Nitefly's Guide to Evolution

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Somewhat inspired by the ‘GordyR’s guide to bodybuilding’, I have decided to make a thread which will help educate some forum members on some misunderstandings they have about the theory of evolution. Whilst not being a totally exhausting guide, it will allow those who wish to ask questions the chance to have them explained, and I can update the OP(s) accordingly. Of course, I am far from a professor in the subject, and this material has been pulled from the works of Professor Gareth Jones and Dr. Arthur Goldsmith from the University of Bristol, and I would like to give them all the credit! This guide is split into three sections, titled:

An Evolutionary Overview: What are we trying to make sense of? What evidence is there for evolution? How is it occurring?

Misconceptions about evolution: Your arguments that evolution isn’t occurring are disproved here. Also, the myths of ‘devolution’, ‘statistical chance’ and other poor terminology are corrected here. This is probably the most interesting section, so feel free to read this first.

Evolution in action: For those interested in learning evolution in some greater detail. Also a brief insight of how life might have evolved.

I hope this is at least an interesting read, and I think everyone that does will learn many things they did not previously know. If reading about bizarre whales with legs sounds intriguing then grab a cuppa and a donut and read on….

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An Evolutionary Overview:

First off, it is best to explain what we are trying to make sense of here. Throughout history, humans have struggled to explain what they see around them in terms of living organisms. Firstly, why is there so much complexity? Living things are incredibly complex, and could not have originated by chance. The information content of a single human cell alone is equivalent to all 30 volumes of the Encyclopedia Britannica (A considerably hefty read).

Why is there so much diversity? Why are there so many different forms of a single species, let alone all the different species of butterfly on the planet? Why not just one all-purpose butterfly?

Why is there a seemingly apparent design? Living things show amazing engineering. Different species in different environments have different, and seemingly carefully designed, strategies for surviving and reproducing. Check out these surprisingly sneaky Giraffes:
giraffesdm4.png


Before the theory of evolution, the apparent design of living things was taken as evidence of a designer, i.e. a God. Quite a reasonable assumption really – nowadays if you see a carefully designed machine then you know someone must have designed it.

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So what evidence is there for evolution occurring?

Anatomy:
Organisms share underlying similarities even when they are superficially different and have different lifestyles. e.g. the pentadactyl limb:

pentalimbwa3.png


All of these examples show the pentadactyl limb in different organisms. This consists of the same bones in different proportions. Why is this so? Even more strangely, why do whales have hip bones but no rear legs? This is also true for some snakes inc. boas and pythons and they represent artifacts of the evolutionary process (more later).

whaleoh4.png


Embryology:
Vertebrate embryos share underlying similarities even when the adults are very different (shown below). Why should human embryos show gill pouches during development? Why should the 3 bones of the middle ear develop from the same bones as the jaws of a reptile? More later.

EDIT - The gill pouches example is now believed to be an error from early microscopy studies, and as such should be overlooked as evidence for evolution.

embryosvo5.png


Palaeontology:
Similar evidence to comparative anatomy, but with the dimension ‘time’ added as well. Why do fossils exist? Why are fossils in recent strata like living animals, but ones from
older (deeper) strata progressively more different? Darwin noted that fossil armadillos were very similar (though much larger) than present-day species. Why are there fossils of extinct animals at all, if all species were created at once a few thousand years ago?

Here is an example from fossil horses:
horsesua4.png


The oldest fossils in the deepest strata don’t look very like horses, but as you move up the rock layers to more recent fossils, they become progressively more horse-like. They become progressively larger, and note the loss of digits at the end of the leg bones.

Biogeography:
Similar evidence to comparative anatomy, but with the dimension ‘space’ added as well. Why are the finches on the Galapagos all similar, even though they lead different lifestyles? Why do animals and plants on one continent tend to be similar to each other (and the fossils there), yet differ from animals in similar habitats on other continents?

Taxonomy:
Why do all organisms fall into hierarchical categories?

Molecular Evidence:
Perhaps the strongest set of evidence, this has only been recently discovered as molecular techniques have become available. Why is genetic material more conserved between closely related species? This is possible to observe as DNA sequence, and also amino acid sequence. Whilst I won’t beat about this too much as it gets a bit technical, this is based on the following:

1) Nuclear and organelle genomes evolve at different rates. Useful for study purposes

2)Non-coding DNA evolves faster than coding DNA due to different functional constraints

3) Non-coding DNA can mutate without imposing any selective cost on its host. Synonymous changes accumulate faster than non-synonymous changes.

