I. Origin of Life Hypotheses
A. Origin of Biologically Important Molecules
B. Origin of Polymers
C. Acquiring the Characteristics of Life
1. Membranes
2. Metabolic Pathways
3. Genetic System:
a. Problem:
DNA requires protein, but proteins require a DNA recipe... neither can
function without the other now. Again, an apparent "irreducibly complex
system" - it all must be there at once to work. You need an information storage molecule (DNA), and a catalyst to access the information (Proteins). Both of these functions must be present at the same time for the system to work.
b. Possible Solution:
But there is another component of our genetic system....RNA. And RNA does lots of wild stuff....
a.Even in current systems, RNA is message (m-RNA), decoder (r-RNA), and transporter (t-RNA).
b. RNA's have been discovered that have catalytic ability (ribozymes), so they can act as an information storage molecule (like DNA) and as a catalyst (like proteins).
c. some RNA molecules can self-replicate.
d. So, the possibility exists that genetic systems evolved from self-replicating RNA molecules. Coding for proteins that assist the replication process would be adaptive. And incorporating DNA, which is more stable than RNA, would also be adaptive, producing the system seen today.
c. Hypothesis for the Evolution of a Genetic System:
- GENETIC SYSTEM #1: Self-Replicating RNA Arises Spontaneously:
- Self-replicating RNA formed by polymerization of spontaneously produced nucleotides.
- It replicates. That's all it has to do to be a successful genetic system...replicate. Consider the 90% of your DNA that does nothing but replicate. It is just as successful (it is still 'alive') as the genes that do code for a protein. So, replication is REALLY all that a genetic system has to do to perpetuate itself through time.
- But, it could replicate more effectively if it coded for replicating
proteins. So, m-RNA and r-RNA and t-RNA interact today to make proteins.
If this step happened next, then the replicating RNA might code for
a protein (an RNA polymerase) that increased the efficiency of its replication .
- GENETIC SYSTEM #2: RNA systems produces useful replication enzymes.
- So, now there is VARIATION IN GENETIC SYSTEMS... the old, slow, self-replicating RNA, and the new, more rapidly replicating RNA that codes for replicating enzymes. So, we have variation and DIFFERENTIAL REPRODUCTIVE SUCCESS... different RNA's that replicate (reproduce) at different rates. What will happen????? Well, the more rapidly replicating molecules will be SELECTED FOR.. They will increase in frequency in the "population" of chemicals...this is selection at a chemical level.
- GENETIC SYSTEM #3: Incorporating DNA
- Now, how and why does DNA get involved? Well, first the how. If the RNA has a small mutation, it may make a slightly different protein... the protein might now link DNA nucleotides together, rather than RNA nucleotides (like the old protein did to replicate the RNA). This new enxyme is a a reverse transcriptase - it reads RNA and makes DNA.. So now, the RNA is read and a DNA molecule is made. (Does this ever really happen today? Are there enzymes that do this? Yes, in retroviruses their are genes that code for reverse transcriptases that copy the viral RNA, make DNA, and then the DNA is inserted into the hosts genome. When this viral DNA is transcribed, the new viral genome of RNA is made.)
- So, there is now a DNA molecule, and a DNA polymerase that can make a
copy and make it
double-stranded. There are also RNA polymerases (present already)
which read a nulcei acid and make RNA. So, here we have evolved a
system where DNA codes for RNA codes for protein, and proteins are used
for DNA replication, transcription, and translation, JUST LIKE THE GENETIC
SYSTEM WE HAVE TODAY.
- Why? Why would DNA be advantageous? Because its' double helix is more stable than the single helices of RNA. Greater stability means fewer mutations, which is a good thing (adaptive).
d. How has science tested this hypothesis?
Well, the history goes like this. After the discovery of ribozymes, some scientists saw that RNA could act as both information storage (recipe) AND catalyst (like enzymes). And, since RNA does everything in today's genetic system anyway, the "RNA-first" hypothesis was raised.
So, scientists tested the premise that RNA could self-replicate. They tested and confirmed this hypothesis - they synthesized molecules that, under particular conditions, did self-replicate (Hypothesis tested and confirmed, in part).
