington put all future Mars shots
Sprit had at least survived the initial impact.
on hold due to a loss of confidence in the
The problem was that in our haste to get the
once-proud program.
mission control display software ready for
landing day, we had forgotten to program the In early 2000, a small group of respected en-
computer to stamp the tick marks on the graph gineers, including Manning and future Spirit
with the time of signal receipt. There was no mission operations manager Mark Adler,
way to tell for certain. concocted a seemingly innocuous proposal to
achieve redemption. Their theory was seem-
I looked around the mission control room and
ingly simple and foolproof. Why not re-fly the
saw seemingly optimistic faces, but they were
same landing system that led to the wildly suc-
somehow unable to mask uncomfortable body
cessful Mars Pathfinder landing back in 1997?
language present only when one has a knot
Unlike the ill-fated Polar Lander, Pathfinder
in the pit of their stomach. The supremely ar-
was a proven landing system. “We even have
rogant side of me wanted to tell everybody to
spare parts left over,” they argued.
have a little faith that Sprit was still alive. The
other side of me was experiencing the so-called The catch was that the payload Pathfinder put
“life flashback” phenomena. I was mentally on the surface, a small pyramidal-shaped base
reviewing every decision we had made over the station barely knee-height in size, and a six-
previous 40 months of designing, building, and wheeled rover the size of a small laser printer,
testing the landing system for the rover and be- was scientifically uninspiring with respect to a
ginning to second-guess a fair number of them. second flight. Back in 1997, the goal was sim-
ply to demonstrate that NASA was still capable
One of my first thoughts was to question
of landing something on Mars despite having
whether we should have even attempted
not done so since the Viking missions back in
something this ambitious on such a short time
1976. However, the unwritten laws governing
scale. Unfortunately, we did not have much
efficient use of exploration funds mandated
of a choice. The world of Mars exploration
that the next mission following Pathfinder
not only land safely, but deliver more ad-
vanced science.
“No problem,” countered Manning and Adler.
What if the small base station and tiny rover
was replaced with a single, larger rover capa-
ble of roaming a kilometer from the landing
site over a period of 90 days? For a science
payload, Manning and Adler proposed to tap
into the ingenuity of professor Steve Squyres
from Cornell University. Squyres was a well-
respected geologist who was in the midst of de-
veloping a sophisticated set of tools for a future
mission to return Martian rocks to Earth using
robotic vehicles. These instruments would
allow the rover to both remotely sense the
NASA/nasaimages.org
chemical composition of rocks and drill into
NASA/nasaimages.org
50 test drops between 2001 and 2003 to arrive and put the vehicle at risk of deploying the
at a viable concept. That final design consisted parachute too close to the surface. After a lot
of eight layers of Kevlar in vulnerable areas to of debate with uncertain facts, we made the
keep rocks from penetrating the inner bladder decision to reprogram the flight computer
of inflation gas. And, in a desperate schedule again. This time, we asked it to deploy the
situation similar to the parachute, the actual chute earlier, and while at a faster velocity, to
flight airbags bound for Mars were delivered di- compensate for the thin atmosphere. The down
rectly to the Kennedy Space Center rather than side was an increase in risk to ripping the chute
to the spacecraft assembly facility in California. due to excessive forces during inflation.
With the myriad of technical challenges to Yet another serious problem surfaced with one
overcome on both the landing system and week to go prior to landing. Jason Willis, one
rover side of the design, Spirit and Opportunity of our lead avionics engineers, discovered a
barely made it to the pad in time for their lift- serious flaw in the electronics responsible for
offs in June and July 2003, respectively. After triggering pyrotechnic initiated events such
our hardware left the Earth, I had mistakenly as parachute deployment, heatshield jettison,
thought that we were looking at seven easy and airbag inflation, and retrorocket ignition.
quiet months in transit to Mars. In retrospect, Normally, the flight computer arms these pyro-
I should have realized that our experiences technics for firing only seconds prior to use for
over the past 33 months were an indicator safety reasons. Test results from our high fidel-
that nothing came easily on this mission. In ity electronics testbed indicated a subtle timing
fact, the time between launch and landing bug in the circuit that caused the arming com-
amounted to some of the busiest moments dur- mand to be ineffective. The only viable solution
ing the mission. was to order the flight computer to remove the
safety inhibits and enter the atmosphere with
One of the first things we discovered after
all the pyros dangerously armed.
launch was that our predictions of the vehicle
dynamics during retrorocket firing failed to ac- And, just when I thought we were finally ready
count for all the force disturbances in the sys- despite the risky solutions we were forced to
tem. So, we went out into the California desert implement, I received a phone call from lead
over the summer of 2003 to perform full-scale flight dynamics engineer Prasun Desai the night
test firings in order to gather data that allowed before Spirit’s landing. Right when I was sit-
us to reprogram the flight computer to com- ting down to watch a football game to unwind,
pensate. Then, a few days prior to Christmas, Desai informed me that the team had just
a huge dust storm developed on Mars. This found a programming error in the sophisticated
storm effectively thinned the Mars atmosphere simulations we had been using to prove to
More Objections
Real Conspiracy
Theory
References
‘Apollo Moon Landing — A resource for understanding
the hoax claims: did man really walk on the moon?’,
National Space Centre, UK: www.spacecentre.co.uk.