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These 6 lines of evidence all make sense if organisms share a common ancestry through evolution. So what is the mechanism?

Natural Selection:
If you have:
- Heritable genetic variation between individuals
- Overproduction of offspring
- Struggle for existence


Then you must get:
- Generation by generation increase in the (heritable) traits that aid survival and reproduction.

If the three basic assumptions hold true, it MUST happen. Also it explains the fit, or adaptedness, of organisms to their environment. It explains apparent design, without needing a designer. We can test three assumptions one by one:

Heritable variation:
How did Darwin persuade people that many of the differences between individuals are heritable, when genetics hadn’t been invented as a subject? Well, although he didn’t know the mechanism of inheritance, it was in fact easy to persuade people that heredity ‘happened’. First, family resemblances are obvious to everyone. But more importantly, Darwin did a lot of research on animal breeding – artificial selection. This clearly shows that heredity happens, but it also shows that animals can be changed through systematic breeding – i.e. particular inherited traits can be selected for. It also shows that large changes can happen in a short space of time. St. Bernards and Pekinese have been produced from the same stock of dogs in a few 100 years, just by differential spread of heritable traits. Broccoli, Brussel sprouts, cabbage and cauliflower have all been bred from wild mustard.

Overproduction of offspring:
Darwin was impressed by the work of Malthus, an economist, who noted that unrestricted populations grow exponentially (2 parents have 2 children who have 2 children etc.), but food supplies can only grow arithmetically (if you’re lucky). So there will always be competition for food – a ‘struggle for existence’.

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The ‘Modern Synthesis’ (1950s):
We now consider evolution as that following:

1) Gradual evolution results from small genetic changes that are acted upon by natural selection.

2) The origin of species and higher taxa (i.e. ‘macroevolution’) can be explained in terms of natural selection acting on individuals (microevolution).
 
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Misconceptions about Evolution:

Creationists are very eager to claim evolution is not occurring because it interferes with religious beliefs. I will counter some of the more difficult anti-evolution arguments of evolution here, however I will not deal with questions or claims to disprove evolution that show a lack of understanding or willing to understand, such as these classic:
A dog has never evolved into a cat – FACT!
...
If evolution is happening, why aren’t apes still evolving into humans?
So if you are going to ask such questions, don’t waste your time.

Without further ado…

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Evolution is only a theory

Many claim that evolution is only a theory, in a comparison to conspiracy theories which rely on speculation and a lack of evidence. This could not be further from the truth for evolution, which is a scientific theory.

A scientific theory:
Must be self-consistent
Must be explanatory
Must be testable (falsifiable)


Saying that evolution can’t be proved is a misunderstanding of the scientific method.

No scientific theory can be proved to be 100% true, not even in physics or chemistry. What science can do is REJECT theories, when their predictions fail. Evolution is a good scientific theory because it is not only consistent with the evidence, it has survived every test of it in the last 140 years. So, to say evolution can’t be proved is to misunderstand what science is all about. Evolution can be DISPROVED, but it HASN’T BEEN.

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Evolution violates the 2nd law of thermodynamics:

The second law of thermodynamics states that you can not go from disorder to order without energy input. A stack of cards, on the floor, does not jump up onto the table to form a pyramid without your hands intervening! So how do molecules come together to form complex structures and organs?

But earth is not a closed system; there is continuous input of energy from factors such as the sun. In nature, very complex inorganic structures form from relatively simple components. Some examples might be more obvious than you might think… ********* anyone?

snowflakehc1.png


What about a simple foetus dramatically changing into adult organism? You do not hear many claims that this is breaking the laws of thermodynamics, after all. When organisms grow, or when ********** and crystals form, they use energy in doing so.

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Devolution:

When people talk about humans losing keen eyesight, or losing their ancestral hair, they often use the term ‘devolution’. This is an incredibly misleading term. The genes coding for these features are not being selected for and thus are no longer conserved, therefore they are subject to genetic drift – the effect of chance on genetic material. In summary THERE IS NO SUCH THING AS DEVOLUTION.

