Chapter 5 and 6.

This chapters deals with the nature of life as we have made discoveries about it on earth. Naturally, a large section is devoted to Darwin's theory of biological evolution. There is also an important section in the book on the difference between creationism (and why it is not science) versus the theory of biological evolution (Section 5.6). Read it!

The basics knowledge and ideas on life on Earth that guide us in our search for life elsewhere:

- Six elements critical to life on Earth: Hydrogen, Carbon, Oxygen, Nitrogen, Phosphorus, Sulfur

- Complex molecules, including amino acids can form in gas clouds from which solar system has formed.

- Life originated spontaneously at some early stage after formation of the Earth. Evidence for that: common ancestor, all life on Earth contains same basic DNA characteristics. If it could happen on Earth, it should be possible to happen elsewhere in other stellar/planetary systems.

- Evolution guides the development of life. Evolution is the reaction to the conditions, and life's response to those conditions. Evolution does not have to lead to advanced species.

- Earth's life has also been significantly affected by mass extinction events, and smaller extinction events. Extinctions can lead to very different life forms becoming dominant in subsequent era. But some life forms have been around very long times.



The chapter starts off with a description of how to define "life". The key characteristics for a living organism are:


EVOLUTION

The key individual in the subject of biological evolution is of course Charles Darwin (1809-1892), who published what is perhaps the most famous book in the sciences every written, "Origin of the Species" in 1859. This was based on his voyage on the ship the Beagle, which visited mostly Latin America, and the observations Darwin made there of how species had adapted to the environment.

Clicker questions:

- Biological evolution is entirely the result of random processes.

a. True b. False



- Why may it be difficult for some people to accept that one species can change or branch into other species as a result of biological evolution?

a. Because we have no evidence for this.

b. Because such a change takes a long time.

c. Because we have no transition fossils.



- Discussion: if a species over time could not change into another species, what would we have to conclude about the change in diversity of life on Earth over time?

Key aspect: Central concept in Darwin's theory of evolution is

NATURAL SELECTION

What Darwin observed was that species adapt to their environment by gradually changing their characteristics, to enhance their chances of survival. This process takes places unavoidably, not by some particular controlled process, other than natural selection itself. (Contrast this with modern "selective breeding techniques" which make use of Darwin's observations that species can change in particular ways. In selective breeding, we help nature a hand by focusing on the traits that we want to pass on, in nature, natural selection preferentially picks the traits that enhance survival chances for the species).

So, the species that are best adapted to their environment survive and may even thrive, while those that don't, disappear. Not only do species adapt to the point where they survive (e.g. black crabs on the Hawaiian lava) but the biological changes can lead to entirely different species in the long run.

Natural selection does not always lead to improved ("better") or "more advanced" species, although this is a possible, and in the right conditions, likely consequence of evolution. Very low life forms, like the simplest bacteria, can also survive and thrive in the right conditions.

When a species goes extinct, it is a reflection of the inability of that species to adapt quickly enough to changing circumstances, or maybe even a recognition that over time the species has changed into a different one, which is still genetically closely tied to its origin, but biologically classified as a different species.


Three contributing components leading to natural selection:


1. There is heritable genetic variation
2. Parents over-proliferate
3. Successful offspring are the ones best adapted to the environment


Natural selection does not lead to a particular goal, it is not always leading to more advanced species, it cannot anticipate anything.

The issue of biological evolution is still hotly debated in some circles in the US, though it is not controversial in the scientific world and not an issue of controversy in most industrialized countries. The following objections have been raised, but are all shown to be wrong:

Five Major Misconceptions About Evolution, click here for a discussion

The rest of Chapter 5 discusses cells as the basic units of life, classifications of life on earth, metabolism (the chemistry of life), before getting to DNA and extreme life forms.

For this course, sections 5.1, 5.4, and 5.5 are most important, but do read the other two sections too. Metabolism is important in connection with what is required to create and sustain life, since it specifies internal and external conditions that need to exist for certain life forms to thrive. Water is one of the key ingredients. One can speculate about life forms in environments with no water, but it is clear that water is and has played a crucial role on earth for life to flourish.


The discovery of the structure and behavior of DNA in cell divisions has provided key support to Darwin's theory of biological evolution: DNA is replicated in cell division, significant changes in DNA happen in sexual reproduction when species of opposite sex create new life and this provides a key mechanism for how gradual changes in the living creatures can occur. Changes can also happen randomly due to mutations. It is known that even tiny changes in DNA can produce very important changes in the characteristics of living beings. If the changes provide a benefit, they can continue to evolve in particular directions under the guiding principle of natural selection and in successive generations the species can develop new properties and eventually evolve into other species. Make sure you know what DNA is, and what the connection is between DNA and chromosomes, and genes.

Clicker question. Consider

a. the DNA in a cell

b. a chromosome

c. a gene

d. amino acids


Which is the largest?

Which is the smallest?