Matthews, Robert & Allen, Marcus, ‘Hot debate: did America
go to the moon?’, Focus, February 2003, pp. 73–76.
Jill Tarter
W
e discovered the very first plan-
etary worlds in orbit around
a body other than the Sun in
19911. They were small bod-
ies (0.02, 4.3 and 3.9 times as massive as the
Earth) and presented a puzzle because they or-
bit a neutron star (the remnant core of a more
massive star that had previously exploded as a
supernova) and it was not clear whether these
bodies survived the explosion or reformed from
the stellar debris. They still present a puzzle,
but today we know of more than 350 other
planetary bodies in orbit around hundreds of
garden-variety stars in the prime of their life
cycle. Many of these planets are more massive
than Jupiter, and some orbit closer to their host
stars than Mercury around the Sun. To date we
have not found another planetary system that
is an exact analog of the Earth (and the other
planets of our solar system) orbiting a solar-
type star, but we think that is because we have
not yet had the right observing instruments.
Those are on the way! In the next few years,
we should know whether other Earth-mass
planets are plentiful or scarce.
At the same time that we have been develop- when I submitted this manuscript, and when
ing the capabilities to detect distant Earths, we you are reading it. Today the tally is 353 plan-
have also been finding that life on Earth occurs ets orbiting 294 bodies (including those puz-
in places that earlier scientists would have zling pulsar planets).
considered too hostile to support life. Scientists
Exoplanets are primarily detected by indirect
were wrong, or at least didn’t give microbes
techniques: astrometry, radial velocity studies,
the respect they deserve. We now know that
transits, and gravitational micro-lensing. The
extremophiles can exist (and sometimes thrive)
first two of these detection methods measure
in the most astounding places: at the bottom of
the reflex motion of the star due to the mutual
the ocean around hydrothermal vents, in ice,
gravitational attraction between planet and
in pure salt, in boiling acid, and irradiated by
star; the third measures the minute diminution
massive doses of UV and X-rays. There do ap-
of brightness that occurs periodically when a
pear to be places on Earth that are too dry for
favorably aligned planet passes between its star
even these (mostly microbial) extremophiles, or
and our telescope, blocking some of the star’s
perhaps our sensors aren’t yet sensitive enough
light; the final method measures the brighten-
to find them.
ing of a distant star when another (unseen)
Since life-as-we-know-it is so extraordinarily star and its orbiting planet align perfectly and
hardy, might it exist today (or in the past) on the gravitational masses of the star and planet
any of the exoplanets that are being found?.A bend the light from the distant star causing it
group of scientists known as astrobiologists are to appear brighter. Only very recently have we
trying to answer that question. This lecture will actually seen images of objects we believe to
discuss what appears to be possible in the near be planets in orbits around stellar hosts. The
future, as well as the questions that will likely Hubble Space Telescope was used with a cora-
remain unanswered until new technologies nographic mask to block out the light from the
enable new explorations in the more distant star Fomalhaut (think of holding up your hand
future. It might even turn out that our first in- to block out the light from a distant street light
dication of another inhabited world will be the while you look for something faint in the area
signals deliberately generated by its inhabitants surrounding your hand). In 2004 observations
– that’s right, SETI, the search for extraterres- showed a small (single-pixel) bright object
trial intelligence. located in a large disk of dust, far from the star
(115 astronomical units from the star, or 115
Exoplanets times as far from the star as the Earth is from
the Sun). This object was confirmed as a planet
In his book Plurality of Worlds, Steven J. Dick2 Fomalhaut b when an HST 2006 observation
has chronicled the millennia of discourse about showed that it had moved slightly along a
other inhabited worlds, based upon deeply believable orbital track. A series of rapid im-
held religious or philosophical belief systems. ages of the star HR 8799 using a groundbased
The popularity of the idea of extraterrestrial telescopes allowed observers to remove the
life has waxed and waned and, at its nadir, put effects of atmospheric distortion and to im-
its proponents at mortal risk. Scientists at the age 3 giant-planet point-sources orbiting at
beginning of the 21st century have a marvelous distances of 24, 38, and 68 AU, far from the
opportunity to shed light on this old ques- star. The smallest mass planet to date (exclud-
tion of habitable worlds through observation, ing those puzzling pular planets) orbits the
experimentation, and interpretation, without very low mass star Gliese 581, and has a mass
recourse to belief systems and without risking of 1.9 Earth masses. The reflex motions of the
their lives. A good place to keep track of the star that are induced by the planetary orbit are
newest planet discoveries is the interactive cata- greater and easier to observe if the star mass is
log of the Extrasolar Planet Encyclopedia web small. What we haven’t found is a planet like
site http://exoplanet.eu/catalog.php. At a glance the Earth orbiting its star at just the right dis-
you will be able to see how many new planets tance so that its surface temperature might be
have been announced in the time between
The research described in this paper was conducted within the Constellation
program at the National Aeronautics and Space Administration.