However evolution is not necessarily towards higher complexity. Some organisms (e.g. internal parasites) have evolved towards a simpler structure.

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How can random chance create complex objects?

When a hurricane sweeps through a junk yard, it never creates a jumbo jet by chance. Therefore it is impossible to believe that complex organic molecules are created by chance, surely? For an eye to work there must be a lens, a focusing device, a retina with photoreceptors, etc. One component is no use without the others, so how can the eye have evolved bit by bit?

Mutations are random; natural selection is distinctly NON-random. As such, the jumbo jet analogy is distinctly misleading. Evolution occurs by the power of cumulative selection. Lets use an example to demonstrate this:

Take the word BIOCHEMISTRY. If we were to type any 12 letters to try and match this, the chance we would obtain this in one go is 1 in 26^12. However by cumulative selection it is a mere 1 in 26 x 12. Here is how it works….

Start with eight 12-letter ‘organisms’ (words), one has a letter (O) in a place(3rd letter) that is beneficial to its survival in comparison with the others, and this one survives and breeds, and its offspring all have an ‘O’ in the 3rd position. One of the new offspring also has a ‘Y’ in a beneficial place i.e. at the 12th position; this one survives and breeds, and so on. This is reflected in the diagram below.

biochemyd7.png


To put it into perspective, 26 to the power of 12 is a very large number: If you typed at a rate of one letter per second, 26 to the power of 12 is longer than the age of the earth (4.5 billion years). Conversely, 26 x 12 is about 5 minutes. THAT is the power of cumulative selection.

As for the eye example, complex structures do NOT evolve in one go but “intermediate” structures ARE useful. What matters is being BETTER than other designs around at the time. For example, Darwin went to great lengths to show that structures simpler than the vertebrate eye could be very useful. Indeed, ‘simple’ eyes exist in organisms today (e.g. lens-less eye of Nautilus, acts as a pinhole camera).

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There are no transitional fossils – O RLY?

This is probably the poorest yet most widely used claimed that evolution is not occurring. From any two living groups thought to be evolutionarily related, you can identify the ‘derived’ and ‘ancestral/primitive’ traits, and predict what the extinct forms should look like and also predict what forms should not exist. Evolutionary theory doesn’t just predict what fossils should exist, and what they should look like, it predicts what forms should NOT exist. E.g. We expect to find bird-reptile intermediates, not bird-mammal intermediates. This isn’t trivial -- no other theory makes these predictions.

Reptile – Bird transition:

Here is a simplified fossil record of fossil intermediates between dinosaurs and the common chicken.
chickenbirddd9.png


Here is how these fossils are found, with the oldest fossils further down in older rock.
fossilzx2.png


To the left is the incorrect and often assumed approach that animals evolve into once another. To the right is the correct representation of what is occurring. Note that we are not saying that all the fossils represent a direct line of descent to the present day. Many, indeed maybe most, will be offshoots of the direct lineage. Archaeopteryx didn’t evolve INTO a modern bird, but it was part of a richly branched tree of which modern birds occupy one set of branch tips.

The Archaeopteryx is not a fake. If you feel that this is not sufficient, consider, Eoraptor, Herrerasaurus, Ceratosaurus, Allosaurus, Compsognathus, Sinosauropteryx, Protarchaeopteryx, Caudipteryx, Velociraptor, Sinovenator, Beipiaosaurus,
Sinornithosaurus, Microraptor, Rahonavis, Confusiusornis, Sinornis, Patagopteryx, Hesperornis, Apsaravis, Ichthyornis, and Columba before making any judgements.
There is a very complete sequence of intermediates between dinosaurs and birds

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Reptile – Mammal transition:

Comparative anatomy and molecular sequencing suggest that mammals and reptiles evolved from a common ancestor -- not dinosaurs, but an earlier reptile group. When looking at the ears of a living reptile and a living mammal, the reptile has one bone transmitting sounds in its middle ear, the mammal has three. If you look at embryological development, the two ‘extra’ mammal bones start in a position next to the jaw and migrate to their adult position. They seem to be the SAME bones as two of the reptile’s jaw bones, but they’ve changed their function. So, we PREDICTED to find fossils with such intermediate arrangements.

