Information

What are the evidence that all life today descended from a common ancestor (LUCA), and which organisms (if any) challenge the concept?


If I understand correctly, the concept of the LUCA (last universal common ancestor) is based on the hypothesis that archaea and bacteria share common ancestry.

In the realm of mathematics, the same discoveries have often been made more than once, in different places. Sometimes (like with calculus) these independent discoveries were made almost simultaneously. Sometimes the discoveries appear to be totally unrelated (Hipparchus affirmative compound propositions before 100 BC, and David Hough's work on inserting parentheses in 1944).

If "life" started on Earth in some kind of primordial soup, it is conceivable that it started not once but many times, in different places and at different times.

How strong is the evidence that bacteria and archaea do not represent quite separate discoveries of "life", which (because of the nature of the chemical substances that they use) happen to share a number of features, such as DNA?


It is quite likely (but impossible to study) that the first stages of life originated more than once. However, the evidence that all currently existing life originated from the same population is very strong.

On the most basic level, many of the basic building blocks of life, RNA, DNA, amino acids are chiral, which means they come in multiple forms, but for the basic processes in nature, always the same one is chosen. For example, the DNA double-helix is almost always right-handed in nature, see also here. If there were multiple origins of archaea and bacteria, we would expect some to pick another form, if not other molecules. In addition, many crucial proteins such as DNA- and RNA- polymerases are very similar between all species, the probability that they would have originated independently is simply minuscule.


The genetic code of the tree of life is actively studied. So far, all the living beings have conformed to LUCA model. They are all RNA and DNA dependent, and no other life forms are known. All the RNA and DNA life forms share a tree like inheritance pattern with more simple organisms.

Sometimes there is doubt about wether mushrooms are more closely related to animals or plants.

Sometimes it is debated wether Prions are life forms or not. They are proteins that can reproduce by tricking human cells to making them and then transmit themselves, but they have not developed into anything else than a protein.

Some Virii have a special relationship with DNA, in that they just hyjack and eat DNA using RNA tricks, but their code is basically a lego block of other DNA they have hyjacked, they have fascinating evolution mechanism.

Here is the Tree Of Life, for the moment all genetic testing has found a tree structure shared by common acenstors, in all organsims, hence a LUCA:

here you can see it in detail, so far 50 000 species are on there, from the same philae and DNA -tested, and soon they will have more species, like 200k or something. huge pdf poster: http://www.timetree.org/public/data/poster/timetree24x32.pdf


Evolution: 5 Lines of Evidence

When On the Origin of Species was first published in 1859, to say it caused a scientific and political earthquake would be a vast understatement. The ideas put forward would become the basis of every biological field in existence today.

The foundations of the theory are observations that were made while Charles Darwin and Alfred Russel Wallace travelled the world, but since then there have been many expansions and breakthroughs. I’ve allocated these topics of evidence into 5 categories and I’ll do my best to explain the significance of each. But to start, a bit about natural selection.

The 4 statements of evolution by natural selection.

Evolution (which Darwin referred to as “descent with modification”) is a multi-faceted affair, but the core mechanism proposed, known as natural selection, stands true to this day. It claimed four simple but powerful statements supported by decades of accumulated evidence:

  1. Variation in traits (or characteristics) within a species exists.
  2. These traits are heritable.
  3. Some traits result in individuals having more offspring (or are associated with it).
  4. These traits will increase within a population over time.

As such, natural selection is all about reproduction. Although Darwin was unaware of how variation come into existence (genetics was still some way off), it was only necessary for the variation to exist and for it to be heritable.

There are of course some notable exceptions to the above. As an example, a volcanic eruption, or meteor strike, can destroy an entire group of variants independent of their competitive ability or reproductive success (by chance). This is known as genetic drift, and it’s also an important mechanism that drives evolution.

The Evidence:

1. Biogeography.

The modern field of biogeography revolves around the study of species distribution across the planet, and why such a distribution should exist. Wallace, arguably one of the founders of biogeography, noticed that species in one region were often very different from species in another, even though their climate and geography were the same. This didn’t fit with the conventional 1840s viewpoint of creation for purpose, and soon enough Wallace found many other examples which begged explanation, most famously the “Wallace Line”.

Even though there was a very short distance between them, the species of eastern Indonesia (and Papua New Guinea) are very different from their counterparts in western Indonesia. The eastern species resemble those of the Australian continent, whilst the western species are more Asian. Wallace was able to draw a line between these two groups (see Wallace Line above).

We now know the differences are due to colonisation from the two different continents, with the various species later becoming isolated by rising waters — adapting in isolation and becoming separate species. Colonised volcanic islands follow the same trend: Darwin’s Galapagos finches, isolated far into the Pacific, clearly had a common ancestor on the South/Central American mainland.

Following Alfred Wegener’s plate tectonic theory in the early 20th century (shown above), it became clear that inter-continental similarities between species could be explained by the movement, and breaking, of mega-continents. Indeed, one of the most convincing pieces of evidence behind the theory was that identical fossil plants and animals had been discovered on opposite sides of the Atlantic.

2. The Fossil Record.

Changes in species distribution over time are very clear in the fossil record as the dating of a fossil, or at the very least its surroundings, is possible*. This allows for a timestamp that gives us a tiny snapshot of what the species distribution looked like at certain periods in our planet’s history. The record is highly incomplete for many lineages, due to the rare conditions required for fossil formation, but I’ll focus on the fairly complete lineage of the birds as an example.

*Dating of geological specimens is not just limited to radiocarbon, which has a range of only around 70000 years. There are a variety of other methods, including K-Ar and Uranium-Lead dating, which both have ranges in the billions of years. It is pivotal to understand the vast geological timelines that facilitate evolution, as this is a common sticking point. Read more about the dating of rocks and fossils here.

The fossil record provides us with some inkling of a mass extinction event that wiped out many species some 66 million years ago. The only line of dinosaurs that survived, a small branch of the archosaurs, are the ancestors that led to modern birds.

The first Archaeopteryx fossil was discovered in 1860, and although it looked like a bird, there were some distinct differences (see above). It had feathers, but it also had a bony tail and teeth — both of which aren’t found in modern bird species. The bone structure was also somewhat different. All of this pointed to Archaeopteryx as an intermediary between birds and an earlier dinosaur.

The bone structure and presence of feathers in the fossils of theropods, a ground-dwelling dinosaur, suggest that they were the intermediary between Archaeopteryx and larger, pre-feather dinosaurs (although where the dinosaurs branched into feathered and non-feathered is contentious). As a result, using phylogenies (a family tree for relatedness over time), researchers have been able to piece together the legacy of the dinosaurs.

A complete fossil record will probably never be achieved, for fairly obvious reasons. However, great strides have been made in tracing other lineages: especially our own Homo genus. The fossil record is indicative of evolution, but it is only one piece in the evidence puzzle.

3. Embryology, similarity, and vestigial structures.

Many species share an embryonic larval structure (see above). Darwin postulated that: “community of embryonic structure reveals community of descent”, and there’s a reason for this.

We can view the larvae, or embryos, as a template for shared ancestry. For instance, both human and fish embryos have gill-slits — but these slits are removed in the later development of the human embryo, whilst developing into gills in fish. Genetic factors, developed through adaptation to land-environments, silence gill development in humans but the early, gill-slit stage suggests we share a common ancestor with fish. Other examples include eyes in embryonic moles and teeth in embryonic whales.

Shared features due to a common ancestor are known as homologies, and some can only be viewed in early embryos, whilst others extend into adulthood (see image above). Some homologous structures have no function, like the tail-bone in humans, or the hind leg remnants in whales. These apparently functionless appendages are called vestigial structures, and they can also indicate shared ancestry.

Finally, we have analogous structures: they share function, but not ancestry. An example would be the wings of butterflies and birds, both developed independently as adaptations for similar environmental pressures.

When the discovery of DNA’s double-helix structure was published in 1953, there wasn’t long to wait before the nature of heredity was revealed. DNA was found to be the carrier — but most importantly, through its own replication, it provided a source of variation.

The building blocks of DNA (adenine, guanine, cytosine, and thymine) are shared throughout the living world, from bacteria to humans. Impressively, triplets of these DNA building blocks form a code that is read to build proteins, and this protein code is also shared throughout life. The result: bacterial DNA can be read in a human cell, and the ultimate indicator for a common ancestor for all life was revealed.

Shared mechanisms aside, sequencing of genomes (all a species’ DNA), and the use of mitochondrial “molecular clocks”, confirmed relatedness theories. We humans share around 99% of our DNA with our closest relative, the chimpanzee, and probably split from our common ancestor a few million years ago. Phylogenies, like the one shown below, can be built to map the genetic differences between species, and so indicate relatedness.

Variation is generated through mutations in the DNA. This can occur through a variety of mechanisms, such as UV radiation, but most commonly from errors during replication. These errors change how the DNA is read, which changes the protein product and ultimately the function of the cell. Accumulated changes can be positive (new function), neutral or deadly (cancer), and natural selection ultimately removes changes that are negative relative to the local environment.

Which brings us to our final reason.

5. Observable evolution on small timescales.

Perhaps the most famous of Darwin’s examples of adaptation are the Galapagos finches. Having colonised the volcanic islands from the American mainland, the finches appeared to have different beaks, even though they were similar in all other respects (see image above). It was only much later, after consulting with the ornithologist John Gould, that it was realised that the beaks were adaptations for different food sources. In true natural selection fashion, individuals with better beaks (be it for insects, tough seeds or sucking blood) grew to dominate their local populations. Those who didn’t would slowly die off.

This phenomenon was observed in the Galapagos drought of 2004/5, where average beak size on an island for one species shrank (following mass die-offs of the larger beak variants), likely due to competition for large-beak-associated seeds. The variants with smaller beaks were able to find an alternative food source. Importantly, the genes associated with this trend were identified and their associated increased, or decreased, frequency within the population confirmed.

Another famous example is the peppered moth, as their population drastically changed following the industrial revolution in England (pictured above).

The expansion of industry in the late 19th century had a major effect on the air quality of British towns, but it also appeared to affect the moth population. The black variation of the peppered moth became increasingly common, while the previously common white variant became rare.

In the 1950s, Bernard Kettlewell showed, through an elegant set of experiments, that the moth population was changing because of predation. The trees surrounding British towns, previously light-barked, had become sooty and dirty in colour, providing better camouflage for the black variant. The white variant, no longer camouflaged, became visible to birds and was hunted in greater numbers. His observations were confirmed in a paper published in 2012 as modern, cleaner forests have seen a reversal back to white variant domination.

I couldn’t talk about observable evolution without mentioning bacteria and viruses. The rapid lifecycle of microorganisms means we can observe thousands of generations in a relatively small amount of time.

M. tuberculosis, the bacterial species which causes TB, has been highly efficient at adapting to the selective pressures applied by multiple antibiotics. However, resistance to drugs has developed in various other species of pathogen too. The general mechanism of adaptation to antibiotics is shown in the image above.

Just a theory? Why “scientific theory” is different.

A “scientific theory”, in the ideal sense, is the best representation of the available evidence at any one time. The theory itself is not “fact”, but rather a series of explanations built off observations which are, individually, facts. As such, the theories evolve over time as our understanding of the observations changes, or new observations are made. A scientific theory is always a work in progress.

Of course, there are young, abstract mathematical theories of science, and then there are those which abound with tangible evidence. Evolution, as you’ve seen above, is one of the latter theories.

Currently, there are no observations that have been made which contradict evolutionary theory. It is highly unlikely that there ever will be. But, if some undeniable evidence for a previously unknown mechanism was to suddenly materialize, the scientific community would be forced to revise the affected theories and move on.

Even evolution isn’t infallible in fact, it wouldn’t be a scientific theory if it was.


Five Proofs of Evolution

1. The universal genetic code. All cells on Earth, from our white blood cells, to simple bacteria, to cells in the leaves of trees, are capable of reading any piece of DNA from any life form on Earth. This is very strong evidence for a common ancestor from which all life descended.

2. The fossil record. The fossil record shows that the simplest fossils will be found in the oldest rocks, and it can also show a smooth and gradual transition from one form of life to another.

Please watch this video for an excellent demonstration of fossils transitioning from simple life to complex vertebrates.

3. Genetic commonalities. Human beings have approximately 96% of genes in common with chimpanzees, about 90% of genes in common with cats (source), 80% with cows (source), 75% with mice (source), and so on. This does not prove that we evolved from chimpanzees or cats, though, only that we shared a common ancestor in the past. And the amount of difference between our genomes corresponds to how long ago our genetic lines diverged.

4. Common traits in embryos. Humans, dogs, snakes, fish, monkeys, eels (and many more life forms) are all considered "chordates" because we belong to the phylum Chordata. One of the features of this phylum is that, as embryos, all these life forms have gill slits, tails, and specific anatomical structures involving the spine. For humans (and other non-fish) the gill slits reform into the bones of the ear and jaw at a later stage in development. But, initially, all chordate embryos strongly resemble each other.

In fact, pig embryos are often dissected in biology classes because of how similar they look to human embryos. These common characteristics could only be possible if all members of the phylum Chordata descended from a common ancestor.

5. Bacterial resistance to antibiotics. Bacteria colonies can only build up a resistance to antibiotics through evolution. It is important to note that in every colony of bacteria, there are a tiny few individuals which are naturally resistant to certain antibiotics. This is because of the random nature of mutations.

When an antibiotic is applied, the initial innoculation will kill most bacteria, leaving behind only those few cells which happen to have the mutations necessary to resist the antibiotics. In subsequent generations, the resistant bacteria reproduce, forming a new colony where every member is resistant to the antibiotic. This is natural selection in action. The antibiotic is "selecting" for organisms which are resistant, and killing any that are not.


What are the evidence that all life today descended from a common ancestor (LUCA), and which organisms (if any) challenge the concept? - Biology

Evolution is widely accepted as indisputable scientific fact when, in truth, it is not based on scientific evidences which are measurable by the scientific method.

Our everyday lives revolve around science and technology. The cars we drive, the food we eat, and the vitamins we take are the result of the application of some scientific principle. Just as science is important to everyday life, so it sets foundational principles by which evidence is acquired, analyzed, and transmitted.

Science is a process in which we procure knowledge from empirical data. The data are from what we observe and record with our senses. Science is a systematic study of the world around us based on observations, classifications, and descriptions that can lead to experimental investigation and theoretical explanations. Both deductive and inductive reasoning are employed in the scientific process. The National Academy of Science in the 1998 publication, Teaching about Evolution and the Nature of Science, confines the activity of science to the empirical evidence, stating that, &ldquoExplanations that cannot be based on empirical evidence are not a part of science.&rdquo (Washington, D.C.: National Academy Press) p. 27. (1)

Valid science must have integrity, dependability, reliability, and be trustworthy. How can you come to true conclusions with experimental data that is falsified? Testing and measuring are also important tools for verification. When scientific research is reported in scientific journals, it should be written so that experimental procedures can be repeated, since repeatability is another tool used for validation.

Science can be seen as theoretical a well as strictly experimental. While experimental science relies on the process of factors referred to as the scientific method, e.g. observable, hypothetically testable, theoretically verifiable or repeatable, and falsifiable or possibly untrue, theoretical science observes data and patterns utilizing information from various disciplines to formulate models that can be extremely accurate, e.g. the DNA molecule.

Basic science continues to rely on observation, fact, hypothesis, theory, and law. These can be defined, briefly as follows:

Observations: Describing or measuring what one observes.
Hypothesis: A statement that can be tested so that inferences and conclusions can be explained.
Fact: Based on repeated observations that can be confirmed.
Theory: A general explanation into which facts and experimental conclusions can be incorporated, so as to allow for predictions to be made.
Law: A functional generalization that has stood the test of time and can be relied on to make accurate predictions.

Scientists agree on the importance of peer review and self correction by means of the scientific process detailed above. Why does the evolutionary scientist fail to apply these standards of science to that of evolution? No one was present when evolution of life initially took place, so we are limited by the "observational" requirement of the scientific method. Obviously, we cannot experimentally verify the evolutionary process. We don't know factually any conditions under which evolutionary processes began. Evolution fails to meet the basic requirements of the scientific method and is therefore by definition dead in the water.

Science, by definition, only deals with material things. It is said to be naturalistic. Therefore scientific evidence relates to material questions about the universe. Science is not a worldview. By itself, it is a neutral mechanism that gives us tools to acquire and examine evidence. Evolutionists depend on science to acquire, analyze, and transmit data to build working models to support theories and laws as so do all scientists.

