A Brief Overview of Evolution

[Agent Intellect]

Introduction:

I've noticed a few times that some people have anywhere from a slight misunderstanding to a complete lack of knowledge on how evolution by natural selection operates, and since this is probably the one area that I'm not retarded, I've decided to indulge myself and educate anyone interested in this area. I am writing about the mechanisms of evolution first, and will later make a post on the evidence for evolution. I believe this to be the logical course to take, as the evidence will be more clear as to why it is evidence if one has a better understanding of how evolution by natural selection works.

I will try to make this a broad overview, not getting too far in depth. I will supplement the text with links, which are not necessary for understanding evolution, but supply reading for further inquiry or justification for a claim that I make for people who may find the assertion dubious.

The science of evolution by natural selection does not disprove the existence of God. Whether someone believes in God or not is a personal choice and it falls within the realm of philosophy, not science. Evolution is not concerned with how life came to be; that is a separate field called Abiogenesis. The phrase "On the Origin of Species" simply means that origin of species, ie the diversity of life. The science of evolution does not support an agenda of "social Darwinism", and it is not concerned with the various philosophies based on it's science - anywhere from bioethics to evolutionary psychology, which often refer to evolution, but are not a part of the science of evolution.

Some Things To Know:

Much of the current study of evolution is work done in genetics and biochemistry. In order for this to make sense, it's essential that one knows the difference between what a gene is and what an allele is. Genes are the segments of DNA that a species shares - all humans share 99.9% of their genes across 23 pairs of chromosomes. The differences between us are in the alleles. A gene is what codes for "eye color" while the different alleles of that gene are what code for "blue eyes" or "green eyes" etc. So, when it's said that humans and chimps share 98% of the same genes, it's because both humans and chimps have the same genes (which can be interchangeable, allowing recombinant DNA to be possible) coding for protiens, with only 2% difference in the actual things that our bodies need to code for.

Evolution, in broad terms, is defined as the changes and differentiation in alleles in a population that results in morphological changes over time. Natural selection is defined as a natural process that results in the survival and reproductive success of individuals best adjusted to their environment and that leads to the perpetuation of genetic qualities best suited to that particular environment.

Selection pressures are the causes in an environment that influence the allele distribution. In natural selection, selection pressures are those things that organisms must survive in order to reproduce and pass on their genes. This includes predators, availability of food, disease and parasite, changes in climate and geography, alterations to the environment (ie a new species moves in, a lake dries up, a species goes extinct etc).

How Evolution Works:

Starting broadly (and I'll get slightly more into detail as I go on), the three precepts that Charles Darwin observed that eventually led to the theory of evolution by natural selection are as follows:

1. Individual organisms within a species vary from one another.
2. Traits and characteristics are passed down to offspring through reproduction.
3. Organisms have more offspring than their environment can handle.

To break this down further, we first must consider the first precept. This seems painfully obvious - I am not an exact replica of my parents, and my siblings are not clones of me. We now know that this is due to independent assortment, random alignment, crossing over, as well as genetic mutation, which unfortunately Darwin didn't have the advantage of studying. So already there is change occurring, even if from this point of view it is nothing significant.

The second precept tells us that there is some relationship between the parents and offspring. Once again, this is very obvious, but the true magnitude of this is easy to miss: we are not independent constructs, but must have had to inherit some fundamental part of ourselves from our parents, so that who we are (physically and mentally) is dependent on our parents.

The third part is more difficult to understand, as far as how it is related to evolution; this is what Darwin observed that allowed him to come up with natural selection. Organisms have more offspring than the environment can handle because it is inevitable that some (if not most) will die. The offspring that did not die are the ones that had the variations (from precept 1) passed down from their parents (precept 2) that allowed them to survive better.

Spoiler

So what happens when there is nothing to kill off the offspring? A plague of mice in Australia conveys this quite succinctly:
YouTube- Guinness Worlds records Worst Mouse Plague

To sum this up, what is happening is that an organism gives birth to offspring that each have variations. Some of these variations will be more advantageous for survival, which will allow these individuals to survive longer and reproduce more. The often cited example is peppered moth in which a species of moth, which had variations between light and dark colored (with the vast majority being light colored, giving them camouflage on the light colored lichens on the trees). When factories moved into their habitat, the lichens died out due to pollution, so that the moths had to live on the dark colored bark of the trees. Because of this, the light colored moths were more easily picked off by predators, with the dark colored moths now having better camouflage. Over time, the dark colored alleles became the predominant features in the moth species, essentially changing the moths from light colored to dark colored.

Variations in individual organisms create changes, natural selection causes the changes that are best suited for a particular environment/ecosystem to survive and propagate those changes to their own offspring. Mutations and variations are like a tree branching out in all different directions, and natural selection is shearing off the branches less suitable for survival and allowing the more fit branches to continue growing.

]This can be visualized:

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This is the actual pictured used by Darwin in "Origin of Species":

Where each branch that stops before getting to the dots at the bottom were the lineages that were "sheared off" by natural selection. The split offs happen when a population of organisms becomes reproductively isolated which means that the population essentially splits into two. This causes the two populations of the same species to face different selection pressures. When the two groups are forced to overcome different selection pressures, the alleles and mutations that are best suited for survival will be different between the two formerly homogeneous populations. This causes different traits, behaviors, and characteristics to become more predominate in both populations. After several generations of different alleles and mutations being propagated through the isolated population, they eventually become a distinct species.

