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Community => Science and Technology => Topic started by: Shane for Wax on January 04, 2012, 06:01:21 am

Title: Crash Course in Evolution and What It Is
Post by: Shane for Wax on January 04, 2012, 06:01:21 am
A/N: This was originally posted by Vene. As such all credit goes to him. I am simply bringing it over here.

So, we all know that a big part of biology is evolution. We also know that a big part of apologetics is creationism. Seeing as I have an interest in the science, I thought I might as well write up a post giving an overview of the evidence for it and explain some of the concepts. After all, I know some of the members here get into debates about it with fundies and more information is always helpful.

To start with, I might as well define a few terms so that we're all talking about the same thing. I am talking about biological evolution. The definition being the change in allele frequencies of a population of organisms over successive generations. Essentially, that the genes and traits of a form of life will change over time. There is nothing about it going for something better. As long as it changes, it's evolution. Deletion or gain of genes, it doesn't matter one bit. When I say macroevolution, I mean evolution at or above the level of species, microevolution is evolution within a species. Abiogenesis is the natural explanation for how life came to exist on Earth. Evolution explains why life is as diverse as it is, abiogenesis explains where the first life came from. Refuting one doesn't mean the other is automatically wrong.

Let's go with something easy, macroevolution. Speciation events have been observed in nature. One simple one is the evolution of the London Underground mosquito and the common mosquito. It has been shown both that they have difference overall genetic composition along with reproductive isolation (source) (http://www.nature.com/hdy/journal/v82/n1/full/6884120a.html). This is an entirely artificial environment, there is not way the mosquito could have been there to start with and it has changed to the point where even if a male and a female mate, they don't have offspring. But, the underground mosquitoes do mate successfully with other mosquitoes in the underground and common mosquitoes do mate successfully with those above ground. Even if the populations become mixed at this point, they are separate and distinct.

Macroevolution has also been shown to occur with bacterial. One of the defining traits of the bacteria E. coli is that it cannot digest citrate. Bacterial species have to be separated due to metabolism as they don't exactly reproduce sexually. What was done was that scientists took pure colonies of E. Coli, like the ones that currently live in our intestines, and grew them on petri dishes with high citrate levels, but with low levels of the nutrients they can digest. What happened is that over tens of thousands of generations (31,500 actually) a strain emerged from all of the bacteria that could digest citrate (source) (http://www.pnas.org/content/105/23/7899.abstract). Remember, this is a trait that microbiologists use to tell if a mystery bacteria is E. coli and this organism, from a colony of pure E. Coli, had an enzyme that could use it for energy. So, this enzyme is entirely new and had never existed before this experiment. Entirely new function and entirely new information.

I suppose now is as good of time as to talk about mutations and how new genes and proteins evolve. There are multiple ways that DNA can mutate. But, I think I should give a basic explanation of what DNA actually is and how it works.

DNA is a long chain of nucleotides. Different combinations of nucleotides lead to different shapes of proteins. The shape of a protein is what gives it an unique function. I know that's a very basic, but there is more to it. DNA is transcribed to make a complimentary RNA strand. DNA is a double stranded molecule, each nucleotide has a corresponding nucleotide it form a weak bond to, when it is used as a template for the synthesis of RNA. From the RNA a set of three nucleotides are called codons. Each codon corresponds to one amino acid. Amino acids are the basic unit of proteins, so altering the order of them and the ones used will drastically change the shape of the protein. So, a change to the DNA leads to changing the protein. This is the central dogma of biology (or molecular biology, or biochemistry, or genetics, it depends on who you ask). A diagram outlining the process is below.

(http://www.iusd.k12.ca.us/uhs/cs2/images/centraldogma.gif)

The mutations occur whenever a cell undergoes mitosis and divides. The DNA has to be copied. During this process, errors can occur. Nucleotides are deleted, inserted, copied, and altered. One example of how this happens is with the globin proteins. The one dominate in humans is hemoglobin. Hemoglobin evolved due to DNA duplication. Hemoglobin itself it actually made out of four different domains, or strings of amino acids. The are two types that compose it, alpha and beta. A picture showing the molecular structure is below.