&ldquoThe raw materials of science are our observations of the phenomena of the natural universe. Science&mdashunlike art, religion, or philosophy&mdashis limited to what is observable and measurable and, in this sense, is roughly categorized as materialistic&rdquo. (2)

Science is a tool that gives a glimpse of truth. It is limited because science attempts to exclude all evidence except that which is by definition natural and quantitative. It excludes man&rsquos inner spirit, motivations, and goals. It fails desperately to measure all the qualitative and subjective aspects of reality. It fails to measure inner qualities, such as truthfulness, generosity, and love. Man&rsquos spiritual nature&mdashthe repository of his faith, convictions, and worldview&mdashis not susceptible to scientific inquiry. Science&rsquos reality is the material world only. It is not competent to reach conclusions about realms beyond. This is a limitation that requires further development and understanding. We will take a more in-depth look at this problem later in this paper.

The Basic Premises
In summary, it is important to remember the following about evolutionary presuppositions: First, evolution assumes slow and gradual change over unimaginable eons&mdashmillions of years for life and billions of years for the material universe to evolve. Many different explanations, without consensus, are offered to explain how this process took place.

Second, evolution assumes that the organizing force for life is internal and depends on random chance, a presupposition that eliminates any outside intelligent creative force.

Third, evolution dismisses intelligence and assumes that time, chance and natural process to be the mechanisms responsible for material reality&mdashwhich, owing to its naturalistic presupposition, is the only reality being postulated. Evolution, therefore, is a non-testable, non-verifiable, philosophical, non-scientific belief).

Can Evolution Withstand an Application of the Scientific Method?

The McLean v. Arkansas Board of Education describes the legal decision by U.S. District Court Judge William R. Overton. Out of this case came a description of science in Section 4 of the case. This section states that the essential characteristics of science are:

1. It is guided by natural law
2. It has to be explanatory by reference to natural law
3. It is testable against the empirical world
4. Its conclusions are tentative, i.e. are not necessarily the final word and
5. It is falsifiable.

This declaration of what science is, defeated the Creationist's attempt to have their alternate explanation of origins be presented in the public school system under the concept of requiring a balanced treatment of creation-science along with evolution-science. We are not here to debate the issue again, but what might be more apropos, is to see if evolutionary science can meet the "science test" e.g., Overton&rsquos science test itself. The court believed that "creation-science" as defined in Act 590 is simply not science.

Section three of this court case produced the court's definition of evolution.

"Evolution-science" means the scientific evidences for evolution and inferences from those scientific evidences. Evolution-science includes the scientific evidences and related inferences that indicate:

1. Emergence by naturalistic processes of the universe from disordered matter and emergence of life from non-life
2. The sufficiency of mutation and natural selection in bringing about development of present living kinds from simple earlier kinds
3. Emergence by mutation and natural selection of present living kinds from simple earlier kinds
4. Emergence of man from a common ancestor with apes
5. Explanation of the earth's geology and the evolutionary sequence by uniformitarianism and
6. An inception several billion years ago of the earth and somewhat later of life. (3)

Can Evolution-science Meet the Test of Science Using the Standards Listed Above?

1. Emergence by naturalistic processes of the universe from disordered matter and emergence of life from non-life.

We are looking for a process which takes molecules found in a disordered state and allows them to become ordered in such a way that life is produced. Is there a "law of syntropy" (negative energy in living systems) which would counterbalance or reverse the "law of entropy"? We know of no such law which would allow entropy (the consequence of the second principle of thermodynamics, which states that in every transformation of energy some of the energy is lost in the environment) to be reversed. A second law, the law of biogenesis, says that life arises only from preexisting life. The experiments of Francesco Redi, and Louis Pasteur dealt with the origin of life by spontaneous generation, and this hypothesis was nullified by their experimental results. Where is this law that would give some credibility to the evolutionist's position? What experiments have been run that prove or provide any credence to the emergence of life from non-life by some naturalistic process? Evolution is a theme that runs through all of biological science, yet it fails the first test of science, a search for a process that explains the existence of life via natural processes. With regard to this Michael Behe states the problem as follows:

1. Molecular evolution is not based on scientific authority. There is no publication in the scientific literature - in prestigious journals, specialty journals, or books - that describes how molecular evolution of any real, complex, biochemical system either did occur or even might have occurred. There are assertions that such evolution occurred, but absolutely none are supported by pertinent experiments or calculation.
2. The sufficiency of mutation and natural selection in bringing about development of present living kinds from simple earlier kinds, and
3. Emergence by mutation and natural selection of present living kinds from simple earlier kinds. (4)

Mutations and natural selection are the two processes described by evolutionists to account for the evolution of organisms including the emergence of new species from previously evolved species. Mutations certainly occur as well as natural selection. However, can these processes accomplish all that evolutionists say they can accomplish? The &lsquomolecules to man&rsquo inferences need much more clarification in the scientific literature to be recognized as supporting these inferences as being truly scientific. Mutations are said to be random and unpredictable. But is this so?

Dr. Lee Spetner has researched this area involving adaptive mutations. The following are some of his findings.

Barbara McClintock, who received the Nobel Prize in 1983 for her work on genetic rearrangements, noted that there are indications that these genetic modifications occur in response to stress.

Barry Wanner of Emory University has suggested that genomic rearrangements could be part of a control system in bacteria that would produce heritable changes in response to environmental cues.

John Cairns and his team at the School of Public Health at Harvard University described other experiments with bacteria and concluded: The cells may have mechanisms for choosing which mutation will occur&hellip. Bacteria apparently have an extensive armory of such 'cryptic' genes that can be called upon for the metabolism of unusual substrates. (5)

Dr. Spetner suggests that these experiments, which indicate that adaptive mutations are stimulated by the environment, thus contradicting the basic dogma of neo-Darwinism, e.g. that mutations are random and should be occurring independent of the environment. He further suggests that other organisms, apart from bacteria, also may have latent parts of their genome dedicated to be adaptive to a certain set of environmental conditions that may arise. (6)

How could an organism have part of its genome dedicated to adapt to an environment or a stimulus that it previously had not been exposed to? Evolution must account for serious aberrations in its theory.

There are many other problems with mutations as a mechanism for positive change in an organism. Anyone reading literature on this subject is aware of the destructive effects of mutations. Even granting the occasional beneficial mutation, a concept still lacking in supportive empirical evidence, the accumulation of these in an organism (providing that organism with a new element in its survival) has not been demonstrated in the scientific literature. We understand that the DNA copying process includes an editing system which corrects mutations or errors as they might occur during replication. Does it not seem that the coded information in the DNA is resistant to change by mutations?

Another problem is one of information. Mutations always cause a loss of information. As an organism changes, either to improve some aspect of its being, or to change into or produce another variety or species, information to do these things must come from somewhere. How valid is evolutionary-science when the main claim for improvement involves losing information along the way? Information is a real element in the accumulation of new and novel structures in living things. The scientific literature appears to be deficient to in suggesting where this information comes from. No one has demonstrated that information can arise by itself over time by chance and natural processes.

Natural Selection is a sorting process and doesn't add any new information to the gene pool. According to a popular text natural selection can be described as follows:

Adaptive evolution is a blend of chance and sorting - chance in the origin of new genetic variations by mutation and sexual recombination, and sorting in the workings of selection as it favors the propagation of some chance variations over others. From the range of variations available to it, natural selection increases the frequencies of certain genotypes and fits organisms to their environments. (7)

From this definition scientists are all in agreement to the basic concept of natural selection. The limitations we are suggesting have more to do with the validity of those mutations, in conjunction with sexual recombination, to provide the needed changes and new information to account for all the life forms we see today. These would also have to include the intricacies entailed in the life processes internal and external to those organisms. If mutations lose information and natural selection simply sorts what is already there to give rise to a new variation using the same genes, how does an organism change significantly into another organism?

Let us take a look at an illustration of how a mutation affects the transmittal of information. We will begin with a simple statement:

The boy ran down the street.

Some typical terms for mutations are additions, deletions, and inversions. Remember mutations are random changes in an already existing code of information. You can make your own mutations to a message if you choose. Let us begin by using an addition.

The boy rat down the street, or
The toy ran down the street, or
The boy q ran down the street.

We can see the effects of changing information that already provides adequate meaning.

What would a deletion do to the message?

The oy ran down the street, or
The boy ra down the street, or
The boy ran down the sreet.

What about an inversion, which reverses or turns upside down an element of the message?

The yob ran down the street, or
The boy ran nwod the street, or
The boy ran down the teerts.

With all of these changes information is lost. What affect do these mutations have on the message transmitted in the genetic code of DNA? Below is a section of RNA. RNA is simply the messenger which carries information from DNA.

Each set of three letters "codon" and represents the information in the DNA which allows a single amino acid to be placed in a specified position in a chain, which then becomes a protein after all amino acids are positioned.

UUU - places the amino acid phenylalanine into the chain.
AAG - places the amino acid lysine into the chain.
CUG - places the amino acid leucine into the chain.
GGC - places the amino acid glycine into the chain.

A protein can be made up of hundreds of amino acids all specifically placed in a sequence to allow for a specific protein such as hemoglobin to be made.

What affect would a mutation have on the sequence above?

How about UUU being mutated with UAU? This would change the placement of the amino acid phenylalanine with the amino acid tyrosine. Tyrosine chemically works differently than phenylalanine and will cause the protein to be shaped differently. Proteins are only effective when their shape is correct. A single mutation might not cause the protein to lose function, but several likely would. Obviously, if a protein such as hemoglobin was not able to be produced in an organism that required it, the organism would die or at the very least show no improvement in its ability to survive.

The point we need to make here is this: tampering with something that already exists and that is already working perfectly well, will cause that system to malfunction, or not to work at all. We can see the effects of mutations on fruit flies, which have been mutated for decades. They are all still fruit flies after thousands of generations. However what is more disturbing are the harmful effects those mutations have had on them. Some are blind, some are wingless others have extra wings, which are of no use to them, and so on. If mutations were beneficial, we should have our daily dose of radiation each day to improve ourselves. However, we know better and protect ourselves from excessive x-rays, ultraviolet light and other forms of radiation. Earlier we read the work of McClintock, Wanner, and Cairns who proclaim there is evidence organisms might enact their own mutations in response to the environment. More study certainly needs to be done on this subject, but the preliminary studies have been startling. When an organism initiates such a change, it would appear that a program is already in place to allow an organism to adapt to its environment rather than a hap-hazard process of chance emphasis on "hazard". How would such a program evolve? Can evolution predict what environmental changes or circumstances will happen in the future of an organism?

Until the evolutionist can bring more to the table and describe in scientific terms, through experimental evidence how all this came to be and how it works, we must conclude that mutations and natural selection fail the test of being part of a proven scientific process. Evolution-science is not science.

4. Emergence of man from a common ancestor of apes.

What natural laws are in place that would turn apes into men? Just look around. We see apes we see men but we don't see man-apes or ape-men - unless you are a fan of the Geico commercial. That is a very simplistic response and not meant as an adequate answer to the question. However there are no natural laws that are in the literature to account for the change of apes to men. There might be in the minds of men, but there is no process for this other than mutations and natural selection and these appear to be woefully inadequate.

Our alleged closest relatives are the chimpanzees. Many are convinced that we have a lot in common with these mammals, and at first glance I would agree. The differences however might amaze you.

A considerable amount of new evidence has presented itself recently regarding the actual differences and similarities between humans and chimpanzees. The human genome has been completely mapped, and subsequently attention has been given to the chimpanzee genome as well. Most of those in this field are motivated by their fundamental world view that humans evolved from monkeys or more specifically chimpanzees.

Has this new endeavor provided a closer walk with the chimpanzee? Previous studies of human and chimpanzee DNA indicate a 98-99% match of identical DNA. These studies have focused on a narrow area of the total genome - the gene coding regions. This is a very limited area and a tiny fraction of the roughly 3 billion DNA base pairs that comprise our genetic blueprint. (8) Recent studies have shown that the amount of DNA difference is not 1-2%, but more like 4%. This is at least double the percentage difference claimed by scientists for years. (9)

Percentages are deceiving. For example 1.06 % represents approximately 35 million mutations of single base pair substitutions in the DNA. There are also an additional approximately 40-45 million bases present in humans and missing from chimps, as well as about the same number present in chimps that are absent from man. The presence or absence of DNA is called insertions or deletions (indels). These can be from as few as 20 base pairs in length to several thousand base pairs. (10) A difference of 40 million bases would fill 10,000 pages, if each base represented a letter. Believing that this many changes accumulate by some unconscious zero IQ force and coincidence is like believing that tens of thousands of random changes on the electronic edition of a medical encyclopedia would add new information, transforming it into an encyclopedia of physics. (11) Fazale Rana, PhD, denies even the 96% similarity. He says:

When scientists take into account all the types of genetic differences and do a more global comparison, the similarities drop from 96% to about 85%. (12)

The apparent 4 percent difference is very deceiving, because it doesn't take into account the activity or expression of the genes. For example, we all use the 26 letters of the alphabet to express ourselves. Even though many of the words are identical in our communications, the final messages are of unlimited difference in expression. We would not compare two pieces of literature by counting how often various words were used by percentage, and coming to the conclusion that both pieces of literature were written by the same person because a similar choice of words was used. Obviously two writers are going to have many words, by percentage, in common. Evolutionists make the same mistake in regards to genes. They assume that because the genomes of two organisms use many of the same genes the two organisms have common ancestry.

Chromosomes are not static entities. They are able to move genetic elements around and reorganize themselves. Sections of chromosomes are able to separate themselves and move to another location on the same chromosome or to another chromosome. The locations of DNA swapping between chromosomes, known as recombination hotspots, are almost entirely different between chimps and humans. The finding is reported in a paper just published in Science by Oxford University statisticians and US and Dutch geneticists. (13)

Why these hotspots occur, and what triggers the swapping of DNA at those particular points, is a mystery. One theory suggests that the DNA code on either side of hotspots control the activity. However, when the researchers compared chimps and humans, they were startled to find that despite being so genetically similar, the species have totally different recombination hotspots. Professor Peter Donnelly at Oxford said: "If chimps and humans do not share these recombination hotspots, then it means something other than the surrounding DNA code must be controlling the process of recombination. Since the surrounding DNA code in chimps and humans is pretty much identical, this means that recombination is even more mysterious than we already thought. (14) The point that needs to be made here is simply this there is a lot we don't know, and as new information is revealed, the evolutionist appears to lose ground.

Another area which is different between these two species involves gene duplication. Gene duplication is simply a repetition of the DNA that makes up a gene. There are duplications found in the chimp and not in the human in the human and not in the chimp as well as duplications shared by both species. Each has significant implications as to their impact on developmental disorders. More significantly however, is the impact gene duplication has on gene-expression. Gene expression is the process through which genetic information is changed into structures and functions in a living cell. The formation of your heart, lungs, blood, etc, is an expression of the genes within your genetic code. The genes within the duplicated segments of the genome, many specific to either chimps or humans, are expressed differently in the two species. (15) Also, the two genetic sequences of chimps and humans are littered with duplicated segments that are scattered in different ways in the two species.

The human brain shows strikingly different patterns of gene expression compared to the chimp's brain. This difference isn't seen in other parts of the body such as the liver and white blood cells an international research team reports. The differences between humans and other Primates are more a matter of quantity than quality. Differences in the amount of gene and protein expression, rather than differences in the structure of the genes or proteins themselves, distinguish the two species. (16) It seems probable that how genes are expressed in the two species, particularly in the brain, might account for the difference in the mental capability between the two species.

Researchers have found that gene expression proved to be a very individual thing, with some humans appearing more closely related to chimpanzees than to other humans in overall expression patterns. (17) Essentially what this means is: gene expression is so powerful, that given the same DNA, expression can produce a continuum of individuals with chimpanzees on one end and humans on the other. The differences determined by the activity of other genes on the common DNA shared between the two species.

One can develop a paradox regarding genetic expression. Given a human and chimpanzee, you can easily tell them apart, but given only their DNA, you can't tell them apart easily. (18) Even the same looking DNA can be expressed one way in one species and a different way in the other species. The paradox of the anatomical difference and the genetic similarity is illusionary - it's an artifact of the intellectual history of comparing. How familiar we are in this new millennium with the physical differences and how unfamiliar we are with the whole notion of genetic difference. (19)

A major distinction between chimps and man is the fact that chimps have 48 (or 24 pairs) of chromosomes, while man has 23 pairs or 46 chromosomes. Evolutionists believe that two chromosomes in the chimp to human ancestry were fused to become the human chromosome 2. There is no known selective advantage for this fusion to occur, and become a characteristic of man. (20)

About 29% of proteins are identical between chimps and humans, leaving a large number - 71%, that are different. About 5% of all the proteins produced by chimps and humans have a deletion or addition of three nucleotides together, which code for a particular amino acid. It takes three nucleotides or three bases in the DNA, to code for a single amino acid in a protein chain. This substitution of an amino acid in the protein chain can cause significant changes in the overall structure of the protein and its function. (21) One base change in one nucleotide is the difference between whether one has sickle-cell anemia in humans or not. A single amino acid causes the change in the shape of red blood cells from discus to sickle shape leading to the symptoms of the disease.