This is known as speciation.

Reproductively isolated does not necessarily mean geographically isolated (although this is the way it often happens and is the most obvious example of it happening). Organisms can evolve within the same geography if it is sufficiently large, or if two variations begin to fill a certain niche within the same environment (although the latter is rare).

This was a very basic overview of how evolution by natural selection operates. It is, essentially, a very simple process, but even still it is not intuitively obvious (particularly when thinking about the time scales involved) and there are a lot of misconceptions about it. I will now go over some of the most common misconceptions.

Spoiler

Understanding geological time is almost impossible for humans to comprehend.

The time scales involved are so vast that it can really only be grasped by analogy. If one were to stretch their arms out with the fingers extended and used the span of their arms to represent the time the earth has been around, the amount of time that modern humans have been on earth could be shaved off the fingernail in one swipe of a file. If one were to compress all time down into a single twenty four hour day, humans would not have even been around for the last minute.

YouTube- Evolutionary Timescale

Evolution: Myths and Facts:

1. Evolution = only the strong survive.
In this case, "strong" means smarter, faster, stronger etc. A common misconception (propagated by this popular mantra) is that evolution is the process of making organisms "better". The idea of better is difficult to quantify. Better is true in the sense of being better suited to a particular environment or ecosystem but the popular usage generally suggests the stacking of traits onto an organism, much like an RPG game, where each species is attempting to get to "the highest level". This is untrue in biological evolution, where traits that are better suited, regardless of whether they are more complex or "better" by the qualitative assessment by humans, are the traits that will become predominate in a species. This leads to point 2.

2. De-evolution.
Evolution is not directional. There is no increasing or decreasing of evolution. If losing a trait allows an organism to survive better, it has evolved in that it has changed to better fit its environment. Evolution can explain why organisms can increase in complexity, but it is not necessarily an increase in complexity. There is no such thing as de-evolving.

3. If evolution is true, why are there still "lesser" animals?
This goes back to point number two, but it still requires further explanation. Evolution is not trying to achieve any sort of goal, it is completely passive. It has no foresight and does not anticipate any future changes. The form an animal takes is the product of the selection pressures its ancestors faced. A common question I've heard is "if humans and chimps came from the same common ancestor, how come chimps aren't as smart as humans?" The simple answer is: chimps did not have to face the same selection pressures that humans did to become what we are today. Chimps are suited for their environment; not all animals are stumbling around in the dark on the path to being human.

4. Individual organisms can evolve.
Evolution happens on the scale of populations, not individuals. Once an individual organism is conceived, it has it's specific alleles for the rest of it's life (even epigenetic changes (video on epigenetics) occur within the realm of the organisms genes). Where the change occurs is during reproduction - the offspring has a mixture of it's parents alleles and has accumulated genetic mutations (the rate of genetic mutation is relatively constant).

5. Micro-evolution is happening, but not Macro-evolution.
This is a common and relatively understandable misconception about evolution, since macro-evolution is not something that can really be seen in our everyday life. The simple answer is that macro-evolution happens on timescales that we can't be around to observe, and it can only be seen in the fossil record. Another way to look at it is that macro-evolution is the accumulation of small changes or micro-evolution over geological time. If I start giving you a penny every year, that doesn't seem like much money, but if I continue this for 10 million years, now you have $100,000.

One problem is trying to differentiate between what constitutes micro and macro evolution, which are essentially just terms that biologists just use to talk about the spectrum of change within a species. There is no quantifiable point where a change ceases to be micro and becomes macro, there is no 'force' stopping large changes from happening.

Evolution is a Game of Economics.

To think about this on a more abstract level, one has to remember that a beneficial trait has to have a cost/benefit analysis (by means of natural selection). Thinking about humans, the reason we do not have supercomputer brains is because it would not be economical on in an evolutionary sense. We would require bigger heads to fit bigger brains which a) would be more difficult to fit through the birth canal, b) would require more neck strength and skull protection (more 'recourses' would need to go towards making the bones and muscles in the head and neck stronger) and c) the brains we have are already energy black holes (just our brain uses about 20%~ of the total energy we consume).

So, essentially, natural selection has to do the equation:
Beneficial trait - Cost to body = Total overall benefit.

If the energy cost of having a larger brain outweighed the benefit of having a larger brain, it would make the trait ultimately less beneficial; the person with the smaller brain would actually survive better if, perhaps, there was a food shortage. The person with the large brain would require a lot more food to support the energy needs of the larger brain and the nutrients required for the stronger skull and neck muscles/bones. The selection pressure of a food shortage, or a disease (which would be taxing on the bodies energy), or one had to escape other dangers (being faster or stronger also requires energy), and the limiting factor of the birth canal size all prevent larger brains from becoming a predominant trait.

This can apply to other organisms, as well. Elephants do not become perpetually larger, even though their size make them better able to survive predation from lions. The increase in size would come with an increased need for food as well as oxygen.

In short, natural selection makes sure that organisms stay at a tenuous 'balance' by forcing populations to continually adapt to selection pressures, while at the same time remaining efficient.