Extremophiles are extreme life forms formed on earth that may provide us with clues as to under which conditions life can still exist on other planets. This is a section that discusses work at the forefront of "astrobiology", the new study of astronomy and biology, which tries to apply knowledge of life on earth to conditions elsewhere to see where life might originate and what its properties might be.

A bit of information on some ocean extremophiles


If we combine Darwin's observations with our knowledge of the early earth and the old age of the earth, we arrive at a central question:

HOW DID LIFE ORIGINATE ON EARTH?

It is obvious, that if the Earth and Sun formed from a contracting gas cloud which heated up as it contracted, that the early Earth was very inhospitable to life: life MUST have formed later, or have been "brought there", perhaps in primitive form from organic molecules on comets. Also, the early atmosphere was certainly not an oxygen rich atmosphere.

The early development of life is poorly understood. We don't know how the first "living things" appeared; the formation from simple molecules into amino acids is not that difficult, apparently, given that we do find evidence for amino acids outside earth on meteorites and comets, but the transition from amino acids to the much more complex DNA, RNA, let alone cellular life, is not understood and has not been done in a laboratory.

We know roughly when (within the first billion years of the Earth's history), but it took until the last billion years (out of 4.5) for life to take on more complex forms that left most of the fossil record. A big challenge is that old rocks on Earth to look for evidence are very rare, due to the constantly changing surface or Earth in the plate-tectonic process.

There is suggestive evidence that rocks called stromatolites (click for more info) were likely deposited by microbes , that may have produced early photo-synthesis 3.5 billion years ago.  Early fossilized cells may have existed shortly after that.

Some important results:

- Advanced life, as defined by multi-cellular organisms and far more complex plant and animal life only developed in the most recent billion years of the Earth's history. At least, we have evidence in the fossil record that it existed this long ago; creatures that have no skeletons or other dense supporting structures do not leave much of a fossil record.

- While development of early life is a difficult subject to find conclusive evidence for, the fossil record of the last 750 million years is very strong and provides conclusive evidence for biological evolution. The real "missing link" may not be the ancestor of humans from apes, but the earliest life forms on Earth. We should keep in mind that this is not necessarily a weakness of the theory of how life may have started, but as much a problem that the evidence has been erased due to the active geological and atmospheric processes (weather!) on Earth.

- Even today life can survive in extreme conditions on Earth, from the most frigid environments in Antarctica to hot vents deep inside the Earth's crust where no oxygen is present. This provides hope that life may exist elsewhere in extreme environments, even if only in primitive form. These life forms are called "extremophiles" and were mentioned above (see also Book section 5.5)

- We are very biased in our view of life on Earth. We mostly think of plants and animals, but the actual "tree of life" is broken up into three broad classes (Bacteria, Archaea, Eukarya) and all animal and plant life only forms two branches of the Eukarya category. As the book states: "The true diversity of life on Earth is found almost entirely within the microscopic realm. Biochemically and genetically, we humans (and all other animals) are much more closely related to mushrooms than most microbes are related to one another." (section 5.2). Also, microbes on earth contain about 5000 times more mass than all humans combined.


Experiments in the 20th century (e.g. Miller and Urey) tried to mimic conditions on early earth and create primitive life forms, but this has not (yet) succeeded. The real "missing link" in our understanding of life and evolution is the creation of that first life form. However, this does not mean it is impossible that it happened. It just means that we don't understand it yet. Some day we may. An equally challenging problem is to be able to understand how "easy" or "frequent" this spontaneous formation of life may happen. This is a critical question to which we have no answer now and it determines very much how prevalent life elsewhere in the universe might be.

Modern evidence in strong support of biological evolution is provided by our understanding at the molecular level of the basic building blocks of life, the role of proteins, amino acids, the structure of DNA, the reproduction of DNA in cell division and forming of new life. This shows that indeed all life forms on Earth stem from a "Common Ancestor", that we have a very high overlap in genetic material with other life forms, in particular the ones people are believed to have originated from, and that evolution does indeed occur as a result of RANDOM MUTATIONS of the genetic material guided by Natural Selection which winds up bringing great order to the randomness of the mutations.

Note that while the process of mutations, now understood to be responsible for evolution of species may be random, the influence of "natural selection" imposes a strong constraint on this random process so that the existence of complicated species in itself is not an argument against evolution. Today we still have very primitive life forms, not only advanced ones. Evolution reflects survival of species that are well adapted to their current environment, be it advanced or primitive ones.

The understanding of the basic building blocks of life have helped shape our understanding of biological evolution: all life forms are based on the same set of common building blocks (amino acids), and the entire "model plan" for a species is passed on through the DNA to its offspring.

Set of terms you should familiarize yourself with:

Biological evolution, natural selection, mutations, DNA, amino acid, double helix, gene, genome, chromosome, mutation.

When looking at the evolution of life, get an idea for the basic time scales:

A good way to realize the incredibly fast pace of evolution over the last billion years, and the short time people have been around is through the cosmic calendar by Carl Sagan





You may be interested in: Artifical Intelligence and Artificial Life. See section 6.6 in book.