Darwinists would claim that six million years have passed from the time a common ancestor arose that lead to chimps and humans. This is approximately about 300,000 generations, and is not enough generations to achieve the staggering amount of changes needed. Much of this change is acknowledged to be that of genetic drift, a change in populations occurring by chance processes, and where natural selection is not operating. This makes the problem even greater. For a change to become fixed in a population there must be a selective advantage for the organism. With no selective advantage, the change would not likely be preserved. (22)

We can mathematically estimate how much time in generations and how many mutations it might take for a particular organism to change characteristics. Given the amount of time evolutionists assert and the infrequency of favorable mutations, it becomes mathematically impossible for enough change to occur in order to turn a chimpanzee into a human in 300,000 generations.

So what makes us human? How can a few percentage differences make one species living in a forest and chattering at one another and another species in a biology lab studying the genome of the ones chattering? This is more than a biological problem. As Svanate Paabo of the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany states:

We cannot see in this why we are phenothypically so different from the chimps.
Part of the secret is hidden in there, but we don't understand it yet. (23)

Another scientist, Ajit Varki of the University of California, San Diego, puts it:

A genome is like the periodic table of the elements&hellipBy itself it doesn't tell you how things work - it's the first step along a long road. (24)

As we see a gain in scientific knowledge, evolutionists experience loss. The earlier interpretations on genetic similarity were based on a superficial and deceptive approach. Now, as we look at the broader picture of genetic expression and interaction, the separation between chimpanzees and humans becomes more evident. Since chimpanzees and humans may be about 96% similar, perhaps we should suggest to the evolutionist to allow the chimpanzee about 96% of our human rights. Fortunately we don't call them human, and rightly so. We don't allocate rights on the basis of genetic distance and that distance is significantly greater than 4% when gene expression and other interactions are taken into account.

We therefore conclude this section with this understanding: (i) not only does evolution not provide us with a mechanism, process, or way in which can be plainly stated as to how apes evolved into man (ii) but even looking at an animal such as the chimpanzee, we can see huge gaps in the differences between them and us. The problem is more than meets the eye, and evolution therefore fails as a provable science in this area as well.

5. Explanation of the earth's geology and the evolutionary sequence by
Uniformitarianism and an inception several billion years ago of the earth and
somewhat later of life.

Scottish geologist James Hutton (1726-1797) is credited with the concept or development of the geologic time scale, described in his work Theory of the Earth, published in 1785. This publication proposed the theory of "uniformitarianism", a geological doctrine which assumes that current geologic processes, occurring at today's rates, account for most if not all of the Earth's geologic features.

What is the geologic time scale? The earth's crust consists of many layers of sedimentary rock called "strata". Geologists assume that each layer represents a long period of time, typically millions of years. This is actually a secondary assumption based upon the primary assumption of Uniformitarianism. Among the billions of fossils found in these strata, some of these fossils are unique to certain layers. The layers are catalogued and arbitrarily arranged into a specific order (not necessarily the order in which they are found). This order reflects the assumption of macroevolution (the notion that all life is related and has descended from a common ancestor). The creatures thought to have evolved first are considered to be the oldest and are thus placed at the bottom of the column of layers. Creatures thought to have evolved later are placed at the top of the column. Many competent, accredited scientists have objected to this, stating that this poses a circular argument how can evolution be the basis for geologic conclusions while geology is taught as the basic evidence for evolution? Evolutionists are maintaining on the one hand, that evolution is documented by geology and, on the other hand that geology is documented by evolution? Isn't this a circular argument?" (25)

According to Niles Eldridge:

A variety of fossils from each layer of strata have been chosen to be what are called "index fossils". Index fossils are how we date the sedimentary rock layers. Paleontologists assume the age of an index fossil by the state of evolutionary history the fossil is assumed to be in. They guess how long it would take for one kind of life to evolve into another kind of life and then date the fossils and rocks accordingly. (26)

Once again this is a circular argument: if we date the rocks by the fossils, how can we then turn around and talk about the patterns of evolutionary change through time in the fossil record? The intelligent layman has long suspected circular reasoning in the use of rocks to date fossils and fossils to date rocks. The geologist has never bothered to think of a good reply, feeling that explanations are not worth the trouble. (27)

Upon perusal of these example above we pick out terms such as: assume, assumption, arbitrarily arranged, assumption of macroevolution, considered to be, have been chosen, assume the age of, they guess how long. My arbitrarily application of reason, leads me to assume, that evolution has been chosen to be a scientific methodology based on little direct evidence or experimental data.


What Is “Evolution”?

Whenever talking about challenges to “evolution,” it’s vital to carefully define terms, otherwise confusion can result. There are three common usages of the term “evolution”:

  • Evolution #1 — Microevolution: Small-scale changes in a population of organisms.
  • Evolution #2 — Universal Common Descent: The idea that all organisms are related and are descended from a single common ancestor.
  • Evolution #3 — Darwinian Evolution: The view that an unguided process of natural selection acting upon random mutation has been the primary mechanism driving the evolution of life.

No one doubts Evolution #1, which is sometimes called “microevolution.” Some scientists doubt Evolution #2. But the Scientific Dissent from Darwinism list only concerns Evolution #3, also called Darwinian evolution or Darwinism. The scientists who have signed the dissent statement say this:

We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.

We defined Evolution #1 by equating it with “microevolution”—small-scale changes in a population of organisms. Collectively, Evolution #2 and #3 might be termed macroevolution, which is defined as follows:

Macroevolution: Large-scale changes in populations of organisms, including the evolution of fundamentally new biological features. Typically this term also means that all life forms descended from a single common ancestor through unguided natural processes.

Unfortunately, evolutionists sometimes purposefully confuse these definitions, hoping you won’t notice that they have overstated their case. They will take evidence for microevolution (Evolution #1), and then over-extrapolate the evidence and claim it supports macroevolution (Evolution #2 or Evolution #3). Indeed, sometimes evolution advocates will equate microevolution and macroevolution, the idea being that macroevolution is just repeated rounds of microevolution added up. (Such inaccurate claims are addressed at The Scientific Controversy Over Whether Microevolution Can Account For Macroevolution.)


A Critique On The Dissent Of Common Descent

On Friday night of October 21, a debate titled, "Is Darwin's theory flourishing or floundering?" was held open for students and the public. It was hosted at St. Edward's University and presented by Hill Country Institute, Christ Church, and Associate Professor of Philosophy at St. Edward's University Dr. Stephen Dilley, Ph.D. The debate centered around whether all of life descended from one common ancestor or not.

As a biology major who is taking both Evolution and a philosophy class titled "God & Science," I attended the debate for both intrigue and because I had to. In fact, Dr. Dilley is teaching my "God & Science" class which discusses the relationship (if there is one) between religion and science and particularly centers around the discourse between evolutionary theory and creationism. As a senior science major taking a philosophy class that challenges the basis of evolutionary theory, I found myself in the privileged position of being able to view the debate from both lenses. Thus, I shall discuss the structure, content, and my impression of the debate in the following sentences.

Structure

The debate gave arguments for both pro- and anti- common descent. Dr. Joel Velasco from Texas Tech University defended common descent and Dr. Paul Nelson from the Discovery Institute challenged it. Dr. Velasco received his Ph.D. in Philosophy of Biology in 2008 at the University of Wisconsin-Madison . Dr. Nelson received his Ph.D. in Philosophy of Biology and Evolutionary Theory from the University of Chicago in 1998. They began with an introduction to their respective arguments, followed by their main arguments, a rebuttal, and Q&A. For purposes of this article, I will not discuss the Q&A portion.

Content

Opening remarks

Dr. Velasco argued that all carnivores, mammals, snakes, plants, eukaryotes, and everything else is related. He argued that all life is genealogically related by common descent.

Dr. Nelson asserted that there are four main opinions on the tree of life: design, no design, one tree, or multiple trees. He argued for the multiple trees of life hypothesis by contending that in the recent last decade, scientists such as microbiologist Carl Woese and biochemist Ford Doolittle found that there can be no single common ancestor since we find organisms outside the domain of the tree of life.

Dr. Velasco argued that when we look back at history, over and over again, we find support for common descent because it is, has been, and always will be very well supported by research. We find this data exhibited in the distribution of life on the planet, in the distribution of traits within life, and where fossils are and what they look like. He contended that descent explains these through comparative anatomy, biogeography, and fossil records. In comparative anatomy, we find homologies between species. Velasco used the famous example of the shared radius, ulna, and wrist structures found in human, whale, bat, and frog bones. Velasco argued that all of these species have this comparative anatomy because they all descended from ancestors that had structures just like that. His biogeography argument claimed that all life came from organisms from somewhere else. He illustrated this through the example of the cactus. The cactus is native to the Americas and is not in Africa, Asia, or Europe even though there are desserts there. He claimed that the reason that there are no cacti there is because they descended from a common ancestor which was native to the Americas and did not spread or arise elsewhere because they cannot travel. Velasco also contended that transitional fossils and vestigial structures further attests to the fact that species are related because they share a common ancestor. Lastly, Velasco gave the example of humans having one less chromosome than chimps and instead having the fusion of two chimp chromosomes with telomeres (which are present at the ends of chromosomes). Velasco argued that this fact makes the theory of common ancestry impossible to not be true since this means that humans and chimps shared a common ancestor.

Dr. Nelson argued the opposing argument which he defined as there not being one primordial form from which all of life has originated. Dr. Nelson stated that the main way biologists view common descent is by the notion that all life is related. The way they define "related" is by organism reproduction. He said that if relatedness is defined as organism reproduction, then we should not find a case in which two cells arise independently from each other. He asserted that the similarities between species that is observed could be explained by two ways: material descent and other physical reasons that have nothing to do with descent. Dr. Nelson declared that if there is a violation to the claim that nothing lies outside the tree of life domain - that is, nothing could have evolved outside the tree of life - then the claim that all of life is descended from a last universal common ancestor (LUCA) is false. He then used counterfactual conditional logic to format his argument by making the claim that If we saw X, then common descent would be wrong. Dr. Nelson then listed the following conditions as substitute for X: the machinery that the cell uses should not be divergent from LUCA and that phylogenies built on morphology should be congruent with phylogenies built on DNA basis. Dr. Nelson's strongest argument, and for which he is most known for, was that ORFan genes are divergent from LUCA and thus invalidate the common descent claim. ORFan genes are genes that do not have homologies in other lineages. They are taxon specific and arise through horizontal gene transfer or other mechanisms other than duplication, rearrangement, and mutation. The second argument that Dr. Nelson presented was that since there are multiple topoisomerases (which are cell machinery essential to DNA unwinding) from which come out of nowhere, this violates the counterfactual conditional on machinery. It was also noted that morphological phylogenies, that were created before the advent of DNA sequencing, do not match phylogenetic trees made on molecular data. Dr. Nelson then mentioned scientists who could not believe in the single tree of life model due to the vast genetic diversity of organisms found and summed up his argument by stating that a possible solution would be an intelligent designer.

Dr. Velasco recognized that he only mentioned evidence for the domain of Eukarya. He said that he implied that everything else is related. He also said that though there are variants of the genetic code, they are very similar and only vary in one amino acid.

Dr. Nelson said that the consequence of debunking common descent is that the single tree of life model will break from the bottom up because you lose the significance of history if the origin of an organism can arise multiple times independently and he concluded by saying that this is what is happening right now.

My Impression

First, I found the subtitle on the flier of the debate, "Is evolutionary theory rock solid or deeply flawed?" misleading. The actual debate was not considering whether evolutionary theory itself was correct rather, it discussed whether the majority of biologists are correct in thinking that all of life descended from one single common ancestor or if a few scientists, who think that there are phenomena that lie outside the tree of life, are correct. Since the event was in part presented by an evangelical church, I think that some people who attended this event thought that it was a debate of religion versus science however, this was not the case.

Second, I found the structure of the debate to be inappropriate. It consisted of two philosophers who presented scientific ideas unrelated to philosophy. They discussed evolutionary theory, molecular genetics, and cell biology - all of which are scientific topics and I fail to see how two philosophers could be experts in a field of which they do not reside.

Third, they didn't even really debate each other. Dr. Velasco only addressed the similarities within the domain of Eukarya and did not even mention Bacteria or Archaea - the two other domains of life - in his main argument. He only rushingly mentioned that it was implied that all other life is also related. Dr. Velasco also did not even make any genetic arguments and the topic of which was the entire emphasis of Dr. Nelson's argument. Instead, Dr. Velasco focused on comparative anatomy, biogeography, and fossils which do not apply Dr. Nelson's arguments.

Lastly, the most concerning part about this debate was that I think that some of the audience members left with the idea that all of life did not descend from a single universal common ancestor, which is the opposite of the consensus that the scientific community holds.

Before Friday's debate, nine St. Edward's University science professors, the Dean of Natural Sciences, and the Director of the Wild Basin Creative Research Center all touched on this fact when they signed a Letter to the Editor of the St. Edward's University campus newspaper Hilltop Views. In a portion of the letter, they write:

We write to state clearly that the theory of evolution has undergone significant review in the scientific literature and remains the best, most coherent explanation of the observed development of life on Earth. While specific mechanisms within evolutionary theory remain the subject of modern research, we reiterate that subject of evolution itself is not up for debate in the scientific community.

Numerous scientific societies, including the American Association for the Advancement of Science, the American Astronomical Society, the American Chemical Society, the American Geophysical Union, the American Institute of Physics, the Federation of American Societies for Experimental Biology, and the National Academy of Sciences, have issued statements on the subject of evolution and intelligent design, confirming the demonstrated success of the former and rejecting the scientific viability of latter. The undersigned faculty in the School of Natural Sciences at St. Edward’s University fully embrace this point of view.

Though my view aligns with that of the aforementioned professors, I am not trying to say that the topics discussed in the debate should not be points of discussion rather, I am merely trying to make the point that I think this debate would have been more appropriate if done with scientific experts. In doing so, this would have been a debate of the scientific minority versus the majority done by scientists themselves instead of philosophers.

Regardless, I applaud Dr. Dilley for organizing a successful debate that was very civil and respectful. Both Drs. Nelson and Velasco were very courteous to each other and their friendship, despite their differing opinions, was apparent throughout the discourse of the debate, which I think is one admirable trait we should all adopt.


Universal Common Descent

Scientists continue to research the origins of life, and to investigate the possibility that early lineages of life shared genes so freely that very early living things cannot be separated into multiple discrete lineages. The extent of that sharing is a subject of active research and scientific debate. Explore Evolution misrepresents that ongoing research as if it were between advocates of a single tree of life and supporters of a "neocreationist orchard."

Full discussion:

The nature of the Last Universal Common Ancestor is a topic of ongoing research today, and a book which intended to explore current scientific controversies within evolution would have to address that topic. A growing body of evidence suggests that there was so much sharing of genetic material among the single-celled organisms at the base of the tree of life that the different strands cannot be separated. Some scientists go so far as to treat the entire community of organisms alive at the time as essentially a single superorganism which shuffled genes freely between components. They treat that community of cells as the Last Universal Common Ancestor (LUCA). As particular genes became more tightly entwined with the functioning of other genes, the sharing decreased and lineages began to diverge.

Other scientists hold that gene transfer between organisms is not an obstacle to tracing the lineages of modern life, and insist that the branching trees of life can be traced all the way back to the earliest cell.

Explore Evolution ignores this ongoing and fascinating scientific controversy. To the extent they acknowledge its existence, it is only to misrepresent the views of participants in that debate. This statement, for example, betrays a profound lack of understanding of evolution and could hardly be more inaccurate or misleading about basic biology:

A central point of the Origin of Species is that evolutionary change takes place in populations of organisms, not in individuals. To elide this point, or fail to make it clear, is obviously an egregious error in a book supposed to be about evolution.

Furthermore, even in 1859 Darwin allowed for the possibility of more than one type of early organism. At the end of The Origin of Species , for example, Darwin wrote:

Since then, the evolution of the earliest cells has been and continues to be a dynamic area of research.