Evolution Is A "Messy" Process:

One aspect of evolution, which I just want to mention (I will go into more detail about it in a later installment) is that evolution can only "work with" what is already there. This is why we have suboptimal traits (the reason humans get bad backs and knees is because we fairly recently evolved to be bipedal, and we had to evolve this from being quadrupedal; suboptimal traits is also why we can swallow water down the wind pipe, because the way our esophagus and trachea are arranged is not optimal) and vestigial organs (wisdom teeth, tail bone, gene for synthesizing vitamin C etc).

As can be seen, the Esophagus and Trachea are 'criss-crossed' when it comes to breathing through the nose. Evolution "built" (for lack of a better word) the trachea this way in fish when they first began evolving lungs, then later noses evolved on top of that. In evolution, things are simply "built" on top of each other.

Coming Soon:
Evidence for evolution.
Human evolution.

 

[Claverhouse]

Murky and Underwhelming

I can scarcely comment on this, but I compliment your thoroughness and admirable clarity.


Still, I can't help adding a review I read just last night of a duo's book refuting an aspect of Darwin's theory: it is awe-inspiringly brutal.

Spoiler

From Publishers Weekly

The authors of this scattershot treatise believe in evolution, but think that the Darwinian model of adaptationism—that random genetic mutations, filtered by natural selection, produce traits that enhance fitness for a particular biological niche—is fatally flawed. Philosopher Fodor and molecular-biologist-turned-cognitive-scientist Piattelli-Palmarini, at the University of Arizona, launch a three-pronged attack (which drew fire when Fodor presented their ideas in the London Review of Books in 2007). For one thing, according to the authors, natural selection contains a logical fallacy by linking two irreconcilable claims: first, that creatures with adaptive traits are selected, and second, that creatures are selected for their adaptive traits. The authors present an ill-digested assortment of scientific studies suggesting there are forces other than adaptation (some even Lamarckian) that drive changes in genes and organisms . Then they advance a densely technical argument that natural selection can't coherently distinguish between adaptive traits and irrelevant ones. Their most persuasive, and engaging, criticism is that evolutionary theory is just tautological truisms and historical narratives of how creatures came to be. Overall, the scientific evidence and philosophical analyses the authors proffer are murky and underwhelming. Worse, their highly technical treatment renders their argument virtually incomprehensible to lay readers.

(Feb.)


Copyright © Reed Business Information, a division of Reed Elsevier Inc. All rights reserved.

http://www.amazon.com/What-Darwin-Wrong-Jerry-Fodor/dp/0374288798

Claverhouse

 

[Agent Intellect]

I do think there is an essence of tautology inherent in the theory of evolution by natural selection, mainly because on one level it's so painfully obvious. What most people seem to have a problem with is the idea of common descent, and more than that, people have a rather visceral reaction to the idea of humans being animals.

The reason I wrote this (and plan to make at least one or two more installments) is firstly because I'm a self indulgent bastard and I find it interesting to write about; but secondly, because I think that most people who do not 'believe' in evolution either don't understand how it works (and that review made it sound like the authors of the book in question didn't understand it) or they are unaware of just how much evidence there actually is backing it up. Other than being ill informed, the only reasons I could think for anyone to not believe in evolution is simply because it's such a slow process that it can't be seen, or they choose not to believe in it, successfully ignoring the available evidence.

I am all for critical inquiry on Darwin's theory of evolution by natural selection, and in fact made a post about it a while back, but discounting evidence or arguing from ignorance is not a good way to go about it - hence, if there is to be any real critical discussion on the subject, I think it's imperative that people know what they are disagreeing with.

 

[Kuu]

Though I do know the great majority of this, I also applaud your efforts AI, you are one of the few in this forum that tends to provide any reference at all (I am notoriously prone to forget them :/).

Hopefully this will clarify things to people that have been misinformed or confused on the subject...

 

[Da Blob]

I suppose I am expected to assume the role of honored opposition, but there are few facts to contend in this definition of evolution as the science of genetics. Again my principle complaints have been with the various philosophies that claim to based upon this science.

However, a couple of points and again it concerns the unverifiable assumptions made above, concerning the distant past. Contrary to what is believed there is no "evidence" of a continuum in the fossil records. Geological history is actually marked by discontinuities, in which there are no fossil records. The Cambrian, Ordivician, Silurian, etc. geological formations are separated by discontinuities (usually in the form of thick beds of shale) which are the products of millions of years of erosion, in which the fossil record is missing or only partially preserved. These discontinues mark the passages of tens or hundreds of millions of years - vast periods of time lacking in evidence of 'evolution" more or less.

The second assumption involves the whole concept of Macro-evolution. This is nothing more than speculation, there is and can be no real evidence of such, as that would have to consist of samples of DNA from every generation for millions of years. And again, as far as selective pressure causing new species to be created, as mentioned before, the selective pressure that has been put on the domesticated species by man, a much greater pressure to adapt, than is found in most environments, has yet to yield a new species. (I even wonder if this is true of botanical species as well?)

 

[EloquentBohemian]

Very clear and informative, A.I. Thanks.

 

[Agent Intellect]

Part 2: Evolutionary Theory

Introduction:

Time for some more self-indulgence from me (actually, this is helping me study for my biology class, too). It's been a while since the last post, but I've been really busy with school, so haven't had much time to do much of anything on the forum.