(http://themedicalbiochemistrypage.org/images/hemoglobin.jpg)

Hemoglobin's function is to carry oxygen through the bloodstream, but the is another protein that can do the same thing, myoglobin (pictured below). Myoglobin has a structure that is nearly identical to that of a single domain of hemoglobin. What happened was that the myoglobin gene was duplicated. This lead to the rise of both alpha and beta hemoglobin (source) (http://biomed.brown.edu/Courses/BIO48/12.Molecular.Evolution.HTML). These two distinct domains were then used to form the hemoglobin protein. The duplication of a single gene is also what leads to many protein families. One of them is preserved and the other can mutate without harming the organism.

(http://themedicalbiochemistrypage.org/images/myoglobin.jpg)

Since I'm speaking about mutations, I might as well talk about junk DNA. Junk DNA is DNA that has absolutely no function. Only about 2% of the human genome actually codes for proteins and even if there are non-coding regulatory regions, over half of it is completely useless (source) (http://www.ornl.gov/sci/techresources/Human_Genome/project/info.shtml). There's even been studies done where sections of DNA have been removed from mice in order to see if it's detrimental (source) (http://www.nature.com/nature/journal/v431/n7011/abs/nature03022.html) and it has been shown that large chunks of the genome can be safely removed. This is important for evolution because not only does evolution explain where it comes from, such as duplication events that don't grab the entire gene, it also provides raw materials for evolution to work with. Junk DNA can be drastically altered without any harm coming to the organism and novel genes can evolve from it. The odds of any given gene are low, yes, but with so many organisms and with so many generations occurring, it can and does happen. And, like the E. coli experiment showed, a successful change can lead to the new trait permeating through the entire population very quickly.

Since we know how genes arise and how they can change, it is possible to map them out backwards. And since we also know the DNA directly leads to the protein, we can do it with just proteins instead of having to look at the gene itself. This is what is done with phylogenetic maps. A protein that is common to multiple forms of life is sequenced so we know the amino acids it's composed of along with their order. The differences between different organisms can then be compared, base by base, and organized with the changes shown in sequential order. The greater the difference between the protein, the further apart the organisms are and the less the difference, the closer they are. This also has the side effect of showing that there is more than one way to accomplish a task as different organisms have different chemicals accomplish the same function. Anyways, one of the best examples of phylogenetics in action is cytochrome c. Cytochrome c is an essential part of metabolism and is present in a wide variety of organisms. The sequence of it is shown below (each letter just represent a different amino acid, don't worry about which one it means) (source) (http://chemistry.umeche.maine.edu/CHY431/Evolve2.html).

(http://chemistry.umeche.maine.edu/CHY431/Cyto-Seq.jpg)

From this data it is possible to chart out the information in an actual tree, like below.

(http://chemistry.umeche.maine.edu/CHY431/Cyto-tree.jpg)

This is one of the most powerful techniques for mapping out evolutionary pasts and trees can be confirmed by looking at different proteins. If special creation was true, we would expect different proteins to make different trees, instead proteins create phylogenetic trees that match up with each other.

I think I'll end this post with a little bit on abiogenesis, because even if it's not evolution, it's important for this subject as it leads into evolution. The science on this is still in the early stages, there hasn't been a single theory that unifies all the data. But, it has been shown that biologically important molecules can form in conditions close to early Earth. There's the Miller-Urey experiment which started showing the plausibility of the concept by making some amino acids from methane, ammonia, hydrogen, and water (source) (http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/miller.html). So, the formation of amino acids is plausible at the least. Lipids, another major group of biomolecules, have also been shown to form abiotically or outside of a cell (source) (http://www.springerlink.com/content/g3r357k5l8279047/). Finally, the sugars and nucleotides needed for DNA and RNA have been synthesized in conditions the same as early Earth (source) (http://www.springerlink.com/content/aq10866526v08u65/). There is no doubt the ingredients needed for life were present, the question at this point is only how they formed the first protocell and evolution started to occur.