Copyright 2009 California Institute of Technology.
Government sponsorship acknowledged.
Image courtesy NASA/John Frassanito & Associates
I magine waking up after eight hours and
floating down off your bunk onto the
floor. You bounce down the hallway
to the food station where you make a
hot cup of instant coffee and hydrate your pre-
packaged breakfast before quickly showering
and checking in with mission control. Passing
by a small window in the corridor, you pause
for a moment and take in the magnificent
desolation surrounding the outpost. Lucky for
you, your lunar base location also provides
for a spectacular view of Earthrise out of a
small window. You have been anxiously await-
ing today because you are headed out on an
enclosed, pressurized dune buggy to monitor
the cargo offloading of a resupply lander that
arrived a day ago. It brought not just logistics
(food, water, supplies), but also a new and im-
proved in-situ resource tool that should make
helium-3 harvesting three times faster than
what the outpost can process out of the lunar
rocks and soil today.
Sound like science fiction? Exciting? By 2024
the United States, along with the help of
international partners, plans to establish a
permanent outpost on the moon where we proper operational functionality before setting
master how to function and survive in a new course to intercept the moon.
and harsh environment far from home. The
Three days later, the crew is prepped and ready
Constellation Program, NASA’s implementation
to transfer into Altair, the vehicle that lands on
of the bold policy for American space explora-
the surface, while Orion stays in orbit for the
tion in the 21st century, is currently developing
duration of their stay on the moon. In conjunc-
and testing new technologies to enable multiple
tion with many “go’s” from mission control,
astronauts to live and work on the moon, or
the vehicles separate, and Altair positions itself
places even further away such as Mars. The
to align with the desired landing site. A high-
moon has no breathable atmosphere, tempera-
thrust engine burn slows the 45,000-kilogram
tures that range from +100 to -173 °C on a
vehicle down from orbital velocity to a compa-
daily basis, and gravity only 1/6 that of Earth’s.
rably slow 1 meter per second at touchdown in
Though we have sent humans to the moon
approximately 14 minutes. The initial missions
before, we did so for a very limited amount of
are expected to last for seven days on the sur-
time and with limited capability to explore. By
face, allowing the crew to explore scientifically
increasing requirements such as the number
interesting and challenging locations on the
of astronauts we want to send simultaneously,
moon such as ice, geographic formations, and
the locations we want to visit, the amount of
unique mineralogical terrain. Future missions
time we want to stay, and the goals we want to
are more focused on assembling and utilizing
accomplish, there are many details and exciting
the outpost. Once established, mission dura-
technology challenges waiting to be solved in
tions may last for up to 210 days at a time.
the next decade before we launch.
The Exploration Systems Architecture Study
How do we get there? performed by NASA identified ten preferred
Constellation’s purpose is to execute a challeng-
ing space-faring plan that includes developing
and operating spacecraft for transportation to
and from the moon, and resources to sustain a
semi-permanent human presence on the lunar
surface. Two primary spacecraft, Orion and
Altair, serve as the backbone of the program’s
transportation architecture. Orion, a dual-pur-
pose vehicle for missions to the International
Space Station (ISS) as well as lunar orbit, is
responsible for the safe launch and return of
the crew to Earth. Altair’s primary purpose is
to take the crew down to the moon’s surface, as
well as any cargo that needs to be transported,
and then safely launch the crew back into low
lunar orbit (LLO) to mate with Orion for the
journey home. Each spacecraft utilizes a dif-
ferent launch vehicle to boost it into space: the
Ares I for Orion and the Ares V for Altair.
Orion and Altair are designed to launch within
90 minutes of each other from the same launch
pads currently in use by the Space Shuttle
at the Kennedy Space Center in Florida. The Figure 1: Shackleton Crater taken by
two vehicles plan to mate in low Earth orbit the European Space Agency’s SMART-1
(LEO) where the crew checks out both to verify spacecraft in January of 2006.
ESA/Space-X (Space Exploration Institute)
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locations of interest on the moon based on ei- to the ISS. Because of the relative difficulty
ther scientific rationale such as geomorphology, in executing a lunar mission, Orion is being
or for exploration to seek out elements avail- developed in two phases known as “Block 1”
able for resource utilization. The Aitken Basin and “Block 2.” This two-phase development
at the lunar south pole is one of these locations. scheme allows the design to quickly reach ini-
It is the largest and oldest basin known on the tial operating capability for Shuttle replacement
moon, and the primary conceptual destina- by 2015, but incorporate the more technically
tion for an outpost. Shackleton Crater (Figure challenging upgrades for lunar missions a few
1) is a point of interest internal to the Basin. years later. The major difference impacting
Its center is completely shadowed year round vehicle design for the lunar upgrade is the du-
resulting in temperatures near -170 °C, while ration for which the system must remain func-
its raised edges see almost perpetual sunlight, tional. The short-duration lunar stays where
a noteworthy feature due to the feasibility of astronauts operate in a science-gathering mode
using solar cells for power generation. At 19 last for seven days on the surface, resulting in a
kilometers across, relatively small for a lunar total Orion mission duration of approximately
crater, it is one of many difficult places to land, 16 days. For the long-duration mission where
but is an exciting destination due to the po- astronauts spend up to 210 days at a lunar
tential presence of ice in the crater that could outpost, Orion must remain in orbit around the
provide life-sustaining resources for an outpost. moon that much longer before returning the
crew home. (Figure 2).