Neo-creationist orchard: From Kurt Wise (1990) "Baraminology: A Young-Earth Creation Biosystematic Method," in Robert E. Walsh (ed.) Proceedings of the Second International Conference on Creationism, Vol. 2. Creation Science Fellowship, Inc.: Pittsburgh, PA. p. 345-360. Furthermore, Explore Evolution badly misrepresents the state of science when it states "Other scientists doubt that all organisms have descended from one and only one common ancestor" (p. 9). While some scientists dispute the strict monophyly of the early history of life, but only because they think that genes from other branches of the tree of life moved between lineages, not because they dispute that life can be traced to a common ancestor. Researchers in the field do not "say that the evidence does indeed show some branching groups of organisms, but not between the larger groups" (pp. 9-10, emphasis original), and scientists absolutely reject the notion that "the history of life should be represented as a series of parallel lines representing an orchard of distinct trees" (p. 10). In fact, that way of talking about life's history was originated by creationists, as shown in the figure at right. In describing his "orchard" view of life, young earth creationist Kurt Wise explains:

In this passage, Kurt Wise introduces his explicitly creationist concepts in the exact terms that Explore Evolution uses. Dr. Wise, is undoubtedly one of the "critics" EE refers to, but he is never cited in EE . Not surprisingly, the book doesn't mention that the young earth creationist group Answers in Genesis states that the same figure shows "the true creationist 'orchard' model."

"Creation model": Explore Evolution co-author Paul Nelson's preferred "creation model," copied from a German creationist textbook.

Paul Nelson (2001) "The Role of Theology in Current Evolution," in Intelligent Design Creationism and Its Critics Robert Pennock, ed. The MIT Press:Cambridge, MA pp. 685.

Nor does the book point out that one author, Paul Nelson, previously presented the "polyphyletic" model shown at left, writing that "creationists defend the dynamic pattern of figure 32.2," rather than the models like the lawn illustrated by part a) of Wise's figure (Paul Nelson, 2001. "The Role of Theology in Current Evolution," in Intelligent Design Creationism and Its Critics Robert Pennock, ed. The MIT Press:Cambridge, Ma. pp. 684-685). Elsewhere, Nelson and a co-author defended their young earth creationist views by arguing that "The overall geometry of the history of life depict[s] a forest of trees, each with its own independent root" (Paul Nelson and John Mark Reynolds, 1999, "Young Earth Creationism" in Three Views on Creation and Evolution , J. P. Moreland and John Mark Reynolds, eds. Zondervan Publishing: Grand Rapids, MI. p. 45).

This vision of multiple trees of life, totally independent of one another is a creationist concept, and bears no relationship with any position being advanced in the scientific literature. There are challenges to the idea that diversity of life followed a strict branching pattern from the earliest days, but as shown in the figure at the right, this view rests heavily on exactly the sort of mixing (or "anastomosis") that Nelson and Wise reject. The figure EE uses to illustrate its proposed alternative view of life also does not include the complex exchanges of genetic information proposed by the authors Explore Evolution cites as critics.

A modern view of the tree of life: From W. Ford Doolittle (2000) "Uprooting the tree of life." Scientific American, 282(2):90-5. Note that distances are not necessarily to scale in this image. This image reflects a view held by some practicing scientists (including Dr. Doolittle, the author of the original article) that there was a period in life's early history when genes swapped so frequently that it is impossible to treat those earlier lineages as truly distinct, nor to trace those lineages back cleanly to a single ancestor. They do not dispute that life has some common ancestor, but they do seek to clarify how we talk about that ancestor.

The scientists cited as supporting this "orchard" view of life actually advocate a tree very different from the one illustrated by Explore Evolution (figure i:4). As the figure to the right shows, the group of scientists challenging traditional views of the tree of life are not proposing the sort of orchard that EE illustrates. Where EE and its creationist antecedents' embrace "discontinuities between major groups," the objection raised by the scientists EE cites actually object that there aren't enough connections between the branches of the tree of life.

These authors do not dispute that we can talk about a single common ancestor, merely that we should talk about it in a different sense. Doolittle explains:

This is a nuanced view, one that high school students are ill-equipped to understand until they have a fuller grasp on the basic concepts of biology. As Doolittle observes, even "some biologists find these notions confusing." It is hardly reasonable to expect students who are still learning what the genome is to appreciate a debate about the ways that gene swapping between ancient bacteria would have produced the sort of communal superorganism Woese and Doolittle describe. It would pedagogically inappropriate for Explore Evolution to thrust students into the midst of that debate without any background or support. Indeed, many biology teachers would be ill-prepared to lead such a discussion. This does not excuse the failure of EE to accurately describe the nature of that scientific debate.

Woese and Doolittle do not advocate an orchard, they simply thing that the trunk of the tree of life cannot be separated into distinct strands. They are not opponents of evolution, and Explore Evolution does the authors they cite no favors when they misrepresent the underlying science. That loose treatment of the underlying science also would do students and teachers no favors. A truly inquiry-based text might be able to wring some useful educational lessons from the debate going on over the base of the tree of life, but it is doubtful that high school students would benefit from that highly technical discussion, and they could not use Explore Evolution to understand even the basic nature of that ongoing research.


Introduction

The very earliest phases of life on Earth witnessed the origin of life and genetics from the elements. There was a time when there was no life on Earth, and there was a time when there were DNA-inheriting cells. The transitions are hard to imagine. Some dates and constraints on the order of events helps us to better grasp the problem. The Earth is 4.5 billion years (Ga) old [1]. By about 4.4 Ga, the moon-forming impact turned the Earth into a ball of boiling lava [1]. Magma oceans with temperatures over 2,000°K forced all water from early accretion into the gas phase and converted all early accreted carbon to atmospheric carbon dioxide (CO2) [1,2]. By 4.2 to 4.3 Ga, the Earth had cooled sufficiently enough that there was liquid water [3]—those first oceans were about twice as deep as today's [1,2]. Only later, hydrothermal convection currents started sequestering water to the primordial crust and mantle, which today bind one extra ocean volume [4,5]. The first signs of life appear as carbon isotope signatures in rocks 3.95 billion years of age [6]. Thus, somewhere on the ocean-covered early Earth and in a narrow window of time of only about 200 million years, the first cells came into existence. Because the genetic code [7] and amino acid chirality [8] are universal, all modern life forms ultimately trace back to that phase of evolution. That was the time during which the last universal common ancestor (LUCA) of all cells lived.

LUCA, the tree of life, and its roots

LUCA is a theoretical construct—it might or might not have been something we today would call an organism. It helps to bridge the conceptual gap between rocks and water on the early Earth and ideas about the nature of the first cells. Thoughts about LUCA span decades. Various ideas exist in the literature about how LUCA was physically organized and what properties it possessed. These ideas are traditionally linked to our ideas about the overall tree of life and where its root might lie [9–18]. Phylogenetic trees are, however, ephemeral. It is their inescapable fate to undergo change as new data and new methods of phylogenetic inference emerge. Accordingly, the tree of life has been undergoing a great deal of change of late.

The familiar three-domain tree of life presented by ribosomal RNA [19] depicted LUCA as the last common ancestor of archaea, bacteria, and eukaryotes (Fig 1A). In that framework, efforts to infer the gene content, hence the properties of LUCA, boiled down to identifying genes that were present in eukaryotes, archaea, and bacteria. When the first genomes came out, there were a great many such investigations [20–22], all of which were confronted with the same two recurrent and fundamental problems: 1) How are the three domains related to one another so that gene presence patterns would really trace genes to LUCA as opposed to another evolutionarily more derived branch? 2) Does presence of a gene in two domains (or three) indicate that it was present in the common ancestor of those domains, or could it have reached its current distribution via late invention in one domain and lateral gene transfer (LGT) from one domain to another?

(A) The three-domain tree: based on rRNA phylogeny, the three domains were of equal rank. (B) The two-domain tree: modern trees show eukaryote cytosolic ribosomes branching within the diversity of archaeal ribosomes. (C) As eukaryotes are not just grownup archaea, the eukaryote ancestor possessed mitochondria. If mitochondrial-derived genes are taken into account, the tree is no longer a bifurcating graph. (D) If plastids are included, the tree becomes even less tree-like because the photosynthetic lineages of eukaryotes also acquired many genes from the plastid ancestor [23].

The first problem (the root of the domains) has been the subject of much recent work. Phylogenetic advances and new metagenomic data are changing the three-domain tree [19] into a two-domain tree [24,25]. This is partially a development around phylogenetic methods [24,26–28] but also entails new archaeal lineages that are now being assembled from metagenomic data and that appear to be more closely related to the host that acquired the mitochondrion than any other archaea known so far [29,30]. The two-domain tree showing an "archaeal origin of eukaryotes" [24,28] (Fig 1B) only tells part of the story, though, because eukaryote genomes harbor more bacterial genes than they do archaeal genes by a factor of about 3:1 [31–33], and those bacterial genes furthermore trace to the eukaryote common ancestor [23]. Eukaryotes are not just big, complex archaea genomically and at the cellular level, they are true chimeras in that they possess archaeal ribosomes in the cytosol and bacterial ribosomes in mitochondria (Fig 1C) [34]. That polarizes cellular evolution in the right direction (there were once debates about eukaryotes being ancestral [10,13,14,22], as discussed elsewhere [35–37]) and identifies eukaryotes as latecomers in evolution, descendants of prokaryotes [38].

Current versions of the two-domain tree focus on the phylogeny of a handful of about 30 genes, mostly for ribosomal proteins (Box 1) but also on sequences from metagenomic samples. The metagenomic studies [29,30] have generated debate. Metagenomic data can bring forth alignments of genes that were sequenced accurately but have the wrong taxonomic label. For example, Da Cunha and colleagues [39] reported that published trees [29] hinge upon a strong signal stemming from one gene out of 30 and that the gene in question (an elongation factor [EF2]) might not be archaeal but eukaryotic instead. Spang and colleagues [40] defended their tree, eliciting more debate [41]. Errors can also occur in the assembly pipeline [42] en route to alignments [43], independent of contamination. Notwithstanding current debate about metagenomics-based trees of life [24,39,40,42,43], we should recall that rRNA itself produces the two-domain tree when various tree construction parameters are employed [24,26,27]. Both data and methods bear upon efforts to construct trees of life. It remains possible that some aspects of domain relationships might never be resolved to everyone's satisfaction—even the endosymbiotic origin of mitochondria is still debated [37]. But the bacterial origin of mitochondria and their presence in the eukaryote common ancestor [44–47], together with the tendency of eukaryotes to branch within archaeal lineages as archaeal lineage sampling [29,30,48] and phylogenetic methods [24,26,27,32] improve, indicates that eukaryotes arose from prokaryotes and that genes that trace to the common ancestor of archaea and bacteria trace to LUCA.

Box 1. The tree of 1% and the tree of everything else

A traditional approach to LUCA has been to simply look for the genes that are present in all genomes. That is easy enough, but the results are sobering. What one finds is a collection of about 30 genes, mostly for ribosomal proteins, telling us that LUCA had a ribosome and had the genetic code, which we already knew [63–65]. That collection of about 30 genes has been in use for about 20 years as concatenated alignments to make trees of lineages based on larger amounts of data than rRNA sequences have to offer [66]. The genes that are present in all lineages (or nearly all) inform us about how LUCA translated mRNA into protein, but they do not tell us about how or where LUCA lived. That information concerns ecophysiology, and physiological traits are not universally conserved—they are what makes microbes different from one another. One can relax the criteria of universal presence a bit and allow for some gene loss in some lineages, in which case, one finds about 100 proteins that are nearly universal [67]. If one puts no size constraints on LUCA's genome and allows loss freely, then all genes present in at least one archaeon and one bacterium trace to LUCA, making it the most versatile organism that ever lived [51]. New insights about microbial phylogeny are emerging from concatenated alignments [24,29,30,42,48,68]. But one has to take care not to get genes from different lineages mixed up, which can be difficult when metagenomes are involved [39,43]. Furthermore, data concatenation has its own pitfalls [66,69,70]. Most modern concatenation studies [29,30,48] employ site-filtering methods in an attempt to remove "noise," but even sites that look "noise free" can still contain bias and conflicting data [63]. Another problem is that popular methods of phylogenetic inference produce inflated confidence intervals on phylogenies and branches [71]. Trees of ca. 30 concatenated proteins are no more immune to phylogenetic error than rRNA is and are prone to additional kinds of error [72]. As it relates to LUCA, regardless of the backbone tree, we still need to know what all proteins say individually about their own phylogenies.

The second problem (how much LGT has there been between domains) that has impaired progress on LUCA has arguably been more difficult to resolve than the rooting issue. If a given gene is present in bacteria and archaea, was it present in LUCA, or could it have been transferred between domains via LGT? As one important example, early studies pondered the presence of bacterial type oxygen (O2)-consuming respiratory chains in archaea [21]. Does that mean that archaea are ancestrally O2 consumers? As O2 is the product of cyanobacterial photosynthesis [49] if we presume archaeal O2 respiration to be an ancestral trait of archaea, it means that archaea arose after cyanobacteria, which are only about 2.5 billion years old and gave rise to plastids (Fig 1D) only about 1.5 billion years ago [50]. If ancestral archaea were oxygen respirers, and ancestral bacteria were too, suddenly neither the two-domain tree nor the three-domain tree (Fig 1) make sense because everything is upside down and rooted in cyanobacteria. Similar issues are encountered for many genes and traits [51]. Lateral gene transfer among prokaryotic domains helps to resolve such problems because it decouples physiology (ecological trait evolution) from phylogeny (ribosomal lineage evolution) [52], but it also makes genes more difficult to trace to LUCA.

Has lateral gene transfer obscured all records?

That takes us to the other extreme. If all genes have been subjected to LGT, as some early claims had it [53], then LUCA would be altogether unknowable from the standpoint of genomes. Early archaeal genomes did indeed uncover abundant transdomain LGT [54], and many bacteria to archaea transfers can be correlated to changes in physiology [55], including the transfer of O2-consuming respiratory chains [55–58]. For reconstructing LUCA, the issue boils down to determining i) which genes are present in both archaea and bacteria, ii) which of those are present in both prokaryotic domains because of LGT between archaea and bacteria, and iii) which are present because of vertical inheritance from LUCA. For that, there are currently two methodological approaches. One involves making a backbone reference tree from universally conserved genes that are present in each genome—the tree of 1% [59] (see Box 1)—plotting all gene distributions on the tips of that tree, and then estimating which genes trace to LUCA on the basis of various assumed gain and loss parameters [60–62]. If we permit loss freely, many genes will trace back to LUCA if we assume many gains, LUCA will have few genes [61]. Constraining ancestral genome sizes helps constrain estimates of which genes trace to LUCA [61] but only if we assume that the tree of each gene is compatible with the reference tree, which is a very severe assumption and unlikely to be true. Each gene has its own individual history (Box 1).

Each gene records its own evolutionary history

If any protein-coding genes have been vertically inherited from LUCA, their trees should reflect that. To find such trees, one has to make all trees for all proteins, meaning one has to make clusters for all protein-coding genes from large numbers (thousands) of sequenced genomes. Clusters correspond to "natural" protein families of shared amino acid sequence similarity. Given modern computers, making alignments for all such clusters and making maximum likelihood trees for all such alignments is a tractable undertaking. Because LGT among prokaryotes is a real and pervasive process shaping prokaryote genome evolution [55,58,73–77], one has to treat each gene as a marker of its own evolution, not as a proxy for other genes or as a function that is subordinate to ribosomal phylogeny.

Genes that are present in several bacterial lineages and one archaeal lineage (or vice versa) might have been present in LUCA, but they might also have been the result of LGT [55,56,58]. An example illustrates how each gene tree can discriminate between vertical inheritance from LUCA and interdomain LGT. A recent study investigated the 6.1 million proteins encoded in 1,981 prokaryotic genomes (1,847 bacteria and 134 archaea) [78]. The proteins were clustered using the standard Markov Cluster (MCL) method [79]. The first step in that procedure is a matrix containing 18.5 trillion elements ((n 2 -n)/2), each element corresponding to a pairwise amino acid sequence comparison. The clustering of such a matrix requires substantial computational power and is aided by the availability of several terabytes of memory in a single machine. The MCL algorithm samples the distribution of values in the matrix and then starts removing the weak edges, with the value of "weak" being specified by the user. Two kinds of thresholds are typically used in MCL clustering: BLAST e-values and amino acid identity in pairwise alignments.