And we found them! The bones in ‘intermediate’ forms probably transmitted vibrations arising from the ground as well as through the air. Today, some snakes hear by placing their jaw to the ground to feel vibrations.

fossil2qf9.png


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Land mammal – whale transition:

A lot of people have had difficulty swallowing that whales evolved from a cattle ancestor, provoking comments such as these, with amusing results:
Gish said:
There simply are no transitional forms in the fossil record between the marine mammals and their supposed land mammal ancestors . . . It is quite entertaining, starting with cows, pigs, or buffaloes, to attempt to visualize what the intermediates may have looked like. Starting with a cow, one could even imagine one line of descent which prematurely became extinct, due to what might be called an “udder failure
Behe said:
Finally, and most glaringly obvious, if random evolution is true there must have been a large number of transitional forms between the mesonychid and the ancient whale: Where are they? It seems like quite a coincidence that of all the intermediate species that must have existed between the mesonychid and whale, only species that are very similar to the end species have been found.
Ladies and gentlemen, may I present to you:

hellocj1.png

Ambulocetans, described 1994. Other intermediates have since been found.

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Ape - Human transition:

Finally, probably the most complete record of transitional fossils for any animal is that of Apes and Humans, shown below:

skullsar8.png

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But intermediates are missing from parts of the fossil record!

There are lots of features for which we have no known intermediates, but this does not by any means prove or disprove anything. Expecting a perfect fossil record where everything is preserved is unreasonable - the fossil record gives up snapshots of events with relatively large gaps in them (A short time for a geologist is a long time for biologist). Having said that, there are excellent examples of intermediates in other areas, e.g. Archaeopteryx and the evolution of powered flight, adaptations for flight improvements over time in the fossil record of birds.

Whilst some argue that the human knee joint has had no known intermediates due to an incomplete fossil record, it is assumed we may find such an intermediate in the future - think of the revolutionary 'land mammal - whale' intermediate above. However, our educated guesses allow frequent scientific discussion of bipedalism (Remember other Apes can only walk in water), including this proposed rearrangement of the knee joint.

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Evolution has never been observed

A false statement. Evolution is constantly observed, throughout biology. Pesticide resistance in insects, antibiotic resistance in bacteria and beak size/shape in Darwin’s finches (more later) are all key examples.

.... But no-one’s ever observed a new species form!

Oh yes they have, although admittedly not through natural selection. Plant species in particular can undergo a process known as polyploidisation. This is where a chromosome number of an organism doubles due to errors during meiosis, and it can no longer breed with its parental species. This can be advantageous in arid environments as polyploidy plants tend to have larger cells so they can store more water. The origin of new polyploid plant species is common enough and rapid enough that scientists have documented several such speciations.
 
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Evolution in Action:

This section is simply to expand on knowledge that one may know on this subject to gain a greater, more educated understanding. This could go on for a very long time, but I shall keep it relatively brief.

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The 4 Postulates of Evolution by Natural Selection:

Natural selection produces descent with modification, i.e. evolution and the following postulations describe this method. All postulates are testable.

1) Individuals within species are variable (because of mutation creating new alleles and subsequent shuffling of alleles).

2) Some of the variations are passed on to offspring (genes are passed on to offspring intact and often independently of other genes).

3) In most generations, more offspring are produced than can survive.

4) Survival and reproduction are not random: individuals with the highest reproductive success are those with the most favourable variations (with alleles and allelic combinations that best adapt them to their environment)- they are ‘naturally selected’.

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Darwin’s Finches – Testing the postulates of natural selection:

Darwin’s finches are a collection of birds from the Galapagos Islands, a series of islands which have been largely undisturbed by human activity and show mass biological diversity. They evolved by allopatric speciation (more later) and adaptive radiation, probably evolved from common ancestor 1-5 Mya. Throughout the 70s and 80s, the Grant team observed and tagged individuals on the islet of Daphne Major, allowing each of these postulates to be tested and proved.

finches1kp1.png


Postulate 1 - Individuals within species are variable:

The normal distribution of bill depth for Geospiza fortis:
finches2ke0.png


The chart shows that there is clearly variation between individual bill depth. A drought in 1977-1978 caused a huge population crash, shown by the second chart. The drought caused a reduction in small seeds, leaving only seeds which birds with large bill depth could consume.