Orion For a crewed lunar mission, the astronauts
Orion, currently being developed by Lockheed launch from Earth to LEO in the Orion vehicle.
Martin for NASA, has the responsibility for not (Figure 3). Once in LEO, the crew performs
only transporting four astronauts to the moon a precision docking maneuver to mate Orion
and home again, but also taking over the Space with Altair prior to heading for the moon. In
Shuttle’s role of ferrying six crew members today’s concept, the crew has access to Altair
Figure 3: Orion vehicle in low earth orbit with solar arrays deployed.
NASA/John Frassanito & Associates
Figure 7: The Ares V approximately 6 seconds after ignition as it lifts from the launch
pad at Cape Kennedy. Image courtesy NASA/John Frassanito & Associates
Surface Systems
The technologies to sustain life on the moon
and beyond are in the earliest stages of devel-
opment, but already have some very exciting
prototypes under test in exotic locales such as
the Mojave Desert and Antarctica. One element
of living on the moon is mobility, both for
people and objects such as science experiments
and living quarters. The moon, while much
smaller than the Earth, is still a large place to
explore. The Apollo astronauts walked around habitat location. Today’s rover concept is a six-
in spacesuits, and used their “open air” lunar legged vehicle with 12 wheels. The prototype
rover to explore up to a few kilometers from was recently taken out to the Arizona desert
the landing site. Constellation astronauts can where engineers tested it to understand its
also perform walking excursions near the land- maneuverability, obstacle avoidance capability,
ing location, but a small enclosed rover is being and ease of controllability.
designed to provide a shirt-sleeve environment
Similar to the enclosed rover, the design of the
for two crew to live for days at a time while
habitats and workspaces is challenging due the
driving 20 to 30 kilometers away from the
Melanie Manetsch
Emma E. Ramsay
Alaina J. Ammit
A sthma is a chronic disorder of
the airways affecting millions of
people worldwide. Airways are
remodelled, or thickened, result-
ing in airway obstruction and a decline in lung
function. Airway remodelling is considered
to be a consequence of long-term inflamma-
tion. As the current drugs for treating airway
remodelling have side effects, we urgently
need to target the inflammatory pathways that
control the development of the remodelled
phenotype in the airway. A wealth of studies
has implicated the mitogen-activated protein
kinase (MAPK) family of phosphoproteins as
critical signalling molecules that drive pro-
inflammatory pathways. Thus, inhibition of
MAPKs has emerged as an attractive strategy
for reversing inflammation and remodelling
in asthma. This chapter will focus on target-
ing MAPKs as future therapeutics. We will
briefly outline the use of small molecule MAPK
inhibitors, and then explore the potential of
harnessing the power of an endogenous MAPK
deactivator – MAPK phosphatase 1 (MKP-1) –
in inhibiting MAPK-mediated pro-remodelling
functions. Our recent studies demonstrate that What is the cellular
MKP-1 deactivates MAPK signalling in airway basis of asthma?
smooth muscle cells; a pivotal airway cell in
asthma and airway remodelling. Thus, this Asthma is characterized by inflammation
chapter will focus on the role of MAPKs in the and airway hyper-responsiveness. An acute
development of the pro-remodelling phenotype asthma attack can be brought on by exposure
in asthma and highlight the promise of novel to triggers. Exposure to triggers induces air-
anti-inflammatory strategies designed to reverse way inflammation characterized by mast cell
the development of the airway remodelling degranulation and an influx of lymphocytes
phenotype by regulating the anti-inflammatory and eosinophils. These cells secrete various
protein – MKP-1. agents capable of perpetuating inflammation
and provoking airway smooth muscle contrac-
What is asthma? tion (bronchospasm). Accordingly, the majority
of therapeutic agents used for asthma seek to
If you have asthma, you experience episodes minimize the development or consequences
of wheezing, chest tightness and shortness of of airway inflammation (corticosteroids) or
breath in response to a variety of “triggers”. directly promote airway smooth muscle relaxa-
This occurs because the airways in your lungs tion (β2-agonists).
narrow, making it more difficult for air to get
through. Over 2.2 million Australians have What is airway remodelling?
asthma. This includes 1 in 4 children, 1 in 7
teenagers and 1 in 10 adults (Source: National Asthma is a treatable health condition and we
Asthma Campaign). Because “when you can’t have a number of effective drug treatments
breathe, nothing else matters” (American Lung to tackle acute asthmatic attacks. With good
Association), asthma is an important and de- asthma management, asthmatics can lead nor-
bilitating disease that we need to understand mal, active lives. But, there are still a number of
more about so that we can beat it! unanswered questions. We now know that the
airways of asthmatics can become “thickened”
What causes asthma? or remodelled over time. This occurs when the
inflammation that is part of an acute asthmatic
Asthma is a complex disease with both ge- attack is not treated or controlled effectively.