I've decided to expound on the previous section instead of going right into the evidence for evolution, as I think there are more in-depth aspects to evolution that can be explored that will be a) more interesting than the basics and b) make evolution more interesting.

What follows are more conceptual aspects of evolution that build on the ideas discussed in the previous post.

Reproductive Isolation:

Reproductive isolation does not necessarily mean that two organisms are separated from each other spatially. Reproductive isolation is when two organisms are either unable to breed, or do not breed for other reasons.

Spatial Isolation is when a population of organisms is split up due to geography, and then face different selection pressures. One example of this is antelope squirrel, which has speciated due to the grand canyon.

Spoiler

Behavioral Isolation is when two populations, because of facing differing sexual selection pressures, will acquire different mating rituals and behaviors. Some organisms within a population will not breed with another organism if it doesn't have the same mating rituals. In the birds in the follow picture, the mating ritual in the left differs from the mating ritual on the right, and if a bird (even though they look the same) tries to present the ritual between the two variations, the female will not breed with them

Spoiler

Mechanical Isolation is pretty self explanatory. One could say a form of speciation has happened between a great dane and a chihuahua, because even though their seed is still viable, it's almost logistically impossible for them to breed.

Temporal Isolation occurs when two organisms have different breeding times. This is separation in time. As the above chart mentioned, flowers bloom at different times of year, and therefore will not cross pollinate. In this way, two species can be reproductively isolated, yet live side-by-side.

Spoiler

Types of Evolution:

Allopatric Evolution:
This is the most basic form of evolution. When a population of organisms is separated by physical barriers, they will face different selection pressures that select for different alleles. Over time, the split population will diverge enough that if the two populations ever crossed paths again, they would be unable to interbreed (or they may breed, but they would produce sterile hybrids, like the liger or mule). Peripatric evolution is a form of allopatric evolution, but when one population is significantly smaller than the other.

Sympatric Evolution:
This is when organisms evolve in either overlapping or identical environments. This is very similar to parapatric speciation, which is generally referred to when behavioral sexual isolation occurs. One way in which sympatric evolution occurs is in a rain forest, there are several different environments - for example, the canopy and the ground. A single population of insects may separate into two, with one facing different selection pressures in the canopy while the others face a very different pressure on the ground. There is also the famous (in biology circles) Chiclid fish in Africa.

Spoiler

in three lakes of Africa's Rift Valley, a member of a family of fish named cichlids has evolved a range of ecologies and sizes unmatched anywhere else. Those lakes are known to have formed no later than 1.5-2 million years ago, and the hundreds of species of fish in those lakes occupy ecological niches, and exhibit biological forms, unheard of elsewhere. (One species specializes in eating the eyes of other fish.) The range is greater than what you might find at a coral reef, and all from a small number of evolutionary starting points.

(source)

Sexual Selection:

This is a theory that Darwin came up with after natural selection - although the two are under the same umbrella of evolution. The story goes that Darwin was bothered by the peacock:

‘It is curious that I remember well time when the thought of the eye made me cold all over, but I have got over this stage of the complaint, and now small trifling particulars of structure often make me very uncomfortable. The sight of the peacock’s tail, whenever I gaze it, makes me sick!’
Darwin, Charles correspondence 8, 140pp

Spoiler

YouTube- Natural Selection Tale of the Peacock

This is because the tail of the peacock, being so ostentatious and requiring such upkeep would seemingly be detrimental to an organisms survival. This is when he came up with the theory of sexual selection, which is when organisms (usually females) choose male mates for certain traits or behaviors that portray that they have good, healthy genes. A male peacock with the biggest plumage will be a peacock that is healthy and well fed, and therefore have the most fit genes.

This is an interesting (and quite humorous) scientific article where they tested the effect of ovulation on the tip earnings of strippers - with telling results.

Spoiler

YouTube- Evolution Sweaty T-shirts and Human Mate Choice

Also check out this TED video with Helen Fisher.

Ecology:

Spoiler

Evolution ensures what people often times call the balance of nature. Why are there so many herbivores and only a few carnivores? Why are plants so important to the environment? Why is over-hunting so deleterious to an environment?

The above picture shows the 90% reduction in kilocalories every time we move up a level in the "food chain". Herbivores only get 10% of the kilocalories that the plants produce. This, obviously, is because plants have to use most of the calories they produce for their own metabolic functions, and not all of the calories the herbivore takes in will be used - some of it will be excreted as waste. This is decreased once again with carnivores, who only get 10% of the calorie efficiency of the herbivores, as the herbivores also use most of their own caloric intake for metabolic functions.

It's because of this that nature maintains a tenuous balance, with carnivores being few and far between, requiring large hunting ranges; herbivores are much more common, and plants are (ideally) very plentiful.

Of course, this 'balance' is a complex dynamic system and can fluctuate. In a drought, plants die off, which causes herbivores to die off, and that causes carnivores to die off. If the carnivores are killed off, the herbivores will overpopulate and eat all their plant resources and die off. Such is natural selection.