Second, scientists realized that RNA would have to code for DNA to get from SYSTEM #2 to SYSTEM #3. They saw that the existence of retroviruses that confirm this requirement. Retroviruses, like HIV, have an RNA genetic system. They insert this in their host's cell, and this RNA is read like any other m-RNA molecule. One of the genes on the RNA codes for a protein called "reverse transcriptase". This enzyme reads the viral RNA and links together complementary DNA bases - it reads RNA and makes DNA (the reverse of transcription, thus 'reverse transcritpase'). The DNA is then incorporated in the host's genome - it is spliced right into a chromosome. And now, anytime the cell replicates its OWN DNA and divides, teh viral gene gets copied and gets passed to the daughter cells. Eventually, some envrionmental cue stimultes the viral DNA to be read, and its expression (coding for copies and viral replication) kills all the host cells that have descended from this original infected ancestor.
So, parts of this hypothesis have been tested. However, the entire process of evolving a DNA-based genetic system from an RNA-based genetic system has not been done yet. BUT, what HAS been tested has been supported so far. It is certainly intriguing stuff. There is certainly enough evidence, to me, to suggest that the hypothesis "IT CAN'T HAPPEN" (such as intelligent designer's claim) needs to be put on hold for a while. Thankfully there are curious people who continue to ask questions.
Scientists continue to find new properties to RNA. Lately (since 2002), a new class of regulatory molecules have been found that can turn genes off. They are short strands of RNA, called "interference-RNA" (i-RNA). They bind to either DNA or to the m-RNA transcript - they block protein synthesis and effectively turn a gene off. So, RNA not only is a message, a decoder, and a transporter, it is also a genetic regulator. And these short pieces of i-RNA may be important as a blocking agent for genetic diseases.
This pathway is now accepted in the scientific community as a "plausible hypothesis" for the evolution of a genetic system. There is impressive support thus far, but all elements of the hypothesis have not been confirmed. THE SEARCH FOR KNOWLEDGE CONTINUES....!!
D. Summary:
1. STEPS REQUIRED FOR THE SPONTANEOUS, NATURAL FORMATION OF LIFE, and the evidence to date:
1. Spontaneous synthesis of biomolecules - strong evidence; Miller-Urey experiments.
2. Polymerization of monomers into polymers (proteins, RNA, sugars, fats, etc.) - strong evidence; Cairns-Smith experiments.
3. Formation of membranes - strong evidence; behavior of phospholipids in solution.
4. Evolution of metabolic systems - reasonable hypotheses, and genetic similarity in genes involved in particular pathways (suggesting gene duplication and susequent evolution of new genes and elaboration of existing pathways)
5. Evolution of a genetic system - a reasonable hypothesis and significant corroborating evidence that it could happen. But no experimental evidence of the process evolving through all three steps.
6. How did these three elements (membrane, metabolism, genetic system come together?) a few untested hypotheses.
So, as you can see, there are several elements of this hypothesis that have various levels of support. Unlike the Big Bang theory, which is really a single event (with evidence), the evolution of life requires several events. Since all of these events have not been tested yet, it is appropriate to refer to this whole idea as a hypothesis at this point. I hope you appreciate the distinction between "evolutionary THEORY", which describes how life changes, and "origin of life HYPOTHESES", that address the ultimate formation of life. These are very different things, and just as people accepted the heliocentric theory long before anyone had any testable scientific hypotheses about how suns and planets formed, we may accept the consistency of evolution by common descent without the same degree of confidence in knowing how life first arose.
E. Early Life
We will cover these points in more detail as we move forward through the diversity unit, but it seems like a good time to consider some of the key epochs in the evolution of early life, and some of the misconceptions of life's common ancestry that are presented by anti-evolutionists. So, even since Aristotle, humans have been grouping organisms together. Ever since Darwin, these groupings have been interpreted as "family trees". At one time, there were just three kingdoms: bacteria, animals and plants. Fungi were seen as more 'plant-like" and protists that swim were more animal like. However, subsequent analyses produced the 5 (and even 7) kingdom approach, dividing life into Bacteria (Monera), Single celled eukaryotes (Protista), and multicellular organisms (Kingdoms: Fungi, Plantae, and Animalia).
With the advent of large scale gene sequencing, we are able to look directly at the patterns of biological relatedness - 'cuz remember - we know where an organisms GOT it's DNA - from it's parents and ancestors. This allows us to see where our morphology-based taxonomy worked (keeping animals separate from plants), but it also identified some areas where morphology, alone, is not the best descriptor of relatedness. (Humans, chimps, and gorillas, for instance).