When the goal of clustering is to make alignments and trees, our group has found that a clustering threshold of 25% amino acid identity is a good rule of thumb. At lower thresholds, amino acid identity starts to approach random values and generates random errors in alignments [80], carrying over as erroneous topologies in trees [81]. That is why Russell F. Doolittle coined the term "twilight zone" for amino acid identity at or below the 20% range [82,83]. Of course, many proteins or domains that clearly share a common ancestry by the measure of related crystal structures do not share more than a random amino acid sequence identity [84]. Such ancient folds will fall into separate clusters at the 25% identity threshold and might thus generate false negatives when it comes to presence in LUCA (but see next section).

From thousands of clusters and trees, a handful remain

Using the 25% identity threshold, the 6.1 million prokaryotic proteins sampled fall into 286,514 clusters of at least two sequences, and 11,093 of those clusters include sequences found in both archaea and bacteria [78]. Many of those clusters involve oxygen-dependent respiratory chains. Did LUCA have 11,000 genes in its genome and breathe oxygen? That is, was LUCA (and hence archaea) descended from cyanobacteria? Neither prospect seems likely enough to warrant further discussion [85]. Knowing that transdomain LGT is prevalent [54–56] and that thousands of typically bacterial genes are shared with only one archaeal group [58], Weiss and colleagues [78] reasoned that a simple way to exclude some LGTs would be to set the minimal phylogenetic criteria that 1) a gene needs to be present in bacteria and archaea, 2) it needs to be present in at least two phylum-level clades, and 3) the tree needs to preserve domain monophyly (Fig 2). Genes that do not fulfil criterion 1 are not candidates for LUCA anyway. The two-phylum-plus-monophyly criteria 2 and 3 make it less likely but not impossible that such a gene attained that distribution via LGT. How so? Criteria 2 and 3 would require one transdomain transfer followed by intradomain transfers to different phyla, while allowing no subsequent, independent transdomain transfers. The last condition is the restrictive one.

The gene presence is indicated with a plus sign, absence with a minus sign. a) Genes found universally in both domains, regardless of their tree, trace to LUCA. About 30 fulfil this criterion. b) Another way to trace genes to LUCA is to say that any gene found in both archaea and bacteria was present in LUCA. However, thousands of these genes will have been transferred between bacteria and archaea by LGT so were not necessarily present in LUCA. c) Genes present in only one bacterial or archaeal phylum could easily be the result of LGT and are removed. But presence in two phyla per domain while preserving domain monophyly yields good candidates to have been present in LUCA. Such phylogenies would only result from LGT under very specific and restrictive conditions. They require exactly one transdomain transfer followed by either i) one additional transdomain LGT from the same donor lineage to a different recipient phylum or ii) retention during phylum divergence in the recipient domain, plus—in addition to either criteria i) or ii)—an additional, more subtle but highly restrictive criterion: No further transdomain LGTs occurred during all of evolution. Subsequent transdomain LGT would violate domain monophyly for the gene. Indeed, transdomain LGT is common, and 97% of the trees examined by Weiss and colleagues [78] did not exclude transdomain LGT (remaining 3%, 355 trees, provided in S1 Appendix). LGT, lateral gene transfer LUCA, last universal common ancestor.

Of the 11,093 clusters that harbored sequences in bacteria and archaea, only 355 (3%) passed the simple LGT filter [78]. Put another way, 97% of the sequences present in bacteria and archaea apparently underwent some transdomain LGT, underscoring the degree to which transdomain LGT has influenced gene history since LUCA and underscoring the need to employ phylogenetic filters in search of genes that trace to LUCA [21,51]. The 97% LGT value is important with regard to the 25% clustering threshold and possible false negatives 97% of all false negatives founded in low-sequence conservation would still not trace to LUCA because of transdomain LGTs. But transdomain LGT has apparently not erased all signals, as 355 genes passed the LGT test, and those genes tell us things about LUCA that we did not know before.

The physiology of LUCA

Most earlier depictions of LUCA focused on what it was like [16] for example, whether it was like RNA [86], like a virus [87], whether it was like prokaryotes in terms of its genetic code [88], or like eukaryotes in terms of its cellular organization [22]. But traditional approaches lacked information about how and from what LUCA lived [16]. Our phylogenetic approach to LUCA [78] uncovered information about what LUCA was doing: its physiology, its ecology, and its environment. The genes for those physiological traits are not necessarily widespread among modern genomes, but the filtering criteria by Weiss and colleagues [78] only require that these genes are ancient. What Weiss and colleagues [78] found is schematically summarized in Fig 3.

Summary of the main interactions of LUCA with its environment, reprinted with permission from [78] (supporting trees in S1 Appendix). Components listed at the lower right are present in LUCA. The figure does not make a statement regarding the source of CO in primordial metabolism, symbolized by [CO]. LUCA indisputably possessed genes because it had a genetic code. Transition metal clusters are symbolized. CH3-R, methyl groups CODH/ACS, carbon monoxide dehydrogenase/acetyl–CoA synthase GS, glutamine synthetase HS-R, organic thiols LUCA, last universal common ancestor Mrp, MrP type Na + /H + antiporter Nif, nitrogenase SAM, S-adenosyl methionine.

LUCA was an anaerobe, as long predicted by microbiologists [89]. Its metabolism was replete with O2-sensitive enzymes. These include proteins rich in O2-sensitive iron–sulfur (FeS) clusters and enzymes that entail the generation of radicals (unpaired electrons) via S-adenosyl methionine (SAM) in their reaction mechanisms. That fits well with the 50-year-old [90] but still modern view that FeS clusters represent very ancient cofactors in metabolism [91–93]. It also fits with newer insights about the ancient and spontaneous (nonenzymatic) chemistry underlying SAM synthesis [94].

LUCA lived from gasses. For carbon assimilation, LUCA used the simplest and most ancient of the six known pathways of CO2 fixation, called the acetyl–CoA (or Wood–Ljungdahl) pathway [95–97], which is increasingly central for our concepts on early evolution because of its chemical simplicity [97,98] and exergonic nature [99–101]. In the acetyl–CoA pathway, CO2 is reduced with hydrogen (H2) to a methyl group and CO. The methyl group is synthesized by the methyl branch of the pathway, which employs different one-carbon (C1) carriers in bacteria (tetrahydrofolate) and archaea (tetrahydromethanopterin), cofactors that are synthesized by unrelated biosynthetic pathways [96]. Carbon monoxide (CO) is synthesized by carbon monoxide dehydrogenase (CODH), the archaeal and bacterial versions of which are distinct but related [96]. The methyl and carbonyl moieties are condensed to an enzyme-bound acetyl group that is removed from a metal cluster in acetyl–CoA synthase (ACS) as an energy rich thioester. Thioesters harbor chemically reactive bonds [102] that play a crucial role in energy metabolism [101] and in metabolism in general, both modern and ancient [101,103,104]. Although CODH/ACS clearly does trace to LUCA [78,96], this is not true for the methyl synthesis branch, which consists of unrelated enzymes in bacteria and archaea [78,96].

A recent report [105] argued that the presence of CODH in LUCA did not exclude a heterotrophic lifestyle for LUCA. This argument is problematic because no single enzyme defines a trophic lifestyle. Even Rubisco (D-ribulose-1, 5-bisphosphate carboxylase/oxygenase), the classical Calvin cycle enzyme, is not a marker for autotrophy because Rubisco also functions in a simpler heterotrophic pathway of RNA fermentation [106–108] that is common among archaea and bacteria in marine sediment environments [109]. Moreover, all heterotrophs are derived from autotrophs due to the former requiring the latter as a source of chemically defined growth substrates. The reason is that CO2 constituted the main carbon source on Earth after the moon-forming impact [1,110], while carbon delivered from space was either too reduced to be fermented (polyaromatic hydrocarbons), too heterogeneous in structure to support microbial growth, or both [108]. Autotrophs with CODH can obtain ATP from CO2 reduction with H2 [98,101,110]. Autotrophs without CODH cannot. If we base inferences about LUCA's lifestyle on broad criteria rather than single genes [105], LUCA was an autotroph [78,108].

Life is about harnessing energy [44]. Thioesters are chemically reactive—they forge direct links between carbon metabolism and energy metabolism (ATP synthesis) as they give rise to acetyl phosphate, the possible precursor of ATP in evolution as a currency of high-energy bonds [111]. Relics of ATP synthesis via acetyl phosphate were found in LUCA's genes [78], as were subunits of the rotor–stator ATP synthase itself. The ATP synthase might appear to present a paradox because no proteins of the proton-pumping machinery that cells use to generate the ion gradient that drives the ATP synthase traced to LUCA [78]. Yet some theories have it that the first cells arose at alkaline hydrothermal vents [91,96,111], meaning that the inside of the vent is more alkaline than the ocean outside. Such naturally existing pH gradients could have been harnessed by LUCA to synthesize ATP (Fig 3). Ancestral ATPases might have harnessed either proton gradients or sodium gradients generated by proton/sodium (H + /Na + ) dependent antiporters [112], or they might have even been promiscuous for both kinds of ions, similar to the ATPase of modern microbes that live near the thermodynamic limits of life [113].

LUCA's environment was rich in sulfur thioesters, SAM, proteins rich in FeS and iron–nickel–sulfur (FeNiS) clusters, sulfurtransferases, and thioredoxins were part of its repertoire, as were hydrogenases that could channel electrons from environmental H2 to reduced ferredoxin, which is the main currency of reducing power (electrons) in anaerobes [114]. A recent report provided phylogenetic evidence that archaea are ancestrally H2-dependent methanogens [62], compatible with an autotrophic, H2-dependent lifestyle of LUCA.

LUCA had a reverse gyrase, an enzyme typical of thermophiles, suggesting that LUCA liked it hot. But independent of the reverse gyrase, simple chemical kinetics provide strong evidence in favor of a thermophilic origin for the first cells [115,116]. The reason is that only uncatalysed or inorganically catalysed reactions existed before there were enzymes. Their rates of reaction were lower than the enzymatically catalyzed reactions. Between 0°C and 120°C (the biologically relevant temperature range), organic chemical reaction rates generally increase with temperature [115,116]. Before there were enzymes, high-temperature environments were more conducive to organic chemical reactions than low-temperature environments [115,116]. Taken together, LUCA's requirement for gasses (CO2, H2, CO, nitrogen [N2]), the prevalence of sulfide, its affinity to high temperature and metals, plus an ability to use but not generate ion gradients all point to the same environment: alkaline hydrothermal vents.

In addition to shedding light on physiology, the 355 trees that showed domain monophyly (S1 Appendix) [78] also have another interesting property: they are reciprocally rooted. That is, the bacteria are rooted in an archaeal outgroup and vice versa. Genes present in LUCA contain information about their lineages and about the groups of bacteria and archaea that branched most deeply in each domain. In both cases, the answer was clostridia (bacteria) and methanogens (archaea). Those are strictly anaerobic prokaryotes that use the acetyl–CoA pathway live from CO2, H2, and CO fix N2 and today inhabit hydrothermal environments in the Earth's crust [117–119].

The onset of genetics

Though the organization of inanimate matter into living cells with genetics can be charted in mathematical terms [120,121], the biochemical details remain elusive. For example, it is controversial whether LUCA had DNA or not [87]. Several DNA-binding proteins trace to LUCA [78], so it would appear that LUCA possessed DNA, but it is unresolved whether LUCA could actually replicate DNA. For LUCA, DNA might just have been a chemically stable repository for RNA-based replication [122].

A novel and interesting aspect of LUCA's biology concerns modified bases and the genetic code. Transfer RNA requires modified bases for proper interaction with mRNA (codon–anticodon wobble base pairing) and with rRNA in the ribosome during translation. That is, modified bases are part of the universal genetic code (Fig 4), which was present in LUCA. Many RNA-modifying enzymes trace to LUCA, particularly the enzymes that modify tRNA. Several of those enzymes are methyltransferases (many SAM dependent), and they remind us that, before the genetic code arose, the four main RNA bases could hardly have been in great supply in pure form because there were no genes or enzymes, only chemical reactions [123]. Spontaneous synthesis of bases in a real early Earth environment like a hydrothermal vent, an environment that lacks the control of a modern laboratory [124], is not likely to generate the four main bases in pure form. Many side products will accumulate, including chemically modified bases [111]. Chemically modified bases from living cells have been reported since the 1970s by pioneering RNA chemists such as Mathias Sprinzl [125] and Henri Grosjean [126]. There are 28 modified bases, mainly occurring in tRNA, that are shared by bacteria and archaea [127]. The modifications are chemically simple, such as the introduction of methyl groups or sulfur and occasionally of acetyl groups and the like (Fig 4).

Cloverleaf secondary structure representation of tRNA showing post-transcriptional nucleoside modifications that are conserved among bacteria and archaea in both identity and position. The structures of respective conserved modified nucleosides are highlighted in grey. Methyl and acetyl groups are shown in red and dark red, respectively sulfur in yellow and the threonylcarbamoyl group in blue.

Chemical modifications in the tRNA anticodon are essential for codon–anticodon interactions to work [128,129]. Modifications of the rRNA are concentrated around the peptidyl transferase site and are also essential for tRNA ribosome interactions [130]. It is possible that the genetic code itself arose in the same chemically reactive environment where LUCA arose and that modified bases in tRNA carry the chemical imprint of that environment [78]. That would forge a link between the early Earth and genetics as we know it. New laboratory syntheses of RNA molecules in the origin of life context now also include investigations of modified bases [131], as it is becoming increasingly clear that these are crucial components at the very earliest phases of molecular and biological evolution.

Moving forward

Investigations of LUCA based on phylogenies of all genes pose new opportunities and new challenges. As environmental sequencing and metagenomics progresses, the number of microbial sequences and new lineages is exploding [48,109]. How will that aspect of metagenomics affect investigations of LUCA? If the criteria for gene age are phylogenetic (prokaryote domain monophyly, presence in at least two bacterial and archaeal “phyla”), then the correct taxonomic assignment of each sequence is very important. A problematic aspect of metagenomic data is that some data handling steps can assign incorrect higher taxon labels to genes [39,41,43], which in turn can falsify phylogenetic relationships. Analyses of cultured microbes or complete genome sequences limit the available sample size but deliver reliable taxon labels, at least at the level of archaea versus bacteria. Clearly, there are trade-offs.

At first sight, LUCA's genome appears doomed to shrinkage. As the sample of complete genomes grows, the list of 355 genes that trace to LUCA by domain monophyly criteria [78] will shrink because each new genome offers new opportunities to uncover recent LGT events for the 355 genes. Recalling that only 3% of the 11,093 clusters investigated [78] appeared free of transdomain LGT, it is evident that the inclusion of new genomes will eventually cause the number 355 to asymptotically approach zero, unless some genes never undergo transdomain LGT, which seems unlikely. What to do? Filtering out recent LGT events would help save LUCA's genome from shrinking to zero. For example, the tree for gene X might violate domain monophyly by one LGT event. If the LGT was recent, affecting members of only one recipient genus or family, it would hardly affect inferences about LUCA, adding gene X to LUCA's list. To identify recent LGTs in prokaryote phylogeny, standard criteria like incomplete amelioration [132], anomalously high-sequence identity [133], or presence in the auxiliary genome [134] will be useful, as will new methods that root unrooted trees [135]. Identifying recent LGTs should allow us to trace more genes to LUCA.

There is also the issue of clustering thresholds to consider, as discussed above. Stringent thresholds produce many small clusters and more relaxed thresholds produce a smaller number of very large clusters [136]. One can argue that large clusters (low stringency) allow one to look further back into time, but they also can generate clusters whose origins trace to duplications in LUCA, in which domain monophyly is violated but not because of LGT. Another factor concerns gene fusions. Genes tend to undergo fusion and fission during evolution [137,138]. In clustering procedures, gene fusions tend to slightly reduce the number of clusters because when they occur, they can bring two fused genes into one alignment, and the weaker phylogenetic signal in the fusion is obscured [23]. Methods to detect fusions exist [139,140]. By detecting gene fusions and dissecting them into their component parts, it might be possible to increase the number of trees that trace to LUCA by phylogenetic criteria.

Investigations into early evolution always elicit protest. For example, there were criticisms [141] of the term "progenote," which Woese and Fox [142] introduced to designate a state of organization below that of a free-living cell [143,144], as shown in Fig 3. In addition, multiple LGTs can, in principle, generate false positives by mimicking vertical inheritance from LUCA [78], but very specific conditions have to be fulfilled (Fig 1C). The challenge is to distill a chronicle of microbial evolution that takes all genes and LGT [145] into account and that conveys information about physiology [146], the energy-releasing reactions that power microbial evolution.