Life On The Edge Of Chaos and Sensitivity To Initial Conditions:

“Deep in the chaotic regime, slight changes in structure almost always cause vast changes in behavior. Complex controllable behavior seems precluded.”
-Stuart Kauffman

“Of self-organizing behaviors, two are of particular interest to the study of evolution. One is adaptation. We see it everywhere. Corporations adapt to the marketplace, brain cells adapt to signal traffic, the immune system adapts to infection, animals adapt to their food supply. We have come to think that the ability to adapt is characteristic of complex systems, and may be one reason why evolution seems to lead toward more complex organisms. But even more important is the way complex systems seem to strike a balance between the need for order and the imperative to change. Complex systems tend to locate themselves at a place we call ‘The Edge of Chaos’. We imagine the edge of chaos as a place where there is enough innovation to keep a living system vibrant, and enough stability to keep it from collapsing into anarchy. It is a zone of conflict and upheaval, where the old and the new are constantly at war. Finding the balance point must be a delicate matter. If a living system drifts too close, it risks falling over into incoherence and dissolution; but if the system moves too far away from the edge, it becomes rigid, frozen, and totalitarian. Both conditions lead to extinction. Too much change is as destructive as too little. Only at the edge of chaos can complex systems flourish.”
-Michael Crichton

This is a theoretical model of evolution that says that the "balance of nature" maintains a place on the edge between chaos and stagnation. It's in this area that complexity can arise, that evolution can innovate new solutions to selection pressures.

Spoiler

Of course, life doesn't follow a single line across the edge of chaos, but fluctuates as the complex dynamic system evolves, subject to the sensitivity of initial (or previous) conditions. Complex dynamic systems are non-linear systems, essentially meaning that the output will be disproportional to the input, and do not have single cause-and-effect variables.

What this means is that a change in a single variable (for example, a small change in an environments climate, or the introduction/extinction of a single species) will have unpredictable and disproportional effects on the system. The popular example of this is the butterfly effect - a small input (the butterfly flaps its wings) has a disproportionate output (causes a hurricane or some other large impact elsewhere).

This is on account of the sensitivity of initial conditions, which is often represented with a logistic map:

R = a single number representing birth rate and death rate.
x = carrying capacity of population.

Small changes in R (birth rate and death rate) creates large distortions in the logistic map of a population when plotted on a graph:

Spoiler

The logistic map for 100 generations of x (plotted left to right) as r moves from 0 (red, first frame) to 4 (purple, last frame)

A cobweb diagram of the logistic map, showing chaotic behaviour for most values of r > 3.57.

With specific increases in the value of R making bifurcations:

Spoiler

If x is set to different values, even with very tiny alterations, the logistic map will make what is called strange attractors (some of you may remember Ian Malcolm talking about this at one point in the movie Jurassic Park).

Spoiler

Time series for Logistic map r=3.99, x(1)=.3, 48 iterations.

Two time series for r=3.99, x(1)=.3 compared to x(1)=.3000001

Two time series for r=3.99, x(1)=.3 compared to x(1)=.301

What does this all mean for evolution? The sensitivity of the initial condition is the small changes in R and x (R being a single number representing birth and death rates for a single iteration or "generation" and x being the carrying capacity of an environment for that organism, as discussed in the ecology section).

Tiny changes in the environment alter these initial conditions (initial here essentially meaning previous conditions) which causes the selection pressures of an environment to change, which causes populations of organisms to increase and decrease the frequency of alleles from generation to generation, as these new conditions select different traits - this changes the value of R as organisms with different traits will 1) breed at different frequencies (more fit (suitable to the environment) organisms breeding more, less fit organisms breeding less) and 2) die at different frequencies (more fit organisms living longer, less fit organisms dying quicker).

Still To Come:

Evidence for Evolution.
Human Evolution.

Spoiler

Some pictures in this presentation were taken from my Biology textbook, which I jacked from my professors PowerPoint slide shows

 

[Deckard]

Really good posts. Might want to mention the forces other than selection that can affect evolution (genetic drift, gene flow, (possibly) GC-biased gene conversion...).

 

[Agent Intellect]

Really good posts. Might want to mention the forces other than selection that can affect evolution (genetic drift, gene flow, (possibly) GC-biased gene conversion...).

I agree, they are an important mechanism for differentiation, but they don't seem as important for speciation - at least, not to the extent that natural selection is. I have also neglected to mention horizontal gene transfer, polyploidy, and outlaws/modifiers*.

This doesn't mean they aren't an integral part of evolution, but I'm not writing a textbook here



*

Spoiler

Outlaws and Modifiers were talked about quite extensively in "The Extended Phenotype".

Outlaws are replicators (genes) that don't "cooperate" with the genes at other loci, promoting it's own survival while possibly harming the organism at large.
This is split into two:
Allelic Outlaw: "a replicator (gene) that has a positive selection coefficient at its own locus but for which, at most other loci, there is selection in favor of reducing its effect at it's own locus. It is favored at it's own locus through getting itself into more than 50% of the gametes produced. At the same time, genes at other loci whose effect is to reduce the segregation distorition will be favored by selection at their respective loci." (Extended Phenotype, p. 133)
"Junk DNA": non-coding DNA that survives simply by being passed along from organism to organism without contributing anything to it's fitness.

Modifiers are genes that effect the phenotypic expression of genes at other loci. This alters the fitness of an organism, but not the fitness of a gene, but can result in changes in allele frequency within a population that are not due to selection pressures.