netic and environmental causes. Why do we The consequence of uncontrolled asthma is
get asthma? The causes are many and varied. that permanent changes in the airways can
Allergy may play a big role. According to the occur and unfortunately, these cannot be
National Asthma Campaign, 8 in 10 Australians completely reversed with current treatments.
with asthma have positive allergy test results. As development of remodelled airways is cor-
Allergy occurs when your immune system related with deterioration of lung function,
reacts to substances (known as allergens) in the we urgently require therapies that reduce
environment that do not bother most people. and reverse structural changes in remodelled
These allergens can be found in house dust airways. Although corticosteroids can inhibit
mites, pets, pollen, moulds and foods and some aspects of remodelling, side effects ex-
can “trigger” asthma. You may be born with ist and thus, corticosteroid-sparing strategies
a genetic tendency to develop allergic dis- to prevent airway remodelling require further
eases (called “atopy”); or allergy may develop investigation.
throughout life. There are still a large number
of unanswered questions about the develop- Airway smooth muscle plays an integral role in
ment of allergic disease but currently much acute asthma and airway remodelling
intense research is being performed all around In the Respiratory Research Group at the
the world to understand more about the links University of Sydney we have focussed on the
between allergic disease and asthma. role of the airway smooth muscle in asthma
and airway remodelling. Airway smooth mus-
cle is no longer viewed simply as a bystander
on the post-transcriptional and on the post- regulation so that we can increase MKP-1 and
translational level. Shortly after exposure to reduce MAPK-mediated signalling.
the diverse stimuli (such as stress and growth
factors) the transcription of MKP-1 is induced Our current work: how
and mRNA levels are highly increased. The is MKP-1 degraded?
mechanism by which the transcriptional induc-
tion is mediated is currently not completely Thus, because MKP-1 serves a crucial negative
understood but since MKP-1 can be induced feedback role in regulating pro-remodelling
by various stimuli the transcriptional induc- signal transduction, discovering mechanisms to
tion and regulation seems to be a promising regulate the protein level or enzymatic activity
target for the modulation of the inflammatory of this endogenous MAPK-deactivator may be
response (42). The post-transcriptional regula- exploited as a novel anti-inflammatory strategy
tion of MKP-1 stability is another mechanism in asthma and airway remodelling. Thus, in
to alter the enzymatic activity of this phos- order to achieve our aim of increasing MKP-1
phatase. It has been shown that the MKP-1 to reduce MAPK-mediated signalling, we need
stability can be increased through phosphoryla- a greater understanding of the three levels of
tion by ERK1/2 and that leads to an accumula- MKP-1 regulation: (i) transcriptional; (ii) post-
tion of MKP-1 in the cell and therefore may transcriptional; and (iii) translational. We are
enhance the activity of MKP-1 (42, 48). To currently examining how MKP-1 is regulated
what extent the enhanced expression of MKP-1 at the translational level, that is, how MKP-1 is
has positive or maybe also negative outcomes is degraded by the proteasome – the garbage bin
not completely known. The modulation of the of the cell. As mentioned earlier, stimuli which
interactions between MKP-1 and its substrates activate MAPKs also induce MKP-1 protein.
is a subject of the post-translational regulation However, the increase in MKP-1 protein levels
of MKP-1 activity. The substrate specificity de- is transient, as MKP-1 then undergoes rapid
pends on diverse structural elements of MKP-1 degradation by the proteasomal machinery.
and the modulation of this interaction could If we can understand how and why MKP-1
also be a mechanism to enhance the phos- is degraded, we could design molecules that
phatase activity and hence the inactivation of could specifically block MKP-1 degradation
the MAPK pathway and therefore the efficacy of and thus allow MKP-1 protein levels to remain
the anti-inflammatory reaction in the immune high. We are currently a long way from our
response. If it is possible to inhibit or attenuate goal but our preliminary evidence obtained in
the proteosomal degradation of MKP-1, that airway smooth muscle cells shows that stimula-
would provide another promising opportunity tion increases MKP-1 protein levels (peaking
to regulate the MKP-1 activity. We are currently at ~ 2 hours) but the protein degrades over
working on achieving a greater understanding time. We have used a non-specific proteasome
of the multiple levels of regulation of MKP-1 inhibitor – MG132 – and confirmed that we
can inhibit proteasomal degradation and keep
3. Mauad, T., E. H. Bel, and P. J. Sterk. 2007. 12. Johnson, P. R., J. K. Burgess, Q. Ge, M.
Asthma therapy and airway remodeling. J. Poniris, S. Boustany, S. M. Twigg, and J.
Allergy Clin. Immunol. 120(5):997-1009. L. Black. 2006. Connective tissue growth
factor induces extracellular matrix in asth-
4. Wiggs, B. R., R. Moreno, J. C. Hogg, C. matic airway smooth muscle. Am. J. Respir.
Hilliam, and P. D. Pare. 1990. A model of Crit. Care Med. 173(1):32-41.
the mechanics of airway narrowing. J. Appl.