This is only a small overview of some of the lines of evidence for evolution. Hopefully it wasn't too terribly long and hopefully it has some useful information for somebody. And if there's a creationist reading this by some chance, please, I dare you to refute this.
Title: Re: Crash Course in Evolution and What It Is
Post by: D Laurier on January 04, 2012, 08:29:29 am
Evolution: An ongoing process of imperfect genetic replication leading to ever increasing genetic diversification.
Evolution was recognized by neolithic farmers, but was not understood untill the 19th century when several researchers figured it out independantly of eachother.
Alfred Wallace, Charles Darwin, and Thomas Huxley all figured out sexual selection... And Gregor Mendel discovered genes.
Title: Re: Crash Course in Evolution and What It Is
Post by: Cataclysm on January 07, 2012, 09:56:31 pm
You and Vene +1

I've heard this one theistic evolutionist say that Evolution is impossible with a guiding force, and cited analogous structures, such as bat's and whale's Prestin evolving in an extremely similar fashion for echolocation as a reason. I don't think it is really evidence against natural selection, but it is interesting.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 07, 2012, 10:03:02 pm
The guiding forces would be the laws of physics & the situations of the environment.
Title: Re: Crash Course in Evolution and What It Is
Post by: The Right Honourable Mlle Antéchrist on January 07, 2012, 10:09:18 pm
Someone should really buy Vene a drink for writing this. Or a particle collider, which he'd probably enjoy more. Buy the man something, though, 'cause this is awesome.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 07, 2012, 10:23:45 pm
I could buy him a sweet tea from McDonald's, but I'm not sure I could pay the shipping & handling.

I'm po'!
Title: Re: Crash Course in Evolution and What It Is
Post by: The Right Honourable Mlle Antéchrist on January 07, 2012, 10:29:34 pm
Lithp! I was wondering when you'd show up. Smite me immediately, in order to complete your initiation to the new forums.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 07, 2012, 11:11:10 pm
Smite? Is that a penis lightning reference, or am I missing something here?
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 07, 2012, 11:14:41 pm
Smite? Is that a penis lightning reference, or am I missing something here?
I missed your Lithping so much.

AC, I'll take the drink. I have little use for particle accelerators as I am not a physicist.
Title: Re: Crash Course in Evolution and What It Is
Post by: Cataclysm on January 07, 2012, 11:27:23 pm
Smite? Is that a penis lightning reference, or am I missing something here?

Unless you missed her post on the Karma thread, it is a penis lightning reference.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 07, 2012, 11:50:26 pm
Checked the thread, smote her, will now fire penis lightning as a bonus.
Title: Re: Crash Course in Evolution and What It Is
Post by: The Right Honourable Mlle Antéchrist on January 08, 2012, 03:39:37 am
Checked the thread, smote her, will now fire penis lightning as a bonus.

So your penis shoots lightning and your clit shoots the Sheriff... what, pray tell, does your anus shoot?
Title: Re: Crash Course in Evolution and What It Is
Post by: Oriet on January 08, 2012, 11:11:56 am
Checked the thread, smote her, will now fire penis lightning as a bonus.

So your penis shoots lightning and your clit shoots the Sheriff... what, pray tell, does your anus shoot?
The Deputy, I'd imagine.
Title: Re: Crash Course in Evolution and What It Is
Post by: D Laurier on January 08, 2012, 03:56:48 pm
Ok,
Not to spoil the party but...
...   could we post more solid info about evolution please.
Title: Re: Crash Course in Evolution and What It Is
Post by: Cataclysm on January 08, 2012, 06:02:09 pm
Irreducible complexity is bogus.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 08, 2012, 06:35:31 pm
Irreducible complexity is just another term creationists misuse. An irreducibly complex system isn't one that could not have evolved, it is a system that no longer functions when any part of it is removed. However, that system could have been different in past ancestors, with extra parts, missing parts, or modified parts that did other things.
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 08, 2012, 07:59:39 pm
Ok,
Not to spoil the party but...
...   could we post more solid info about evolution please.
http://www.amazon.com/Why-Evolution-True-Jerry-Coyne/dp/0670020532 (http://www.amazon.com/Why-Evolution-True-Jerry-Coyne/dp/0670020532)

ETA: Unless you have a more specific question
Title: Re: Crash Course in Evolution and What It Is
Post by: Auri-El on January 17, 2012, 09:03:50 am
I have some questions! Okay, background: I'm taking the complaints about my geology class to people who can do something about it, per yours and a trusted professor's advice. the last thing I want is to be dismissed as a silly girl because I didn't do my research. So I'm doing research, and I thought it would also be good to ask for help here, since there are a lot of people here who know a lot about science and evolution.