Conclusions

More clues about LUCA's lifestyle are emerging. Investigations of modern biochemical pathways hone in on the same kinds of reactions as the phylogenetic approach [103]. Similarly, laboratory experiments also demonstrate the spontaneous synthesis of end products and intermediates of the acetyl–CoA pathway, the mainstay of LUCA’s physiology new findings show that formate, methanol, acetyl moieties, and even pyruvate arise spontaneously at high yields and at temperatures conducive to life (30°C–100°C) from CO2, native metals, and water [98,147]. Those conditions are virtually impossible to underbid in terms of chemical simplicity [98], yet they bring forth the core of LUCA's carbon and energy metabolism [78,96,97,101,103] overnight. Did the origin of genetics hinge upon hydrothermal chemical conditions that gave rise to the first biochemical pathways that in turn gave rise to the first cells? Genes that trace to LUCA [78], ancient biochemical pathways [103], and aqueous reactions of CO2 with iron and water [98,110] all seem to converge on similar sets of simple, exergonic chemical reactions as those that occur spontaneously at hydrothermal vents [148]. From the standpoint of genes, physiology, laboratory chemistry, and geochemistry, it is beginning to look like LUCA was rooted in rocks.


Evidence from Life

Darwin recognized that the fossil record, as it existed, had serious problems. He admitted that the record, as it stood then, offered an argument against evolution. It was Darwin’s hope that continued fossil exploration would reveal more evidence demonstrating an unbroken succession of life forms from simple to complex.

During Darwin’s lifetime, a rich repository of some of the oldest fossils ever discovered was found in Cambria (the classical name for Wales). It is called the ‘Cambrian Explosion’. Because of its place in the geological column, only the simplest life forms should have been found in the Cambrian layer. According to the theory, rock in this layer should contain fossils that would give us insight into the very first stages of evolution. Surprise! What was found was totally unexpected! Paleontologists discovered what they call ‘bursts’ of life forms that appear abruptly, representing the major groups of animals with their radically different body plans. It confounded evolutionary thinking, because greatest distinctions between life forms appeared first, before the smaller variations.

These fossils were said to date back to what came to be called the Cambrian period—making them 485 to 542 million years old. Rocks assigned to the Cambrian have also been found in Utah, Canada, Siberia, Greenland, and China. During the time of Darwin (in the mid 1800s) the rock layer below the Cambrian stratum was believed to be older yet and was devoid of fossils, because it was believed that the heat and pressure from above had destroyed any traces of life. This pre-Cambrian section comprises most, some 88 percent, of the geological column.

More recently, an effort has been made to divide the pre-Cambrian rock into other geological layers. The Ediacaran Period allegedly precedes the Cambrian in time and is 542–635 million years old—a period in which fossilized soft body organisms or extinct worm-like creatures were found. There is uncertainty as to what fossils belong in the Ediacaran. Some that may belong in the Ediacaran are simply blobs. The Ediacaran Period is contained within the Proterozoic Eon, which evolutionists have assigned to be between 542 million and 2.5 billion years old. Fossils found in the Proterozoic are microscopic organisms including bacteria, fungi, protists (amoeba, paramecium, algae) and others. The fossils found in this eon are very much like what we see today and can be found on any other layer.

Cambrian fossils are of every basic body type. It is because they are so numerous and appear so abruptly in the geological record that this find has been called the Cambrian Explosion. Organisms from hard-shelled clams to mollusks to extinct trilobites, and even fish, have been discovered in this layer. This vast array of organisms, all found on one layer, is a huge problem to the evolutionary thesis that slow change over eons accounts for all life forms now in existence.


The Big Problem
Fully-formed fossils, representing so many kinds of animals without any ancestral forms, present a tremendous problem to evolution. Darwin’s theory states that all life forms evolved from simple to complex, from molecule to man. But in the Cambrian layer, where one would expect to find fossil evidence of lower forms—organisms in an earlier stage of evolution—none have been found. Even if one goes down further to the next layers, in the Proterozoic, no fossils that show any connection to the organisms found in the Cambrian appear. Again, the Cambrian explosion can not be explained by evolution, while creationists interpret this layer as the fossil record of those creatures that lived on the bottom of the ocean at the time of the Flood.


The Amazing Trilobite
Trilobites are extinct soft body animals that once moved along the bottom of the sea and had features similar to a horseshoe crab. They typically vary in size from 3–10 cm (1.2–3.9 inches) and have a ridged shell divided by three distinct lobes, the feature for which they are named. A few trilobite fossils have been found that measure 72 cm (2.4 feet). These creatures are found in the Cambrian layer, accompanied by many different kinds of creatures. Evolutionists get excited about old-age fossils, particularly the trilobite, because it is found in the Cambrian layer and thought to be some 500 millions years old. One would assume from evolutionary theory that the trilobite, given its putative age and place in the geological column, would be simple in form. Not so.

Like any other living system, trilobites have inherent complexity. One of the most revealing examples of complexity found in trilobites is their aggregate eye, a feature found in some, though not all trilobites. This very unique eye features an upper lens, which is hardened calcite, and a lower lens designed to correct the ray pattern to a focal point. It has rods in slightly different positions, similar to an insects’ compound eye. The aggregate eye is also called schizochroal and is one of the finest optical systems designed.

The design of the schizochroal eye makes it unique among eyes perhaps even to the point of being the best optical system known in the biological world. This design, in fact seems to far exceed the needs of the trilobite. The origin of the design of the schizochroal eye is not understood by means of any known natural cause. Rather, it is understood as being due to an intelligent (design-creating) cause, through a process involving remarkably high manipulative ability. Among available hypotheses, creation of God is the most reasonable hypothesis for the origin of the complexity of the trilobite’s schizochroal. 1

The Fossil Record’s Real Testimony

Randomness
The evolutionary hypothesis holds that simple organisms will change into more complicated forms slowly through time. For that reason, evolutionists divide the fossil record into theoretical periods, such as the Cambrian and Ediacaran, in order to show from the fossil record the progress of life up the evolutionary scale. It is not working out that way. As more and more fossils are discovered, these theoretical divisions are disappearing. Fossils keep appearing at the wrong places, suggesting that the system needs to change. As fossils are discovered, it is apparent that the organisms are not simple and that they challenge, by their unexpected complexity, evolutionary assumptions about the fossil record.

Living fossils
Living fossils are fossils of plants and animals that are not extinct, but still exist today. For example, more than 84 percent of insects still in existence have been found in the fossil record as far back as what evolutionists tell us was 100 million years ago. Other living fossils include the following:

    The Chambered Nautilus
    “It remains essentially the same as its ancestors of 180 million years ago
    . . . a living link with the past.” National Geographic, January 1976

Even More Complex Than You Think
Michael Behe, an outspoken biochemist, is challenging the foundations on which biological evolution rests. With the publication of Darwin’s Black Box in 1996, he presented an academic challenge to traditional Darwinian thought. As a biochemist, he began to question how small microorganisms could evolve from raw components. Although he is not a biblical creationist, he came to the conclusion that, given the fine details of these living systems, they could not have come from any known natural processes. This led him to the only alternative answer: an outside Intelligent Designer.

Biochemistry explains how all the component parts of a living system work together and how the molecules act together. The light microscope, pushed to its limits, could reach down to one-tenth the size of a bacteria cell. Many of the substructures could not be visualized completely, and many were still hidden. In the 1950s, with the aid of the new electron microscope, cell structure took on a new meaning. The electron microscope has the capacity, with the aid of an electron beam, to magnify an object 500,000 times.

With the capacity to view the cell in such incredible detail, many new subcellular structures were discovered. Behe, in his book, reflects on the fact that each of these substructures have their own set of biochemical instructions. Such detail exponentially increased the complexity of the cell. A hundred years after Darwin, the simple cell suddenly became immensely complicated, with countless systems all entwined with each other to contribute to the total biological purpose of sustaining life.


Molecular Machines
The molecular machines of the cell are the proteins. These molecular protein machines are the basic material of which cells are made. They provide structure and chemically interact with other molecules and particles of the cell. Proteins are composed of 100 or more amino acid units strung together in different sequences to make a long chain. An amino acid chain needs help from a molecular machine called a chaperonin so that it can properly fold into the three dimensional shape of a protein. These folded proteins have their own complexity and are useful for specific cell functions, as in building structures or chemically reacting with other molecules.

It is in the details that evolution fails so miserably. The molecular structures from which proteins are made have always been challenging. Today they continue to give biochemists new revelations of how living systems work. These proteins make up the different structures of the cell, which include the nucleus, mitochondrion, ribosome, cell membrane, vacuole and many others.

Cells are mobile and move with the help of different protein structures. Bacterial cells move in a variety of ways. A moving tail, called a flagellum, propels one type of bacteria cell. This tail is made of hundreds of different types of proteins that function just like a rotary propeller moving at impressive speed. Behe suggests that the flagellum paddling mechanism is made of three substructures: the paddle, a rotor, and a motor. The bacterial flagellum is a marvelously designed substructure with the following unique characteristics:

• Moves in two directions:
forward and reverse

• Reversing after ¼ of a turn

• At least 40 operational parts

• Rotary motor cooled by water


Irreducible Complexity
Behe introduced the concept of ‘irreducible complexity’ to describe what he found in the myriad micro systems all functioning together within a cell. He found component parts as simple as a molecule synchronized with other molecules, like the mechanical gears of an expensive Swiss watch. Just as the watch would stop if one of the gears failed—if a molecule were altered in a biologically elaborate system—the organism could die. In the words of Behe:

By irreducibly complex, I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. 2

This principle of irreducible complexity can be seen at every level of biological function—from molecules to cells to organs to organisms. The simple tail of a one-cell bacteria, as described above, has at least 40 moving parts. If one of those parts failed to function, the tail would cease to work. Without the tail, the cell could not move and without movement, the cell would die for lack of nutrients.


No Room for Evolution
Irreducible complexity makes a powerful argument for design. For a system to function, not only are all parts needed, but a set of instructions are needed as well for how the parts should work together. To assemble a new lawn mower out of the box, not only do you need all the parts, you need an instruction manual (hopefully, with lots of pictures) to put it together. Cell assembly is a far more complex task than putting together a lawn mower. The parts and instructional manual for the cell did not produce themselves. They had to come from a divine planner, the Creator—Jesus Christ.

The study of biochemistry demonstrates how the basic materials in a cell or other living system function together. This academic discipline majors on the details of life and is usually taught in the upper level of undergraduate or the graduate level at colleges and universities. It is interesting to note that evolution has no place in this discipline. Many biochemistry texts completely ignore evolution. When mentioned, it is usually in passing. By its nature, biochemistry deals with measurable, empirical data. It seeks out the order and design in living systems, a process that, if one is open-minded, leads to the deduction that there is an intelligent Creator. This, after all, was Behe’s final conclusion:

The simplicity that was once expected to be the foundation of life has proven to be a phantom instead, systems of horrendous, irreducible complexity inhabit the cell. The resulting realization that life was designed by intelligence is a shock to us in the twentieth century who have gotten used to thinking of life as the result of simple natural laws. 3


DNA from a Higher Source
It was front-page news nationwide. “Genetic Code of Human Life Is Cracked by Scientists,” the New York Times announced on June 27, 2000. This marked the first time the whole human DNA code—the blueprint of life—had been mapped. This enormous project, formally called the Human Genome Project, involved hundreds of scientists in a multibillion-dollar experiment funded by medical research grants from several countries. They found the exact sequencing of 3.2 billion chemical building blocks (abbreviated with the letters A, T, C, and G) in the DNA of a human. All sorts of wonderful benefits were predicted with this discovery, including a cure for cancer.

Unfortunately, the press reacted too quickly. Now it appears that there is a long road ahead, with many difficult hurdles to clear. What was really uncovered was similar to four letters strung out in a sequence of 3.2 billion base pairs. Much work still has to be done to understand the meaning of those letters. The term ‘cracking the genetic code’ implies that scientists understand what the code means. The mapping of all that human genetic information is a great accomplishment. But to say that it is understood? This is nothing but a puffed-up exaggeration by the press.

Evolutionary scientists once concluded that out of the billions of bits of DNA base pair data, only 5 percent are actually used. Beyond that extremely small percentage, the rest was labeled as ‘junk’ DNA, or evolutionary ‘leftovers’. This so-called ‘junk’ DNA is something we don’t fully understand at the present time, but as research continues, new insights are being revealed as to its genetic function. Creationists argue that junk DNA performs important regulatory functions, and could have been used to enable a rapid post-Flood biological adjustment.

Presently, there are still large gaps of knowledge that remain. To illustrate this even further, the geneticists have recently found that genes can have more than one function. For instance, the Distal-less gene develops the appendages of mice, sea urchins, spiny worms and velvet worms. The same gene produces different structures. This phenomenon is being intensely studied and is still a big mystery. Clearly, the genetic code is extremely complicated.


What Does DNA Look Like?
James Watson, an American biologist, and Francis Crick, a British physicist at Cambridge, England, worked out the structure of DNA in 1953. DNA is the foundational information storage system of life. Finally, the mysterious chemical structure that controls every living organism was revealed to all mankind. All life is controlled by a simple double helix structure. This is like a nanoscale spiral staircase, where the stairs are made by four chemical bases: Guanine (G), Cytosine (C), Adenine (A), and Thymine (T). The ‘stairs’ connect two strands comprising alternating deoxyribose (a type of sugar) and phosphate. This explains the name of DNA: deoxyribonucleic acid.

The DNA molecule is a very long, microscopically thin string that is tightly bound together. When it unravels, it unzips the double helix, and the two segments open up, exposing a sequence of the four base pairs listed above. Since the molecule is very long, the sequence of base pairs on each side carries an immense amount of information. When both sides of the DNA molecule open, the four base codes send instructions from the nucleus of the cell to build proteins. The simplicity of two base pairs is amazing—being sequenced over a long molecule and having the potential to contain the information from which all life is derived.

Amazing Properties

DNA has extraordinary properties, including the following:

• DNA is a very thin filament measuring 0.000,000,002 meters thick in diameter.

• DNA is so thin that a strand of DNA long enough to reach the sun would weigh only half a gram.

• The DNA in each human cell would be about 2 m (6 feet) long if totally unraveled.

• If an adult human’s entire DNA were to be unwound, it would extend 184 billion kilometers. That is an unimaginably long molecular string that would go to the sun and back, a distance of 310 million kilometers (or 186 million miles), some 596 times.

• DNA weighing an amount equivalent to 1/15 of a postage stamp contains all the DNA needed to make 5 billion people.

• The information in the DNA of each human cell would fill 850 Bible-sized books.


How is the Information Stored?
Information is derived from the order in which the four bases, or chemical ‘letters’ appear. But this order is meaningless unless decoded by many decoding machines, including the ribosome. This is a real chicken-and-egg problem: the instructions to build these decoding machines are in the DNA, but these instructions can’t be decoded without already-existing decoding machines.

The code produces genetic information for proteins to do their work, making cells to form a plant, frog, turtle, human or any living system. There are at least 50,000 different proteins in living systems. In DNA, the base pairs function in three groups. In threes, the information code is given to produce amino acids. The amino acids then bond together, usually in the thousands, to make the proteins essential for living systems.

The intelligence center of the cell is the nucleus where the DNA is found. The DNA molecule is considered the greatest information carrier known to man. The tiny DNA molecules are tightly wound up. For example, the E. coli chromosome has 300,000 twists in the space 1 mm. DNA’s information density is a staggering 1.88 × 10 21 bits per cm 3 . The sum of all human knowledge in all books is 10 18 bits. All the libraries of the world combined could never match the amount of information in one cubic centimeter, or 0.4 of a cubic inch, of DNA.

The sum total of knowledge currently stored in the libraries of the world is estimated at 1018 bits. If this information could be stored in the DNA molecules, one percent of the volume of a pinhead would be sufficient for this purpose. If, on the other hand, this information were stored with the aid of mega chips, we would need a pile higher than the distance between the earth and the moon. 4

DNA: Self-Replication
Not only is DNA a magnificent information machine, it also has phenomenal replication accuracy. After all, its basic function is to transfer genetic information in order to continue living processes. Since cells make every living organism, it is of extreme importance that no information is lost in the duplication process. Cells, after they divide, must have identical genetic information without any transfer of mistakes. To replicate, the DNA molecule in a bacteria cell unravels at an amazing speed of 10,000 revolutions per minute.