Physiol. 69(3):849-860. 13. Ammit, A. J., L. M. Moir, B. G. Oliver, J. M.
Hughes, H. Alkhouri, Q. Ge, J. K. Burgess,
5. Pare, P. D., B. R. Wiggs, A. James, J. C. J. L. Black, and M. Roth. 2007. Effect of
Hogg, and C. Bosken. 1991. The compara- IL-6 trans-signaling on the pro-remodeling
tive mechanics and morphology of airways phenotype of airway smooth muscle. Am.
in asthma and chronic obstructive pulmo- J. Physiol. 292(1):L199-L206.
nary disease. Am. J. Respir. Crit. Care Med.
143:1189-1193. 14. Ammit, A. J., A. T. Hastie, L. C. Edsall, R.
K. Hoffman, Y. Amrani, V. P. Krymskaya, S.
Figure 3: The best photo ever taken of the Big Bang. The photons detected to make
this map travelled for 13.7 billion years and are the oldest photons we can detect. They
were emitted from the surface of last scattering at the edge of our observable universe
when the universe was about 380,000 years old and had a temperature of ~3000 K. As
the universe expanded, these 3000 K photons became redshifted and cooled to the 3K
photons we now observe. The pattern of hot (red) and cool (dark blue) spots has been
used to obtain the most accurate estimates of the contents, age and size of the universe.
Image: NASA/WMAP Science Team.
dominated by matter. Then at 10-3 seconds During the 13.7 billion years since the Big
after the Big Bang, matter – in the form of a Bang, the universe expanded, the heat bath
quark-gluon plasma – cooled and condensed cooled and life (at least on Earth) emerged. Life
into protons and neutrons. Within three did not emerge simply because the universe
minutes these particles had condensed into cooled down to have the right temperature
light nuclei during a period called “Big Bang for H2O to be a liquid. Life needed a source of
nucleosynthesis”. As the universe continued to free energy unavailable from an environment
cool, atoms formed for the first time about half in chemical and thermal equilibrium. The ori-
a million years after the Big Bang. The universe gin of all sources of free energy can be traced
was a thermal heat bath of photons and atoms back to the initial low gravitational entropy of
in chemical equilibrium. Figure 3 is a full-sky the unclumped matter in the universe (e.g.,
map of the cosmic microwave background Lineweaver & Egan 2008). The gravitational
radiation. It shows the thermal heat bath of collapse of this matter produced galaxies, stars
the universe 380,000 years after the Big Bang. and planets and is the source of all dissipative
There were no stars or galaxies. Life is not pos- structures and activities, (including life) in the
sible in such an environment. In thermal and universe. Notice in the upper right of Figure 4
chemical equilibrium, no free energy is avail- the small interval of logarithmic time during
able, and free energy, not just energy, is what which free energy from stars has been available
life requires (Lineweaver & Egan 2008). to power life in the universe. The first stars
formed about 200 million years after the Big
Bang ( ~ 1016 seconds) when hydrogen cooled fusion accumulated to contain enough oxygen,
down to 50 – 100 K. Before this time there carbon, nitrogen, sulfur and phosphorus to
were no stars and therefore no free energy to produce watery environments and allow the
drive life. There was also no oxygen to make chemical evolution of carbon molecules into
H2O until several million years after the first hydrocarbons, carbohydrates and life.
generation of massive stars.
Four elements make up more than 99% of
Life as we know it is based on molecules; the atoms in terrestrial life: hydrogen, oxygen,
clumps of atoms that froze out of the cooling carbon and nitrogen or HOCN. Add seven
universe when the temperature of the universe more elements to this mix (S, P, Cl, Na, Mg, K
fell below molecular binding energies (Figure and Ca) and we have more than 99.99% of the
4). Thus, the expansion and cooling of the atoms in terrestrial life. Of all these ingredients,
universe has been the most basic prerequisite only hydrogen was made in the Big Bang, the
for the origin of molecules and molecular life. rest were produced in the hot fusing cauldrons
But life cannot be made out of the cooling of massive stars. Their ubiquity ensures that
hydrogen and helium produced in the Big the ingredients for life are present throughout
Bang. Many generations of massive stars had the cosmos.
to form and die before the ashes of nuclear
Figure 9: The Evolution of Relative Brain Size in Groups of Vertebrates Over the Past 200
Million Years (adapted and updated from Jerison 1976, p 96, Jerison 1991, Figure. 17). This
plot purports to show an evolutionary trend towards increasing relative brain size ( = E.Q.
= Encephalization Quotient) and is probably the most well-documented evidence for
such a trend. Average living mammal E.Q. is defined as 1. The broken lines indicate gaps
in the fossil record. Variation within groups is not shown. The lineage that led to humans
is drawn thicker than the other lineages. Lineweaver (2008)
the y-axis of a plot 2) plot yourself in the upper useful, we should see many independent ex-
right 3) plot your ancestors who, since you are amples of it in biology, and we could cite many
the extreme, will fall on a descending line into creatures that had evolved on independent
the lower left. Thus Figures 9 and 10 are not continents to inhabit the “intelligence niche”.
evidence for any general trend toward bigger But we can’t. Human-like intelligence seems
brains or noses. to be what its name implies – species specific.