 

[Vrecknidj]

For more, read all the recent stuff by Sarah Hrdy (yes, the last name is spelled correctly).

Dave

 

[Ska]

I got to "Abiogenesis" before I ended up reading about sigma bonds on Wikipedia. Let's try this again XD

 

[Jah]

Speaking of Abiogenesis; I came across The Miller-Urey Experiment after I spent an entire night (to 5 am) trying to imagine the origin of the first life-forms, and it does seem to me a very plausible explanation, especially for those of us who have seen Volcanic electrical storms.

It's interesting to see the evidence for evolution and I'm thrilled that you've published such lengthy, in depth posts on this topic.
Keep up the good work.


btw. Are you as easily charmed by Sir David Attenborough as I ?

 

[Kevin Stratocaster]

However, a couple of points and again it concerns the unverifiable assumptions made above, concerning the distant past. Contrary to what is believed there is no "evidence" of a continuum in the fossil records.

What are you talking about? The fossil record is not perfect, but instances of a highly detailed record whenever the conditions are right show us that it is very gradual and very continuous.

The second assumption involves the whole concept of Macro-evolution. This is nothing more than speculation, there is and can be no real evidence of such, as that would have to consist of samples of DNA from every generation for millions of years. And again, as far as selective pressure causing new species to be created, as mentioned before, the selective pressure that has been put on the domesticated species by man, a much greater pressure to adapt, than is found in most environments, has yet to yield a new species. (I even wonder if this is true of botanical species as well?)

You evolved from an ape like ancestor and the proof is in the DNA. So to call macro evolution speculative is absurd. There is no need to sample every generation for millions of years. You have a very detailed record of your ancestry in every cell in your body. 7 mega-bases of DNA is alot of information and if it is always consistent with Darwinism, in every species we have examined, then Darwinism has already been verified beyond any REASONABLE doubt.

Evolutionary biology is my passion and AI is right on the money. Da Blob, I am inclined to think that you don't understand it very well and that you are precisely the audience intended for his post.

 

[Oblivious]

(He is assuming that this is another God thread, which thread is not about. I will personally smite the next person who tries to derail it into such faggotry)

The science of evolution by natural selection does not disprove the existence of God. Whether someone believes in God or not is a personal choice and it falls within the realm of philosophy, not science.

Awesome thread AI, kudos.

 

[Puffy]

Thanks for posting this A.I., evolution was on my mind today after watching a documentary on it last night. I will read when I have a free evening.

 

[onthewindowstand]

The reason evolution is often associated with religion, is because it is astonding how inconsistent people are in regards for demands for evidence. A religious person will believe something contrary to evidence and logic, and yet to everything else that could contradict that they place a standard so high that nothing could ever reach. And yes, God can be a philosophical idea, but evolution contradicts virtually all ideas of God that exist in religion today. Lets not play pretend, the religious have to think all of science is a farce.

 

[Puffy]

Depends what you classify as 'evidence' - bit of a blanket term. And no, a theist would just hold that God guides evolution. But it is a discussion for a different thread, as A.I. set out this isn't a 'God' thread.

 

[Agent Intellect]

Perhaps it's time for another installment:

Evidence For Evolution

The Fossil Record:

The fossil record is one of the most referenced compilations of evidence for evolution. One of the reasons is because the fossil record is what tells the actual story of evolution. It's through the fossil record that we can get a glimpse of what actually happened eons ago. Unfortunately, the fossil record is fraught with "holes" (that skeptics are often quick to point out as evidence against evolution). But, we are actually lucky to have any fossils at all:

This is a short video about how fossils form (requires Quicktime).
A short video about dating fossils.

The conditions required for something to be preserved as a fossil at all are very stringent - in addition, it's highly unlikely that we have found all the fossils there are to find.

The fossil record is what allows us to fill out phylogenic trees which show the 'story' of how a lineage evolved. With radiometric dating, the age of fossils can be estimated to within a certain degree of accuracy, along with the age of their surroundings. Through this we can not only look at which organisms in a lineage came before and after one another, but we can also get an idea for what sorts of environments and selection pressures the organisms faced. Also, when fossils are uncovered we can compare their anatomy and observe the geological paths that the organisms took as they evolved, which leads to the next two points: anatomical homology and biogeography.

Anatomical homology:

The basic idea of this is that, organisms that appear vastly different often have surprisingly similar structures.

This comparative homology can also be used to compare lineages through time. For instance, in whale anatomy, the changes in bone morphology of pakicetidae can be followed along it's phylogenic tree to the modern whales and dolphins.