The chemical structure of the bases provides the means for replicating the information—as a cell divides, and from parent to child. The letter A of one strand always matches a T of the other, and vice versa and G always matches C. So the each DNA strand can be copied to make another strand which is analogous to a photographic negative. Here as well, there are complex machines needed for the copying, in particular DNA polymerase. This is another chicken-and-egg problem: the instructions to build DNA are also stored on DNA, but they can’t be passed on to the next generation without pre-existing copying machines.

This replication is also very accurate, thanks to error-checking machines:

The replication is so precise, that it can be compared to 280 clerks copying the entire Bible sequentially, each one from the previous one, with (at most) one single letter being transposed erroneously in the entire copying process. 5

Once again, there is a chicken-and-egg problem: the instructions to build the error-checking machines are stored in the DNA. But without pre-existing error checking machines, these instructions would be degraded when the DNA is replicated. This would lead to worse error-checking machines, which would allow further degradation of the instructions, causing even worse machines. This would be an error catastrophe.

Only from an Intelligent, Outside Source
The DNA code contains information that is translated into a program to make a specific protein. The protein is made to fulfill a biological need so the living system can function. There is a molecular transfer of information from the DNA molecule, which is programmed to be aware of the total needs of the whole living system. Biochemists have classified this marvelous process as ‘the language of life’. It is apparent that the information system for all life is a wonder. The fact is that DNA is designed with such an ultimate excellence that it far surpasses what man has done and what he can do in the future. The amount of information stored and the way it is replicated is nothing but a miracle.

The code reveals a language that is in every gene. The complexity of this language, as mentioned above, far exceeds all human knowledge. It could not come from a material source. It is classified as a language not unlike a computer language. One would consider it ridiculous to assume that computer programming came from the computer chip. Every computer language was made from an outside source. Language uses a higher form of conceptual intelligence.

The late Dr. Wilder Smith demonstrated by a simple illustration the preposterous nature of the evolutionary idea that life came from inert matter. He compared the claim that life could be produced from inert matter to the idea of a blank book producing letters on its pages. In the case of the book, once all 26 letters are produced, they would then randomly combine to make words. These words would randomly mix to make sentences expressing complete thoughts. The random process would continue until a paragraph is formed. After that, paragraphs would randomly combine to make chapters and, finally, the same random process would produce the final product, the book. Not likely.

It is obvious that books are the product of an outside intelligence and that language is used to translate information. But evolution offers the irrational argument that the DNA code came from randomness. Dr. Smith’s illustration makes it clear that the DNA code must originate from an outside intelligent source who has a plan and will use the letters to give us words or proteins. These proteins combine and form complete sentences—or cells. These cells combine and form paragraphs—or tissue. These tissues come together to form chapters—or organs. And the last step … these organs come together to form the book—or organism. All of these steps are programmed by an outside source, just as an author writes a book.

There is no man in the universe who could come up with this wonderful and awesome design for life. The evidence is clear. The complexity of any living system points to God. It is written in our genes that there is a God … so we are without excuse.

Statistically Impossible!
As mentioned above, the protein molecule adds structure and function to every living cell. It is a long molecule that contains many subunit molecules all bonded together. These subunit molecules are called amino acids and are composed mainly of the elements nitrogen, oxygen, hydrogen, and carbon.

There are twenty kinds of amino acids involved in living plants and animals. A typical protein will have between 100 to 300 amino acids connected in a definite sequence. These amino acid sequences give the protein its shape and its potential to function as a basic unit of a component of the cell.

It should be noted that 19 out of the 20 types of biological amino acid molecules have a mirror image. Just as one’s right hand is a mirror image of the left hand, so amino acids have a left- and a right-hand side to their molecular structure. If these amino acids were really formed in a primordial soup, as most evolutionists believe, they would be in a 50-50 (racemic) mixture. Amazingly, all observable living things are made of left-handed amino acids.

The protein is encoded with information based on the sequencing of its amino acids. Different sequences give different information which, in turn, allows the protein to perform various functions. This works because DNA operates with a several coded languages. The best known code operating on DNA is to make proteins: every three-letter sequence is called a codon, because it codes for one protein ‘letter’ or amino acid, or to start or stop the protein being made.

The sequencing of the amino acids begins in the DNA of the cell. Because DNA starts the process, it is very often called the information center of the cell. The big question is: Where does the DNA molecule receive its information? The answer is obvious—from an outside source—an intelligent Creator.


The Improbable Protein
A simple protein must have at least 100 amino acids bonded together in a set sequence. There are twenty amino acids to choose from, and, assuming they were available in number, the probability for the formation of a protein molecule would be impossible. The probability comes out to a staggering chance of one out of 10 115 . That is 1 followed by 115 zeroes. This impossible-to-imagine number completely exceeds the statistical odds that it could ever happen. (Borel’s Law holds that any probability less than 1 out of 10 50 could not happen).

There is a 50 percent possibility that amino acids will be right- or left-handed. All protein molecules have left-handed amino acids. If a right-handed amino acid is added, it could be extremely toxic to the living system. With this new variable added to the above calculation for the statistical likelihood of the formation of a protein, one is confronted with an even greater problem. Given the criteria that not only do all 100 amino acids have a specific sequence, but they are all left-handed, the probability that this will occur works out to one in 10 145. This last calculation overwhelmingly demonstrates the massive problem evolution has in getting inert matter to form a protein. The statistical improbability for the next step, the formation of a single cell from all these improbable proteins, is beyond comprehension.

Seeking Help in the Heavens
When faced with these cold, hard statistics, what chance did evolution have? Francis Crick suggested life itself may be likened to a ‘miracle’.

An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going. 6

Thus some evolutionists looked heavenward for answers and came up with the idea of ‘Directed Panspermia’. Crick helped popularize the hypothesis that some kind of extraterrestrial intelligence, aided by a UFO, carried life spores to the earth. Most evolutionists find this nothing but fantasy. In the real world, though, many do hope that an asteroid or trip to the planet Mars might reveal a life form that may have made it to earth untouched and ready to be incubated.
However, this is not only unscientific, it merely removes the very same problem to the untouchable reaches of the distant cosmos.


Kind After Kind
Researchers have, by means of genetic breeding, changed a two-wing fruit fly into a four-wing fruit fly. The four-wing fruit fly consistently reproduces four-winged fruit flies. But although a new variety has been produced, it is not a new ‘kind’. The mutant fruit fly is still a fruit fly. As a matter of fact, the four-winged fruit fly is a weakened form. The second set of wings do not help the fruit fly they actually get in the way. Its ability to take flight is dangerously hindered. Having been selectively bred in the laboratory, this variant would not survive without the caring assistance of researchers. This is a poor example of evolution by mutation. The bottom line is that mutations always weaken an organism and never change it into something fundamentally different. The fruit fly remains a fruit fly.


Beneficial Mutations?
Evolutionists often offer sickle cell anemia as an example of a beneficial mutation because those who have it have a reduced likelihood of getting malaria. Sickle cell anemia originates in a mutation in the hemoglobin molecule found in the red blood cells of our body. This mutation distorts the normal biconcave (concave on both sides) shape of the red blood cell. Presently, this disease affects millions of people worldwide in the United States alone there are some 70,000 cases of active sickle cell anemia.

Sickle cell anemia is a hereditary blood disorder that is most common in people who trace their ancestry to Africa or India, regions where malaria outbreaks have taken many lives. However, those who have one sickle-cell gene and one healthy hemoglobin gene (i.e. are heterozygous in this trait) have minimal sickle-cell symptoms but also have malarial resistance. So since the mutant gene benefits its possessor, it is a beneficial mutation by definition. However, as will be shown, this is irrelevant for evolution.

Definitely a Defect
Even this beneficial sickle cell mutation is most definitely a defect. There is no substitute for the optimal biconcave shape of normal hemoglobin molecules. This shape is tolerant to quick movement and designed perfectly for the effective transfer of oxygen to every cell in our body.

In the case of sickle cell anemia (SCA), the DNA that produces the proteins to make the hemoglobin in the red blood cells actually transfers one coding error. This error or genetic defect produces hemoglobin molecules that stick to each other when oxygen is released to the tissues. The defective hemoglobin molecules form long rigid chains that completely distort the shape of the red blood cell. Some of these distorted red blood cells actually form a distinct crescent shape and look like ‘sickles’—hence the name ‘sickle cell’.

These distorted red blood cells grow in size and can clog the capillaries, which limits the transfer of oxygen and causes severe pain to the extremities and throughout the body, including the chest cavity. It also leads to shortness of breath, infection, organ damage, and, in severe cases, can cause death. It also should be noted that sickle-shaped red blood cells die prematurely because of their large unstable shape. A normal red blood cell will last 120 days while a sickle cell can only survive 10 to 20 days. Patients with this disease often need blood transfusions to replace their lost hemoglobin.

However, a person who is heterozygous with the SCA gene usually doesn’t have the misfolding that leads to the anemia. But when the malarial parasite (Plasmodium) invades one of his blood cells, it causes the hemoglobin to ‘sickle’ and deform the blood cell. The spleen detects this defective cell and destroys it along with the parasite.

It’s important to note that this has nothing to do with evolution of more complex features. Rather, it is more akin to guerilla war against an invading army: guerillas might destroy a bridge on which the enemy is crossing. However, although it is ‘beneficial’ for the country to destroy the enemy, the country is poorer by one bridge. Similarly, the person destroys the malarial parasite but loses a blood cell in the process.

In any case, resistance to malaria at the cost of a dangerous blood disorder that leads to premature death does not confirm Darwin’s idea that species evolve upward over time. 7

Beneficial Mutations “Exceedingly Rare”
Mutation statistics accumulated over several decades show that there is very little data to build a theory that evolutionary progress takes place by means of beneficial mutation. First, as shown, the usual examples of beneficial mutation are still destructive. Also, the late Motoo Kimura, a Japanese mathematical biologist, introduced in 1979 a statistical method for handling data on genetic mutations. He clearly demonstrated that most mutations are neutral in their effect. Very few are lethal and no beneficial mutations are represented in his graphical representation because the number is too small to be mathematically significant. According to J.C. Sanford, a geneticist from Cornell University who invented the ‘gene gun’, beneficial mutations “are exceedingly rare—much too rare for genome building.” 8

The development of bacterial resistance to antibiotics is often suggested by evolutionists as another proof for upward evolutionary progress through beneficial mutations. A careful molecular analysis shows quite the contrary. Mutant strains of bacteria that show resistance to antibiotic are hindered by a degradation of genetic information—meaning they have become less fit over time. “Clearly, the fitness of some mutant strains is permanently reduced (sometimes dramatically), and evolutionists have typically ignored such effects in their rush to promote antibiotic resistance as ‘evolution in the Petri dish,’” according to microbiologist Dr. Kevin Anderson.9 Just like SCA above, the resistance is caused by information-destroying mutations, even if they are beneficial.


Statistically Insignificant
Dr. Jerry Bergman searched for the term ‘beneficial mutations’ in two biomedical journal databases containing 18.8 million records. While the term ‘mutation’ turned up 453,732 times, the phrase ‘beneficial mutation’ was used just 186 times, a statistically insignificant number (.041 percent) that agrees with Kimura’s statistical analysis. As Bergman researched further he found that so-called ‘beneficial mutations’ always involved a loss of genetic information. He concluded: “Not a single clear example of an information growing mutation was located. It was concluded that molecular biology research shows that information-gaining mutations have not been documented.” 10

Perhaps the best way to summarize the overuse of the evolutionists’ blind faith in ‘beneficial mutations’ is with Sanford’s own words, “In conclusion, mutations appear to be overwhelmingly deleterious, and even when one may be classified as beneficial in some sense, it is still usually part of an over-all breakdown and erosion of information.” 11

No New Information
A basic information principle must be violated for evolution to be true. For an organism to evolve upward from simple to complex, there must be an increase of genetic information. When mutations take place, however, there is an exchange of information or misinformation, but never an increase. The system is limited to what it has and, therefore, cannot create new information. Most frequently, information exchange leads to a loss of information. The loss of genetic information is consistent with the universal law of entropy.

It can be observed that errors in the genetic code are passed between generations. The rate of mutation is much too high to allow for evolution over millions of years. There are 100 to 300 misspellings of our genetic code passed on from one generation to the next. This might seem insignificant when we consider that the human genome contains 3 billions letters. However, the human race has six billion people, which means some 600 billion to 1.8 trillion genetic mistakes per generation.

Genetic Load
If one includes other types of mutations, such as deletions, insertions, duplications, mitochondrial mutations and others, the number of individual mutations will be 1,000 times more for each person and for the whole population. As a result, our genetic endowment is being corrupted. This phenomenon of accumulating mutations is best termed as ‘genetic load’.

According to Dr. Sanford, “The consensus among geneticists is that at present the human race is degenerating genetically, due to rapid mutation accumulation and relaxed natural selection pressure.” The decline in our fitness as a species is thought to be taking place, Sanford writes, at the rate of one to two percent per generation. 12

Such a great rate of decay in the genetic code does not fit with the six to seven million years it took for man to evolve according to the evolutionary model. It fits best with a biblical time frame of 6,000 years. This range of time was determined using a biological decay curve that was constructed using the rate of genomic degeneration. 13

There is no time for evolution to take place with this type of genetic degeneration. The human race is subject to more variations of disease and sickness as the ‘genetic load’ increases. Man will have to work hard against the law of entropy to stay alive. Genetic deterioration certainly excludes the idea of upward evolutionary progress by which we move from tiny living molecules and organisms to man.

Chimp and Human DNA
There has been a great deal of time, energy, and money invested for the purpose of developing advanced technology to investigate plant and animal DNA. The ability to isolate complete genetic alphabet sequences will no doubt start to give us a better understanding of the bio-molecular process. Evolutionists are at the door anxiously waiting to jump in and chant, “I told you that slow change of our genetic code is how we humans got here after all.”

The October 9, 2006, cover of Time displayed a juvenile monkey’s face just above the shoulder of an infant, with the provocative title, “How We Became Human. Chimps and humans share almost 99 percent of their DNA. New discoveries reveal how we can be so alike—and yet so different.”

Actually, the 99% genetic similarity claim is based on outdated and selective research. The true sequence similarity is unknown, but more recent studies have found dramatic differences that demolish the 1% myth. 14 But even if the difference was only one percent, would that mean men and monkeys are almost alike? Since there are 3 billion letters in our DNA, this would mean 30 million differences! As one writer for Smithsonian admits, “just a few percentage points translate into vast, unbridgeable gaps between species.” 15

No one will disagree after a visit to the zoo that chimps look more like us than any other animal. They rank high in intelligence and have a fairly complex social system in the animal kingdom, but there is a real difference between people and other primates. Physical similarities may exist, but the differences are so huge that we would never confuse an ape with a human. The proportions of the lengths of our arms and legs, the appearance of the neck, skull, pelvis, hands, and soft tissue structures—including our lips—clearly distinguish us from other species. Internally, our proteins are 71 percent different from that of a chimp. We have 46 chromosomes while a chimp has 48, and our Y chromosomes are radically different. 16

More to it Than the Code Itself
The most important point of comparison between genetic sequences is not how similar the genes are but how the genes act or are expressed. Even similar gene sequences may act very differently because of their interaction with other genes. Our physical appearance, for example, is controlled by just a few genes. The length and shape of our nose, eyebrows, complexion, eye and hair color, etc., are all modulated not by an army of genes but by the orders of a very few genes which work in dynamic harmony. Dramatic physical change does not necessarily have to be orchestrated by DNA directly.


Physical Change Without DNA Difference
Giuseppe Sermonti, a distinguished geneticist from Italy, argues that it may not be DNA alone that determines the nature and structure of living things. There is a black box between DNA and the total function and purpose of an organism. Secular evolutionists who suppose that DNA changes can explain evolution need to heed Sermonti’s eloquent warning: “My view is that the problem is rather how the organism makes use of DNA, getting it to work or keeping it silent, and how it selects its areas of interest. DNA is not the starting point.” 17 Just because we find the complete genome does not mean that we understand how DNA functions. Sermonti says we have great mysteries still to explore in seeking to understand how DNA determines who we are.


Common Designer, Not Common Ancestor
Evolution holds that organisms with similar designs must descend from one common ancestor. This argument can be challenged by this question, “Does similarity mean we come from the same ancestry or does it mean we were created by the same designer?” That designer would be the master creator, who could produce an ultimate design for every niche in the physical and living universe. That creator would have to be the perfect designer who knows all things and therefore chose the ultimate design, a universal design that can be utilized with the greatest efficiency to maintain all life. The evidence points to one magnificent, intelligent Creator.