In the 70's and '80's, Carl Woese compared r-RNA sequences from eukaryotes and two types of "monerans" - the eubacteria and the archeabacteria (as they were then known). He found that these three groups were VERY different, and that actually, the archeabacteria were more similar to eukaryotes than to the other bacteria. So, based on genetic similarity, he constructed a new phylogeny and divided life forms into three groups, or "Domains"
Eubacteria - the "common" bacteria
Archaea - exploit extreme environments
Eucarya - eukaryotes.
- As a result of Woese's genetic work, the relationship among life looks like this:
|-------Eubacteria
---| |--Archeaea
|----|
|--Eukarya
- So, it seems that the Archeaea and Eubacteria are very different groups. They are both very diverse, gneetically, as we should expect of these very ancient lineages. They both date back beyond 3.5 bya, while eukaryotic life only extends back about 1.8 by. So, for most of the history of life on this planet, life was bacterial. With such a long evolutionary history, there has been more time for genetic variation to accumulate. thus, these groups are much more diverse, genetically, than all the eukaryotes, combined. (And of course, some of that diversity evolved INTO eukaryotes, so the eukaryote diversity can be seen as a subset of bacterial diversity, like one branch on a limb with many other branches. )
D. Timeline
4.5 billion years ago - Earth formed (Evidence: meteorites and moon rocks date to this age)
4.0 bya - oldest rocks (The oldest rocks are not as old as the Earth because the Earth is tectonically active, recycling its crust)
3.5-3.8 bya - origin of life (oldest fossils date to 3.5 bya, from western Australia)
2.0 bya - oxygen accumulating ("red bed" sediments form, demonstrating that oxygen in the atmosphere was oxidizing minerals)
1.8 bya - first eukaryotes (fossils)
0.9 bya - first animals (fossils)
0.5 - radiation of animals with hard bodies (Cambrain explosion)
So, for half of life's history, life was exclusively bacterial. It has radiated genetically MUCH MORE than eukaryotes... which is sort of interesting, because morphology they are NOT as diverse. But that is largely a consequence of changes in the SHAPES of eukaryotes, not in their basic structure or cellular metabolism.
An aside: Many creationists have long misrepresented the idea of "common ancestry", representing the common ancestor must be "1/2 this and 1/2 that" (like half human, half banana). For example, here's a quote from Ken Forbes:
"We share half our genes with the banana
Robert May is a UK Chief Scientist. In New Scientist magazine (July 1, 2000)
on page 5 he stated, "We share half our genes with the banana." One can only
guess (with a fertile imagination) what the common ancestor between people
and bananas looked like! In addition, there are fish that have 40% the same
DNA as people, but hopefully no evolutionist would claim that the fish are
40% human - or people are half bananas."(my bold italics... this implies that the common ancestor has to be some crazy, imaginary, 1/2 man, 1/2 banana creature...)
They then correctly state that, since this is absurd, the idea that humans and bananas share a common ancestor is absurd. This is a rhetorical strategy called the "argument of absurdity". Take an element of your opponents argument (common ancestry) and draw inferences from it that are absurd. Then, by claiming the inferences are absurd, you imply that the initial argument is absurd. Well, that's rhetoric, not logic. The implication can simply be wrong, not the initial point.
So, if we are dealing with organisms that have a fairly recent common ancestor, then yes - we would expect the common ancestor to look similar to the descendants. You and your sibling might both have your mothers eyes, for example. And the common ancestor between humans and chimps was a primate - it was neither a chimp NOR a human, but it probably looked pretty similar to a chimp (because, as a consequence of comparisons with the outgroup of gorillas, we know that chimps have retained more of the ancestral traits in the ape cluster while humans have diverged more from this ancestral type - by evolving bipedality, big heads, less hair, etc.). As we go back to more distant ancestors, they become less similar to the modern descendants. So, if you look at your ancestors from the 1800's, you probably don't recognize any facial characterists that you have, or that your third cousin has ... (except that your ancestor from the 1800's is human, of course). The common ancestor of humans and cows was in no way primate like or cow-like; but it WAS a placental mammal, of course. It was small, sort of shrew like (but not a shrew). And, if we look at the common ancestor to plants and animals (and therefor bananas and humans), we certainly have something the resembles neither. Biologists suggest that the common ancestor to plants and animals was a primitive form of eukaryotic single celled life. But even this is not imaginary, because cells really do exist. Human-bananas don't.