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Or, with horses, the morphology of their feet can be observed:

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Intermediate morphologies can be observed. For instance, the stapes, incus, and malleus of the mammalian ear are homologues of parts of the fish jaw and gill arches. The changes in this morphology can be traced through the fossil record of reptiles and early mammals:

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A side view of three idealized skulls of mammals, therapsids (mammal-like reptiles), and pelycosaurs (early reptiles). The figure shows the differences between mammal and reptilian jaws and ear-bone structures. The jaw joint is shown as a large black dot, the quadrate (mammalian anvil or incus) is in turquoise, the articular (mammalian hammer or malleus) is in yellow, and the angular (mammalian tympanic annulus) is in pink. Note how, in the reptile, the jaw joint is formed between the blue quadrate and the yellow articular (with the pink angular close by), and how, in the mammal, the jaw joint is formed between the squamosal above and the dentary below. In the reptile, the squamosal is just above and contacting the quadrate. Advanced therapsids have two jaw joints: a reptile-like joint and a mammal-like joint

Biogeography:

The distribution of organisms on earth corresponds, in part, to the relationship implied by biological classification. For instance, trilobites during the cambrian period were unable to swim the vast distances of oceans, yet the same species are found in both North American and Europe:

Which shows that, during this period, the continents drifted together to form Pangea, closing the lapetus suture, and allowed the trilobite species to cross over. After Pangea split, the species became geographically isolated and both took different evolutionary paths - this phylogeny is supported by the fossil record (this phenomenon is actually used as evidence for the theory of continental drift).

The same phenomenon is also seen often on islands (with the Galapagos islands being the famous ones that Darwin explored). When organisms become geographically isolated, their evolutionary path can be observed in the fossil record, but also in more recent observations, like the recent findings of killer whales occupying different niches.

Biogeography allows us to track backwards to common ancestors. Humans are distributed over the entire earth, but if humans and apes share a common ancestor, then the highly mobile and nomadic humans must first have appeared where the less mobile and territorial relatives are still found. The evidence of early human ancestors found in east Africa, and the evolutionary phylogeny can be tracked over several migrations:

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Vestigial Organs:

As was mentioned in an earlier post of mine, evolution is not perfect. It must build upon what's already there, making nested hierarchies, and this often leaves vestigial organs (along with vestigial genes). For instance, the recurrent laryngeal nerve:

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This video contains a relatively graphic dissection of a giraffe, so squeamish people should beware. Also, has some anti-creationist propaganda, but it illustrates the point nicely.


YouTube- Laryngeal Nerve of the Giraffe as Proof of Evolution by Natural Selection [CC]

Some fish have vestigial lungs, such as anabantoidei, snakeheads, and Lungfish. There are also vestigial legs in whales, snakes, and dolphins:

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Human's display a lot of vestigiality. Aside from the well known organs, such as the appendix, coccyx, goosebumps and wisdom teeth, we also retain non-functional ear muscles that other organisms (including some monkeys) can use to move their ears, as well as what's known as Darwin's tubercle, which is only found in 10% of the population. Humans still retain the plica semilunaris of conjunctiva, which is vestigial of the nictitating membrane.

The Occipitalis Minor is a muscle in the back of the head which normally joins to the auricular muscles of the ear. This muscle has varying trends of presence in different races of humans. The Palmaris longus muscle is a seemingly functionless muscle that's absent in some people. The pyramidalis muscle is a muscle in the torso that is absent in 20% of the population, and doesn't seem to have any adverse effects to those missing it. The same goes for the plantaris muscle.




I'll do genetic and molecular evidence in a later installment (this one seems sufficiently long, and I've run out of steam). But, I will address a question raised earlier about the evolution of dogs and why they are still the same species.

Organisms have what are called tandem repeats (1) in their genetic code, where some genes contain repeating sequences of nucleotides adjacent to each other. Wolves (and all breeds of dogs) have a high frequency of these tandem repeats. The differentials in these tandem repeats accounts for the vast diversity within Canis lupus familiaris. For instance, size is influenced by a "single nucleotide polymorphism" in the IGF1 gene (1).

 

[Jill BioSkop]

For the very interested the moth that changed its colour is called Biston betularia.

And again, as far as selective pressure causing new species to be created, as mentioned before, the selective pressure that has been put on the domesticated species by man, a much greater pressure to adapt, than is found in most environments, has yet to yield a new species. (I even wonder if this is true of botanical species as well?)

Pressure to adapt only causes a new specie to form if the adaptation forced on the group makes it different enough from the original specie that they cannot interbreed anymore. Selective pressure does not necessarily cause change. It actually prevents change a lot of the time via balancing selection (http://en.wikipedia.org/wiki/Balancing_selection).

Also, not all domesticated animals have wild versions they can be compared to left. How do you know no new species have technically been formed? Eg: As far as I know there are no truly wild sheep left. If there were there some maybe we would see that they cannot interbreed with the domestic varieties.

In botanics making a new species is easier, because plants can always duplicate the whole genome if a chromosome is on its lonesome and cannot pair up. It can then pair up with itself, and just like that you have a new species (allopolyploidy) on your hands (http://en.wikipedia.org/wiki/Polyploidy#Polyploidy_in_plants)
eg: http://www.newphytologist.org/plantspeciation/speakers.htm (2nd abstract down). Most animals can't do that because the levels of expression of their genes wouldn't be adapted to the sudden increase in copy number and they'd die very very young.

Domestication of plants has yielded many new species: eg: triticale, a hybrid from wheat and rye, several types of wheat (http://en.wikipedia.org/wiki/Wheat).
However, plants typically have very big genomes with lots of redundant genes (with several copies only one of which is used) which gives abundant material for mutation and variety to select from, and different phenotypes are not necessarily different species. Eg: from the mustard plant Brassica oleracea, by selecting for different parts mentionned in brackets, we have: cabbage (leaves), broccoli (stem and flowers), cauliflower (flowers), brussels sprouts (buds), collards (leaves), kale (frilly leaves), kohl rabi (stem), etc. (http://en.wikipedia.org/wiki/Brassica_oleracea) (http://en.wikipedia.org/wiki/Domestication#Plants).