Thus, the terrestrial record suggests that we are
In addition, heads (and therefore brains) are
as unlikely to find a creature with human-like
monophyletic: a single species diversified into
intelligence elsewhere in the universe as we are
all extant species with heads (brains). Not only
to find a sulphur crested cockatoo or a naked
is human-like intelligence not a convergent
mole rat on another planet.
feature of evolution, heads are not a conver-
gent feature of evolution. Heads were once a Even so, I am a strong supporter of the SETI
species-specific feature, thus, all heads and Institute, which uses radio telescopes to search
brains have diverged from a single species that for extra-terrestrial intelligence. I do not expect
had a head. Thus, heads and brains are not the to find creatures on other planets that build ra-
generic products of evolution but are as quirky dio telescopes, but I support the effort to keep
and unique as a single species. looking. Who knows what we will find? SETI
is the exploration of new parameter space with
Humans are unique, just like every other spe-
new instruments – a proven recipe for scientific
cies on Earth. It makes no sense to concoct
discovery. However, we do not need to misin-
an imaginary set of which we are the only
terpret the fossil record to justify continuing
terrestrial member and then suppose that
exploration of our universe.
biological evolution elsewhere in the universe
evolves toward this set. This concoction is The
Planet of the Apes Hypothesis. It is testable.
Paleoneurology does not support it.
Carl Sagan said that our evolution represents
the universe becoming aware of itself (Figures.
12 and 13). If human-like intelligence were so
Figure 13: This cartoon captures the status of a big-brained biped. Our big brains
enable us to ask important questions such as “What’s it all about?”, “How do I fit into
the universe?” On the other hand, our brains may be too big. They deceive us with self-
importance and prevent us from knowing the humble answer that every other creature
seems to know: “Eat, survive, reproduce”. Image Garret Hardin.
seen since the universe cooled below 3,000 at higher redshift have all their blue light ab-
degrees. Far ahead, one of the first stars in sorbed by neutral hydrogen gas, while quasars
the universe is shining. at lower redshift do not. Re-ionisation almost
Eventually, the first objects which produced certainly did not happen all at once; instead,
light were born. This light not only illuminated bubbles of ionised gas formed around stars (or
the darkness, but also stripped the electrons off quasars). As the number of bright objects grew,
the atoms in the interstellar gas again. We are the bubbles merged together and cleared up
still not sure which objects were responsible the “fog” of neutral hydrogen, allowing the blue
for this cosmic re-ionisation. They had to be light to travel freely.
objects producing large numbers of energetic Evidence is beginning to suggest that it was
photons: hydrogen is ionised by radiation with stars that first re-ionised the universe. The most
wavelengths shorter than 91.2 nm, which are distant quasars yet observed already show the
ultraviolet photons. The most likely candidates presence of elements heavier than hydrogen
are either quasars or the first stars. Quasars and helium, which means (as we shall see) that
are supermassive black holes, which are ac- there must have already been massive stars be-
creting gas from a swirling disk and sending fore these quasars were born.
narrow jets of high-speed particles and radia-
tion towards us. We know the universe was Composed only of hydrogen and helium (and a
already re-ionised by the time the universe was tiny amount of lithium), these first stars would
1 Gy old5, at a redshift of 6, because quasars have been very different from the stars forming
today. Theory predicts they would not only
5 Redshift describes how much the wavelength of the light have been much hotter than stars forming now,
which reaches us has been stretched by the expansion of but also that they could have been much more
the universe since it left the source. More distant objects massive. Stars forming today cannot be more
have higher redshifts, and so when we observe an object at massive than about 150 times the mass of our
high redshift, the light has been travelling since a long time
in the past. The relation between redshift and age of the Sun. Beyond that mass, the star produces so
universe is given in Table 1, see end of chapter. much radiation that the outward pressure of
the radiation exceeds the inward pull of grav- from the gas that continues to accumulate.
ity, and the star tears itself to pieces. The very The gas cloud containing our proton gradu-
first stars, however, could potentially grow to ally swirls towards the centre of the growing
be much more massive: several hundred, per- galaxy. As smaller clumps come too close
haps even up to a thousand solar masses. Such and are pulled in, some of the gas is flung
stars would have extremely short lifetimes – a completely away, doomed to swirl forever
million years or less – after which they would in the almost empty regions of intergalactic
explode, seeding the interstellar medium with space. Other gas finds itself being hurled
towards the centre of the galaxy. There it is
heavy elements. Their collapsing cores may
pulled into a swirling, super-heated accretion
even have provided the seeds which grow into
disk around the black hole, where it will even-
the massive black holes we see at the centres of
tually disappear into the event horizon and
quasars and galaxies. be lost forever, or else squirted at nearly the
The region towards which our hydrogen speed of light right out of the galaxy in twin
atom is falling is now perceptibly a proto- jets. Our proton avoids both of these fates;
galaxy. At its centre is a black hole, formed instead, it finds itself near the centre of a
from the embers of one of the dying first dense cloud, which gets denser as more gas
stars. Since its formation it has grown con- collides with it and compresses it.