For example, you may notice that a car dealership has a wide selection of cars. Each car has four wheels, an internal combustion engine, steering wheel, and many other common features. Did you ever wonder if the common design would mean that there would be common descent? In other words, did the cars evolve themselves without any outside help? This, of course, is ridiculous, because we know that enormous diligence was needed to design each car model. Although their basic features are the same, they have many other unique qualities that make them attractive to potential buyers. Each car model began with a preplanned design and an outside intelligent creator.

Since there are ultimate designs that function for the exact purpose for which they were created, one may expect to witness repetitive patterns in the universe. The more repetitive a design, the closer it is to perfection. We observe in nature, for example, many animals that have appendages—such as legs or arms or digits.

Does similarity mean we come from the same ancestry? Evolution holds that all organisms have descended from one common ancestor. Creation holds that all living things come from one common source, and are created by one Creator who set out an ultimate design for the universe … and all that is in it.

For by him all things were created… all things were created through him and for him.
—Colossians 1:16


What are the evidence that all life today descended from a common ancestor (LUCA), and which organisms (if any) challenge the concept? - Biology

In this section, you will explore the following questions:

  • How was the present-day theory of evolution developed?
  • What is adaptation, and how does adaptation relate to natural selection?
  • What are the differences between convergent and divergent evolution, and what are examples of each that support evolution by natural selection?
  • What are examples of homologous and vestigial structures, and what evidence do these structures provide to support patterns of evolution?
  • What are common misconceptions about the theory of evolution?

Connection for AP ® Courses

Millions of species, from bacteria to blueberries to baboons, currently call Earth their home, but these organisms evolved from different species. Furthermore, scientists estimate that several million more species will become extinct before they have been classified and studied. But why don’t polar bears naturally inhabit deserts or rain forests, except, perhaps, in movies? Why do humans possess traits, such as opposable thumbs, that are unique to primates but not other mammals? How did observations of finches by Charles Darwin visiting the Galapagos Islands in the 1800s provide the foundation for our modern understanding of evolution?

The theory of evolution as proposed by Darwin is the unifying theory of biology. The tenet that all life has evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology. As we learned in our exploration of the structure and function of DNA, variations in individuals within a population occur through mutation, allowing more desirable traits to be passed to the next generation. Due to competition for resources and other environmental pressures, individuals possessing more favorable adaptive characteristics are more likely to survive and reproduce, passing those characteristics to the next generation with increased frequency. When environments change, what was once an unfavorable trait may become a favorable one. Organisms may evolve in response to their changing environment by the accumulation of favorable traits in succeeding generations. Thus, evolution by natural selection explains both the unity and diversity of life.

Convergent evolution occurs when similar traits with the same function evolve in multiple species exposed to similar selection pressure, such as the wings of bats and insects. In divergent evolution, two species evolve in different directions from a common point, such as the forelimbs of humans, dogs, birds, and whales. Although Darwin’s theory was revolutionary for its time because it contrasted with long-held ideas (for example, Lamarck proposed the inheritance of acquired characteristics), evidence drawn from many scientific disciplines, including the fossil record, the existence of homologous and vestigial structures, mathematics, and DNA analysis supports evolution through natural selection. It is also important to understand that evolution continues to occur for example, bacteria that evolve resistance to antibiotics or plants that become resistant to pesticides provide evidence for continuing change.

Information presented and the examples highlighted in this section support concepts outlined in Big Idea 1 of the AP ® Biology Curriculum Framework. The AP ® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP ® Biology course, an inquiry-based laboratory experience, instructional activities, and AP ® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 1 The process of evolution drives the diversity and unity of life.
Enduring Understanding 1.A Change in the genetic makeup of a population over time is evolution.
Essential Knowledge 1.A.1 Natural selection is a major mechanism of evolution.
Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question.
Learning Objective 1.9 The student is able to evaluate evidence provided by data from many scientific disciplines that support biological evolution.
Essential Knowledge 1.A.2 Natural selection acts on phenotypic variations in populations.
Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain.
Learning Objective 1.5 The student is able to connect evolutionary changes in a population over time to a change in the environment.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena.
Learning Objective 1.2 The student is able to evaluate evidence provided by data to qualitatively and quantitatively investigate the role of natural selection in evolution.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question.
Learning Objective 1.12 The student is able to connect scientific evidence from many scientific disciplines to support the modern concept of evolution.
Essential Knowledge 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics.
Science Practice 5.2 The student can refine observations and measurements based on data analysis.
Learning Objective 1.10 The student is able to refine evidence based on data from many scientific disciplines that support biological evolution.
Enduring Understanding 1.C Life continues to evolve within a changing environment.
Essential Knowledge 1.C.3 Populations of organisms continue to evolve.
Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales.
Learning Objective 1.26 The student is able to evaluate given data sets that illustrate evolution as an ongoing processes.
Essential Knowledge 1.C.3 Populations of organisms continue to evolve.
Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales.
Learning Objective 1.25 The student is able to describe a model that represents evolution within a population.
Essential Knowledge 1.C.3 Populations of organisms continue to evolve.
Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales.
Learning Objective 1.4 The student is able to evaluate data-based evidence that describes evolutionary changes in the genetic makeup of a population over time.

The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards:
[APLO 1.10][APLO 1.12][APLO 1.13][APLO 1.31][APLO 1.32][APLO 1.27][APLO 1.28][APLO 1.30][APLO 1.14][APLO 1.29][APLO 1.26][APLO 4.8]

The Origin of Life

Humans have adopted many theories regarding the origin of life over the course of our time on Earth. Early civilizations believed that life was created by supernatural forces. Organisms were “hand-made” to be perfectly adapted to their environment and, therefore, did not change over time. Some early thinkers, such as the Greek philosopher Aristotle, believed that organisms belonged to a ladder of increasing complexity. Based on this understanding, scientists such as Carolus Linnaeus attempted to organize all living things into classification schemes that demonstrated an increasing complexity of life.

Over time, however, scientists came to understand that life was constantly evolving on Earth. Georges Cuvier found that fossilized remains or organisms changed as he dug into deeper rock layers (strata), indicating that the organisms present in the area had changed over time. This observation led Jean-Baptiste de Lamarck to hypothesize that organisms adapted to their environment by changing over time. As organisms used different parts of their body, those parts improved, and these changes were passed down to their offspring. Ultimately, these theories were disproven by scientists, but their development contributed to the theory of evolution that was finally formulated by Charles Darwin.

Charles Darwin and Natural Selection

In the mid-nineteenth century, the actual mechanism for evolution was independently conceived of and described by two naturalists: Charles Darwin and Alfred Russel Wallace. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape (//cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#fig-ch18_01_01">Figure 18.2). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the mainland of South America. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that the varied beaks of each finch helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey.

Wallace and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, also known as “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits this leads to evolutionary change.

For example, a population of giant tortoises found in the Galapagos Archipelago was observed by Darwin to have longer necks than those that lived on other islands with dry lowlands. These tortoises were “selected” because they could reach more leaves and access more food than those with short necks. In times of drought when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that couldn’t reach the food source. Consequently, long-necked tortoises would be more likely to be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population.

Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring. Although no one, including Darwin and Wallace, knew how this happened at the time, it was a common understanding. Second, more offspring are produced than are able to survive, so resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came from reading an essay by the economist Thomas Malthus who discussed this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Darwin and Wallace reasoned that offspring with inherited characteristics which allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment it is the only mechanism known for adaptive evolution.

Papers by Darwin and Wallace (//cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#fig-ch18_01_02">Figure 18.3) presenting the idea of natural selection were read together in 1858 before the Linnean Society in London. The following year Darwin’s book, On the Origin of Species, was published. His book outlined in considerable detail his arguments for evolution by natural selection.

Demonstrations of evolution by natural selection are time consuming and difficult to obtain. One of the best examples has been demonstrated in the very birds that helped to inspire Darwin’s theory: the Galápagos finches. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of natural selection. The Grants found changes from one generation to the next in the distribution of beak shapes with the medium ground finch on the Galápagos island of Daphne Major. The birds have inherited variation in the bill shape with some birds having wide deep bills and others having thinner bills. During a period in which rainfall was higher than normal because of an El Niño, the large hard seeds that large-billed birds ate were reduced in number however, there was an abundance of the small soft seeds which the small-billed birds ate. Therefore, survival and reproduction were much better in the following years for the small-billed birds. In the years following this El Niño, the Grants measured beak sizes in the population and found that the average bill size was smaller. Since bill size is an inherited trait, parents with smaller bills had more offspring and the size of bills had evolved to be smaller. As conditions improved in 1987 and larger seeds became more available, the trend toward smaller average bill size ceased.

CAREER CONNECTION

Field Biologist

Many people hike, explore caves, scuba dive, or climb mountains for recreation. People often participate in these activities hoping to see wildlife. Experiencing the outdoors can be incredibly enjoyable and invigorating. What if your job was to be outside in the wilderness? Field biologists by definition work outdoors in the “field.” The term field in this case refers to any location outdoors, even under water. A field biologist typically focuses research on a certain species, group of organisms, or a single habitat (//cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#fig-ch18_01_03">Figure 18.4).

One objective of many field biologists includes discovering new species that have never been recorded. Not only do such findings expand our understanding of the natural world, but they also lead to important innovations in fields such as medicine and agriculture. Plant and microbial species, in particular, can reveal new medicinal and nutritive knowledge. Other organisms can play key roles in ecosystems or be considered rare and in need of protection. When discovered, these important species can be used as evidence for environmental regulations and laws.

Processes and Patterns of Evolution

Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons such as an individual being taller because of better nutrition rather than different genes.

Genetic diversity in a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes on the phenotype. A mutation can affect the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of survival or fewer offspring. Alternatively, a mutation may produce a phenotype with a beneficial effect on fitness. And, many mutations will also have no effect on the fitness of the phenotype these are called neutral mutations. Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring.

A heritable trait that helps the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fit” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.

These adaptations can occur through the rearrangements of entire genomes or can be caused by the mutation of a single gene. For example, dogs have 78 chromosomes while cats have 38. A large number of the characteristics that distinguish dogs from cats arose from chromosomal rearrangements that have occurred since both groups diverged from their last common ancestor. On the other hand, certain mice are white and other mice are black. The difference in fur color occurs through the mutation of a single gene. Thus, as a result of a single mutation, a mouse population can become more adapted to survive in snowy environments versus a dark, forest floor.

Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed, and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.

The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators (//cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#fig-ch18_01_04">Figure 18.5).

In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a common ancestry. The two species came to the same function, flying, but did so separately from each other.

These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change.

Evidence of Evolution

The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader.

Fossils

Fossils provide solid evidence that organisms from the past are not the same as those found today, and fossils show a progression of evolution. Scientists determine the age of fossils and categorize them from all over the world to determine when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years (//cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#fig-ch18_01_05">Figure 18.6). For example, scientists have recovered highly detailed records showing the evolution of humans and horses.

Anatomy and Embryology

Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction (//cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#fig-ch18_01_06">Figure 18.7) resulting from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures.

Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past common ancestor. These unused structures without function are called vestigial structures. Examples of vestigial structures include wings on flightless birds, leaves on some cacti, and hind leg bones in whales.

LINK TO LEARNING

Visit this interactive site to guess which bones structures are homologous and which are analogous, and see examples of evolutionary adaptations to illustrate these concepts.

  1. Things that are analogous look similar and things that are homologous do not.
  2. Things that are analogous have the same function and things that are homologous have different functions.
  3. Things that are analogous are not a result of evolution, whereas things that are homologous are.
  4. Things that are analogous result from convergence and things that are homologous result from common ancestry

Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan, living in the arctic region have been selected for seasonal white phenotypes during winter to blend with the snow and ice (//cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#fig-ch18_01_07">Figure 18.8ab). These similarities occur not because of common ancestry, but because of similar selection pressures—the benefits of not being seen by predators.

Embryology, the study of the development of the anatomy of an organism to its adult form, also provides evidence of relatedness between now widely divergent groups of organisms. Mutational tweaking in the embryo can have such magnified consequences in the adult that embryo formation tends to be conserved. As a result, structures that are absent in some groups often appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and tails at some point in their early development. These disappear in the adults of terrestrial groups but are maintained in adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the time of birth.

Biogeography

The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of members of the plant family Proteaceae in Australia, southern Africa, and South America, for example, is best explained by their presence prior to the southern supercontinent Gondwana breaking up.

The great diversification of marsupials in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands.

Molecular Biology

Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and in the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected from descent and diversification from a common ancestor.

DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events that allow the free modification of one copy by mutation, selection, or drift (changes in a population’s gene pool resulting from chance), while the second copy continues to produce a functional protein.

Direct Observations

Scientists have also observed evolution occurring in both the laboratory and in the wild. A common example of this is the spread of antibiotic resistant genes in a population of bacteria. When bacteria are exposed to antibiotics, alleles that help the organism survive increase in frequency //cnx.org/contents/ This email address is being protected from spambots. You need JavaScript enabled to view it. :[email protected]/18-1-Understanding-Evolution#ep-01">Figure 18.9. This is because individuals that cannot resist the antibacterial die off, leaving only individuals with the resistance gene to reproduce.

Adaptations for homeostasis

One major reason that organisms adapt is to maintain homeostasis, one of the main characteristics of life. All organisms have likely descended from a single common ancestor, which is why so many organisms share anatomical, morphological, and molecular features. However, each organism has adapted these similar features to suit their environment and adapt to environmental changes over time. For example, all organisms use DNA polymerase to replicate their genomes. However, whereas organisms with small genomes can get away with just a single polymerase molecule working at one point in the genome at time, organisms with larger genomes replicate many points of the genome simultaneously. Other organisms that live in extremely hot environments, such as deep-sea thermal vents, have specialized polymerase molecules that can withstand the heat that would quickly denature the polymerases in land-based animals. Although the basis for each of these different DNA polymerase molecules is the same, each one has been adapted to function in the organism’s environmental niche.

Misconceptions of Evolution

Although the theory of evolution generated some controversy when it was first proposed, it was almost universally accepted by biologists, particularly younger biologists, within 20 years after publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound.

LINK TO LEARNING

This site addresses some of the main misconceptions associated with the theory of evolution.

  1. Misconception: Evolution is not a well-founded theory. Correction: Although evolution cannot be observed occurring today, there is strong evidence in the fossil record and in shared DNA sequences to support the theory
  2. Misconception: Humans are not currently evolving. Correction: The environmental pressures humans face are different than the ones they faced several thousands of years ago, but they are still there, and they are still producing (slowly!) evolutionary change.
  3. Misconception: Evolution produces individuals that are perfectly fit to their environment. Correction: Evolution produces random changes in the genetic code that sometimes lead to adaptations
  4. Misconception: Evolution is a random process. Correction: evolution is a force that makes animals adapt to perfectly fit the environment they are living in

Evolution Is Just a Theory

Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a body of thoroughly tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists. In contrast, a “theory” in common vernacular is a word meaning a guess or suggested explanation this meaning is more akin to the scientific concept of “hypothesis.” When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization.

Individuals Evolve

Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is called development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium-ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one measures the average bill size among all individuals in the population at one time and then measures the average bill size in the population several years later, this average value will be different as a result of evolution. Although some individuals may survive from the first time to the second, they will still have the same bill size however, there will be many new individuals that contribute to the shift in average bill size.

Evolution Explains the Origin of Life

It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics believe that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, and presumably it just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things.

However, once a mechanism of inheritance was in place in the form of a molecule like DNA either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties.

Organisms Evolve on Purpose

Statements such as “organisms evolve in response to a change in an environment” are quite common, but such statements can lead to two types of misunderstandings. First, the statement must not be understood to mean that individual organisms evolve. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and therefore producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined.

It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic.

In a larger sense, evolution is not goal directed. Species do not become “better” over time they simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species, despite the commonness of this kind of language in popular discourse. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect as it does the human species.

SCIENCE PRACTICE CONNECTION FOR AP® COURSES

ACTIVITY

Using information from a book or online resource such as Jonathan Weiner’s The Beak of the Finch, explain how contemporary evidence drawn from multiple scientific disciplines supports the observations of Charles Darwin regarding evolution by natural selection. Then, in small groups or as a whole class discussion or debate, present an argument to dispel misconceptions about evolution and how it works.

AP ® Biology Investigative Labs: Inquiry-Based, Investigation 8: Biotechnology: Bacterial Transformation. You will explore how genetic engineering techniques can be used to manipulate heritable information by inserting plasmids into bacterial cells.

THINK ABOUT IT

What selection pressures may affect the survival and reproduction of a group of pea seeds scattered by a person along the ground?