For more on the species concept: http://www.talkorigins.org/faqs/faq-speciation.html

You evolved from an ape like ancestor and the proof is in the DNA. So to call macro evolution speculative is absurd. There is no need to sample every generation for millions of years. You have a very detailed record of your ancestry in every cell in your body. 7 mega-bases of DNA is alot of information and if it is always consistent with Darwinism, in every species we have examined, then Darwinism has already been verified beyond any REASONABLE doubt.

DNA as a raw sequence of bases is neither a proof nor as extensive a record of ancestry as you seem to think. Our 3 Gigabases didn't come with an instruction manual or post-it notes with the origin of each base, not to mention that over half of it is noncoding "junk". Were I to sequence and analyse my DNA it would tell me who my parents were, but not which tripoblast I descended from nor whether I'm closest to flies or mice genetically speaking. I quibble, but all the generational information is an interpretation of our DNA, not a story from a convenient book.

The DNA of an individual is a supposed snapshot in time of a moving process (natural selection). Looking across generations is a closer approximation of what the original film looks like. We cannot get DNA across enough generations to directly prove large-scale evolution, we have to prove it indirectly to a degree of confidence the scientific community accepts. Which means it is technically not a proof.

Additionally, proving we are descended from this one ancestor may not be macro enough. I'm fuzzy on dates but I think humanoids haven't been around long enough to constitute proof for evolution over hundreds of millions of years.

Does anyone know how to include a link as a yellow word? It's make this more readable.

 

[Agent Intellect]

Our 3 Gigabases didn't come with an instruction manual or post-it notes with the origin of each base, not to mention that over half of it is noncoding "junk".

Good response, but just one point of contention here. The notion of junk DNA seems to be one that won't go away. We have a lot of non-coding DNA, that doesn't code for proteins or enzymes on it's own, but it's far from junk. "They [Michael Snyder, Jan Korbel] found that transcription factors – proteins that attach to stretches of non-coding DNA and affect how nearby genes make proteins – act at very different locations on the genomes of different people" (1).

The way our genes are expressed are greatly influenced by the non-coding DNA (which makes sense, since the genes themselves don't carry the code for whether they are switched on or off, or how strongly they should be expressed).

Also: "They [researchers from Princeton University and Indiana University] have discovered that DNA sequences from regions of what had been viewed as the "dispensable genome" are actually performing functions that are central for the organism. They have concluded that the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow" (1). A lot of seemingly epigenetic functions are controlled by non-coding DNA known as transposons.

"The term "junk DNA" was originally coined to refer to a region of DNA that contained no genetic information. Scientists are beginning to find, however, that much of this so-called junk plays important roles in the regulation of gene activity. No one yet knows how extensive that role may be" (1)

 

[Jill BioSkop]

My bad, I thought the quotes around the word junk would carry through the meaning that it wasn't quite actual junk, seems I miscalculated badly. I meant to express that non-coding DNA is even harder to interpret than gene sequences because we have an even vaguer idea of what to look for.

 

[nexion]

I have a quick, probably easy question. If we don't need the appendix, why do we still have it? I know Lamarckian evolution was disproved but still, if 100's of years of people had appendices they didn't need, wouldn't one think they would just go away?

 

[Kevin Stratocaster]

DNA as a raw sequence of bases is neither a proof nor as extensive a record of ancestry as you seem to think.

Sure it is...

http://www.talkorigins.org/faqs/comdesc/section1.html

I dont see how you can reason that DNA analysis can resolve a paternity case but not see that that same reasoning can be extrapolated and applied to to a much more ambitious problem.

 

[Kevin Stratocaster]

I have a quick, probably easy question. If we don't need the appendix, why do we still have it? I know Lamarckian evolution was disproved but still, if 100's of years of people had appendices they didn't need, wouldn't one think they would just go away?

Eventually our appendix may go away. But it would take longer than 100 years. Also the appendix probably isnt entirely useless because it seems to play a role in the immune system.

It may also be the case that it is important for proper embryological development. That is, it may be a kind of scaffold that is necessary for some other organ to develop. I dont really think this is the case for the appendix but this may be a good explanation for the presence of a post-anal tail in vertebrate embryos, especially those species that do not have a tail in their adult form.

 

[Ex-User (5841)]

Just want to bump this because:

1. It seems like I've been discussing evolution in several threads and messages quite a bit recently, and this should be the place to do it.

2. I am technically in the process of earning a M.S. degree in it, so I can provide specific examples/explanations especially centering around mammals, reptiles, and birds.

 

[DetachedRetina]

Yeah, I would love to ask someone knowledgeable on the subject this question:

How does macro-evolution happen?

It is supposed to be a series of micro-evolutionary steps right?

For example how did wings come about?

There was a species without wings and then eventually there was a species with wings right? But every step in between seems dis-advantageous! What good is it to have wing-stubs? And for how many generations did these senseless wing-stubs senselessly grow until they became functional wings? Am I expected to believe that was simply genetic drift? I would ask you to consider the probability of something like that happening.

I have been wondering about this for a while. Please and thank you for your response.