So, once the rhetoric is dismissed, we still have the data. So how do we explain the fact that humans and bananas share 50% of their DNA? Well, biologists explain it as a function of common ancestry from primitive single celled ancestors that lived 2 BILLION years ago. We have the whole history of the indepedent evolution of animals, and the independent evolution of plants, in between to make us different. Also, as we have seen, this theory explains the similarities in both the functional DNA and the non-functional DNA. The functional DNA is similar because we have inherited the genes for the same biological processes that occur in plants and animals: things like respiration, protein synthesis, and DNA replication. The fundamental UNITY of life at the cellular level, even among organisms as DIFFERENT as animals, plants, fungi, and bacteria is strong support for common ancestry. So, yes, we share 1/2 our genes with bananas... these are the genes that govern basic eukaryotic cell functions like respiration, DNA synthesis, and protein synthesis.
How does a creationist explain this similarity ('cuz, uh, they have to, because it is the DATA). Well, here's Ken Forbes again, a couple of paragraphs later:
"The creation science interpretation
What are creationists to make of this latest DNA finding from Detroit?
Certainly we would expect that DNA of chimps and people would be similar
because both drink the same water, eat the same food and breathe the same
air. This necessitates a wide variety of protein (e.g. enzymes) being the
same or at least similar.
Creation scientists would say instead of people sharing a common ancestry
with fish, bananas and chimpanzees we have a common all-wise, all-powerful
Designer who uses the same materials to make different living things."
Well, we've seem this argument.. it's the argument of analogy. "Hey, if you are going to respire, do it this way. So, all organisms that respire (plants and animals) have the same directions for respiratory enzymes". Well, uh, maybe. But first, what about the fact that the non-coding stuff is also 50% similar but has no function? Analogy doesn't work to explain that similarity, and the only explanation left is homology (ancestry). Also, although Forbes is making this argument for humans and chimps, we must assume he would make it to explain the similarity between humans and bananas. But humans and banana's don't interact with the environment in similar ways. And gee, once again we are left with the argument of perfect (all-wise and all-powerful) design. But we've seem that there are alot of imperfections out there. And with all options open to the all-powerful, I can't see that humans and bananas would need to be this similar. In fact, I think I could be a better person if I was less like a banana. But that's me.
OK, I've had my fun... and we laughed at my "banana-me" in class, and had our little joke. But I want to get serious for a moment. It is critically important that you do not make the same mistake as the creationists and use the argument of absurdity. Just because believing in a single divine separate creation of all species is indeed absurd (IN LIGHT OF ALL THE EVIDENCE FOR EVOLUTION), that does not mean that gods don't exist. It simply means that the data support the theory that life has evolved over time from common ancestors. The existence of supernatural agents is beyond the scope of science, as we've discussed, and you will answer that question using a different method. So, we had our little fun, but please don't interpret MY rhetoric as an indictment of believing in a god. That's entirely different. However, the physical evidence suggests that IF supernatural agents are somehow responsible, they did it THIS way - through evolution... or else they are just deceptive and made it look this way - which would be a nasty thing for a benevolent being to do (lie). But those are theological questions/issues beyond the bounds of this class. Of course, as a counterpoint, this natural process of evolution - as we see it happening today - can be explained without recourse to divine action.
I raise these issues in such detail because in recent surveys, 45% of the general population of the Unites States thinks humans were created much as we look now and are not descended from other organisms. That actual facts, discovered by the hard work of scientists in physics, geology, ecology, genetics, population genetics, molecular biology, and biogeography have falsified that idea and have produced one of the most consistent and powerful scientific theories that we have today. It is an educational shame that so many otherwise intelligent people remain in the dark with respect to these scientific facts, and fail to recongize the importnace of these facts to their everyday lives (medicine, for example).
Study Questions:
1. How might a genetic systems evolve (three steps, with adapative significance for each step)?
2. How are evolution and "origin of life" ideas different? (In terms of the nature of the question and replication?)
3. What are the steps required for life to arise, and what is the level of empirical support for each?
4. How do retroviruses replicate?