Postulate 2 - Some of the variations are passed on to offspring:
Regression analysis shows how much the change of a variable is due to one factor. The regression slope of the following chart measures 0.79 (R2 statistic), means that 79% of the variation in bill depth due to the additive effects of genes.

finches3gh6.png


Postulate 3 - Are more organisms born than survive to reproduce?
The huge population crash in 1977 coincided with severe drought (Giving 85% mortality). Most finches died of starvation when seeds became scarce, however some population did surive

Postulate 4 - is survival and reproduction nonrandom??
Yes. There was a survival bias towards birds with deeper bills which could break open the hard seeds of Tribulus cistodes which were still relatively abundant. Only birds with deep bills can crack these seeds, so large bills selected for. This is shown in the chart below:

finches4rw3.png


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The Three Types of Selection:
Directional selection: Fitness increases (or decreases) with trait magnitude.

Stabilising selection: Individuals with intermediate trait values have highest fitness.

Disruptive selection: Individuals with extreme trait values have greatest fitness. This may be important in some modes of speciation.

The three types of selection demonstrated below:
finches5qm6.png
 
The Rate of Speciation

In many taxa, molecular clock evidence suggests that 3 MY may be required for reproductive isolation. However particularly rapid rate of speciation in Lake Victoria cichlids has occured where 300 species seem to have evolved in the last 12,500 years. Speciation rate is increased in habitats that prevent gene flow, low dispersal rates, strong sexual selection, availability of vacant niches and perhaps by genetic bottlenecks.

Despite title of seminal work, Darwin never addressed the problem of the origin of species. Main problem is how different population can be formed without intermediates. Any intermediates allow genes to be mixed between the extreme genotypes, and recombination will generate intermediate forms. Main mechanism in sexually reproducing animals is allopatric speciation – evolution of reproductive barriers in populations that are prevented from exchanging genes by a geographic barrier.

There are two types of allopatric speciation:
Vicariant speciation - Two rather widespread populations are divided by emergence of an extrinsic barrier.

Peripatric speciation - A ‘colony’ diverges from a widespread ‘parent’ population, and acquires reproductive isolation. If the isolated population is small, genetic drift may be important in the evolution of a new species. Also known as ‘Founder Effect speciation’, it may occur during dispersal to new islands or habitat fragments.

Case Study - Hawaiian Drosophila (Fly)

Many species of Drosophila are endemic to single islands and probably evolved from founding populations. Because geological history of Hawaiian islands is well understood, it is possible to relate evolutionary history of flies to island history. As such, scientists predicted a) closely related species should occur on adjacent islands, and b) phylogeny should correspond with island history, with most recently diverged species appearing on the most recently formed islands. Turns out by molecular analysis we were quite correct! Our understanding of Evolution is incredibly powerful for making predictions.

islandskc1.png


Sympatric speciation?
Sympatric speciation is speciation without spatial segregation of the incipient species. The extent of sympatric speciation is a major controversy in evolutionary biology as often it is difficult to reject allopatric hypotheses. The main theoretical problem is how intermediate genotypes are eliminated. However, there are known examples of when sympatric speciation is likely to have occurred.

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Is evolution a quantitative or qualitative theory?

It is difficult to find a clear and applicable definition of both quantitative and qualitative theory, so for this section we will assume a quantitative theory allows relatively accurate prediction of an outcome, whilst a qualitative theory shows the 'why' and 'how' of a process - keep in mind this is only to make this section 'easier and less wordy'.

It is debatable as to which catagory evolution will thus fall in to. Whilst it certainly is a qualitative theory, can we use evolution to accurately predict an outcome? The answer is a yes, and a no.

Using our understanding of evolution we can relatively accurately predict which factors will be selected in a certain upon in different environmental conditions. For example, after the observation of Darwin's finches (above) it was predicted that a drought year would see a rise in the proportion of birds with a deeper bill, and that after a particuarly 'wet' year, we would see a rise in the proportion of birds with a shallower bill. Both of these predictions were shown to be true. In this sense, evolution is arguably a quantitative theory.