siderably, by merging with other black holes,
Whether they were formed in the first stars,
and by sucking down enormous quantities of
or collapsed directly from the gas, or grew
gas. Surrounding it is a cloud of stars formed
from seeds of primordial black holes created
in the first instants of the Big Bang, we know of the galaxy and the black hole are somehow
that massive black holes already existed and intimately linked.
were growing less than a billion years after the
However they began, the evidence suggests that
Big Bang. The most distant quasar currently
both the galaxy and the black hole at its heart
known has a redshift of 6.43, so it was formed
grow as a result of the merging of galaxies.
when the universe was only 0.87 Gy old. Radio
Everywhere we look, we see signs of galaxies in
galaxies are also powered by supermassive
the process of colliding, or showing evidence of
black holes, but the jet is seen side-on, so we
collisions in the not-too-distant past. And the
see radio emission from the jets. Radio galaxies
further back we look, the more common these
are known at redshifts of up to 5.19, when the
collisions seem to be. When galaxies collide,
universe was just over 1 Gy old. So the black
the stars almost never collide: their physical
holes must have been formed very early on
size is so small compared to the vast distances
in the universe. Did they exist first and then
between them that they just pass freely past
galaxies grew around them? Or did the galaxy
each other. However, the enormous gas and
and the black hole both form together? We still
dust clouds in both galaxies do collide: the
don’t know. We do know, however, that almost
gas is compressed, which triggers more star
every galaxy has a massive black hole at its
formation. Meanwhile, some of the gas and
heart, and that the bigger the galaxy, the bigger
stars are flung out in huge tidal tails, while
the black hole. This suggests that the growth
some is sent spiralling towards the centre of
the galaxy, where it can feed the black hole.
energy instead of producing it. The star has the star outwards at tremendous speed. When
reached the end of the line, and can no longer this blast wave reaches the surface of the star,
support itself. Gravity has won. it becomes visible as an enormously expanding
fireball: a supernova.
The core of the star collapses inwards. The
inwards pressure forces electrons and protons Sitting in the layer of carbon, our proton (in
in the core to combine to form neutrons. These its carbon nucleus) has no warning of the cat-
neutrons are squeezed so tightly together that astrophic events that have taken place deep
in less than a second the whole core of the star, below it in the core of the star. The first sign
weighing about one and a half times the mass that something has changed is that the pres-
of our Sun, is compressed to a sphere only 15 sure beneath the layer suddenly drops; the
km in diameter: it has become a neutron star. star begins to collapse. With nothing sup-
porting it from beneath, the outer layers of
Meanwhile, the outer layers of the star are still the star, including the carbon atom contain-
falling, oblivious to what is happening to the ing our proton, begin to fall inwards. Seconds
core. When these layers meet the newborn later, however, the blast wave exploding
neutron star, they bounce off it so hard that outwards through the star roars past, and the
they are ejected outwards again at a substantial gas is exploded outwards. All around, nuclei
fraction of the speed of light. This creates a are being fused with other nuclei to form
shock wave which blasts the whole envelope of heavier elements, and bombarded by a flood
Here are some suggestions for popular-level books covering some of these ideas.
• “The First Three Minutes: A Modern View Of The Origin Of The Universe” by Steven Weinberg
(Basic Books, 1993)
• “Big Bang” by Simon Singh (Fourth Estate, 2004)
• “The Birth of Stars and Planets” by John Bally and Bo Reipurth (Cambridge UP, 2006)
• “Cosmic Catastrophes: Exploding Stars, Black Holes, and Mapping the Universe” by J. Craig
Wheeler (Cambridge UP, 2007).
• “The Story of the Solar System” by Mark A. Garlick (Cambridge UP, 2002)
Table 1: Redshift and lookback time
Biomedical physics is an increasingly im- We are also part of the worldwide collabora-
portant area of research in the School, with tions researching fundamental particle physics
academic staff investigating the interaction with the Large Hadron Collider at CERN, near
and effects of radiation with matter to apply Geneva in Switzerland. As well as high-energy
to radiation oncology and diagnostic imaging particle physics, there is a group investigating
as well as modelling ion transport across cell accelerator-driven sub-critical nuclear reactors
membranes. Surface modification to produce as a safer option for nuclear power generation.
bioactive sensors are carried out by the applied To add to our diversity, we accommodate a
physics group. Among other experimental group working on the quantitative analysis of
developments they are pioneering the prepara- humanity’s impact on our environment, and
tion of novel nanolaminate materials for high one with a focus on physics education and the
temperature operations in industry, using question “how should we best teach physics?”
plasma deposition.
Many of the research groups are led by ARC
The School has strengths in many areas of Federation Fellows, which is the most prestig-
theoretical physics, including single atom ious research fellowship offered in Australia.
modelling to understand the properties of mat- In 2008 there were 6 in the School, the largest
ter and surfaces, and working with quantum number in any research area in the country and
entanglement to advance quantum information more than the total awarded to several entire
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