However, since the environment is dynamic and ever changing, predicting what all of these factors may be is an impossible task and as such it is impossible to put an evolutionary prediction into equation form. For Darwin's finches, remember there will be subtle factors involved such as distrabution of seed which will affect the extent of natural selection. Since all inputs are either unknown or not constant, it is therefore arguable that evolution is not a quantitative theory as aiming to predict with total accuracy is an impossible and foolish.

As such, it is debatable to what extent evolution is a quantitative theory, if at all. If you are defining a quantitative theory as something which must be described mathematically to predict an outcome, evolution fails to meet these standards, although it is possible to predict the change in a phenotypic dimension caused by natural selection.

*Thank you to both Arcade Fire and Duff-Man for their contribution for this section*

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What is life and how did it evolve?

Three important features of living organisms are:

1) They can replicate themselves. Replication needs energy, which can be obtained indirectly (e.g. by eating), or by capturing energy from the sun or from simple organic compounds like H2S (autotrophs).
2) They contain proteins, which among other things, catalyse reactions.
3) They store and transmit information (in a genotype) and express it (in a phenotype).

So how did life evolve on earth?

Life forms have not yet been synthesised in the lab, but some plausible stages in the origin of life have been suggested through lab experiments. One significant hypothesis is the Oparin-Haldane hypothesis, which involves 3 stages.

1) Simple organic molecules are produced by abiotic chemical reactions
In 1953 Stanley Miller simulated electrical discharges in conditions that he thought resembled the early atmosphere (methane CH4, ammonia NH3 and water. He produced amino acids, and compounds like hydrogen cyanide (HCN) and formaldehyde (H2CO) which underwent further reactions to produce nucleotides (both purines and pyrimidines). These organic molecules may have accumulated in a pre-biotic soup. However we now think that the early atmosphere may have been dominated by carbon dioxide rather than methane, and nitrogen rather than ammonia. This mixture is less conducive for the formation of organic molecules.

2) The organic building blocks assemble into polymers.
This could happen if the first polymers formed on the surfaces of clay crystals, which reduces the chances of polymers being broken down by hydrolysis. In the lab chains of >40 nucleotides formed from initial chains of 10 by letting the nucleotide chains bind to a common clay mineral, montmorillonite.

3) The polymers start self-replication.
Some scientists argue that clay minerals may self-replicate. Polymers may have hijacked the clay replication, and eventually replicated themselves. Alternatively, early self-replicators may have been made entirely of RNA. The most conserved and universal component of information processing in cells is concerned with translation, and is built on a frame of RNA. RNA can both store genetic information and act as a catalyst, perhaps even catalysing its own replication. Once a population of self-replicating RNAs appears, mutation and natural selection will drive evolution.


Panspermia hypothesis:

This states that life evolved elsewhere, and arrived on earth perhaps on a meteorite. However, this does not solve how life evolved, and simply moves the problem elsewhere. Interestingly, complex molecules found in the large meteor that formed the Sudbury crater in Canada 1.85 billion years ago. Recent trips to Mars claim to have found objects resembling fossils of bacteria, or bacterial biological processes. Jupiter’s moon Europa has volcanoes and water, and life could conceivably evolve in hydrothermal vents there.

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You made it to the end - that was a bit epic! I hope you enjoyed the read, and don't hesitate to ask any questions. I will get back to you as soon as possible with an acurate answer :)
 
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Wow, a lot of effort put into writing that, nice one... I assume that was for a project or something, not just for this forum? :D



Do Creationists say that god may not have Adam and Eve, but just the whole Universe/ Earth in general?
 
ArmyofHarmony said:
Wow, a lot of effort put into writing that, nice one... I assume that was for a project or something, not just for this forum? :D



Do Creationists say that god may not have Adam and Eve, but just the whole Universe/ Earth in general?
I made it specificaly for the forum as I was tired of futile arguments revolving around the subject.

As for your question, you will have to consult a creationist as that goes beyond the call of my thread. Maybe someone else can help :p
 
That was really clear Nitefly - well done. It does make you wonder how even the most stubborn and closed minded moron can argue against it. It's not the 100% end of the story but it's pretty well on it's way.
 
SteveOBHave said:
That was really clear Nitefly - well done. It does make you wonder how even the most stubborn and closed minded moron can argue against it. It's not the 100% end of the story but it's pretty well on it's way.

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This post of mine was misleading, see Arcade Fire's post below
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