Okay, most of what he's said I've found easy enough to disprove in the notes I'm taking to the meeting. Just a couple of questions here (and I apologize if this is the wrong place for it). One, what's the deal with the "missing links"? He said that Darwin himself said that if we don't fill in the gaps, then the theory is wrong. I've not read "Origin of Species" and I don't have time to read it before the meeting, so I don't know if that quote is taken out of context or if it's even true. But there are missing links in the fossil records, no? If so, how is that explained?

Two, what's up with Gould's hypothesis of punctuated equilibrium? I had never heard of it before (not saying much) but it seems like conjecture rather than science, based on what the dude said in class.

Three, he claims there was more oxygen in the atmosphere way back when, and that's why dinosaurs got so big. That sounds very Hovind-esque to me, but I have no idea whether it's true and what the evidence is.

Again, I am doing research on my own, I'm not trying to be all "do my work for me!!!wah!!" I'm just hoping for some insight from people who obviously know more about dealing with these issues. Okay then.
Title: Re: Crash Course in Evolution and What It Is
Post by: Yla on January 17, 2012, 10:50:24 am
Whenever such a "missing link" is discovered, it is usually labeled a new species (species being an entirely human-invented concept). Some fundies/other people who don't understand this like to claim that because of this, there are no "true" "missing links", i.e. transition stages between species.
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 17, 2012, 11:03:04 am
I have some questions! Okay, background: I'm taking the complaints about my geology class to people who can do something about it, per yours and a trusted professor's advice. the last thing I want is to be dismissed as a silly girl because I didn't do my research. So I'm doing research, and I thought it would also be good to ask for help here, since there are a lot of people here who know a lot about science and evolution.

Okay, most of what he's said I've found easy enough to disprove in the notes I'm taking to the meeting. Just a couple of questions here (and I apologize if this is the wrong place for it). One, what's the deal with the "missing links"? He said that Darwin himself said that if we don't fill in the gaps, then the theory is wrong. I've not read "Origin of Species" and I don't have time to read it before the meeting, so I don't know if that quote is taken out of context or if it's even true. But there are missing links in the fossil records, no? If so, how is that explained?
At the time Darwin published, they had no transitional fossils and a prediction of his theory is their would be some discovered. Shortly afterwards (two years later) there was a major discovery, Archaeopteryx. (http://en.wikipedia.org/wiki/Archaeopteryx) Archaeopteryx has characteristics of both modern day birds and modern day reptiles. Actually, without the feathers its skeleton looks like that of a reptile. More recently, another major fossil has been found, Tiktaalik. (http://en.wikipedia.org/wiki/Tiktaalik) Tiktaalik is between a fish and an amphibian. It has some fish anatomy like scales and gills, but also some amphibian anatomy like a neck and a flat snout. Its forelimbs are also a cross between the fins of a fish and forelimbs of a terrestrial animal.

There have been a plethora of other transitional fossils discovered, but there are still gaps (and will always be gaps). Part of the reason is due to the rarity of fossilization. Fossilization requires extraordinary events, one of which is that the body of the organism is not consumed by another organism. This is why most fossils are of sea life, they fall in the sediment and are quickly buried. Soft tissue also does not fossilize, which is why most of the fossils discovered are things like vertebrates and trees. Another reason is more abstract. When Archaeopteryx was found, there was a gap between birds and reptiles, but after its discovery we have two gaps; one between birds and Archaeopteryx and one between reptiles and Archaeopteryx. But, this is okay as far as the theory is concerned as even the existence of a single transitional fossil validates the theory.

Quote
Two, what's up with Gould's hypothesis of punctuated equilibrium? I had never heard of it before (not saying much) but it seems like conjecture rather than science, based on what the dude said in class.
Gould was a paleontologist, so he worked with geologic time scales. As a result, it looked like new forms of species appeared very rapidly after a significant period of not change. As such, this theory on evolution was that species were stable for a long period of time, but changed very rapidly when the environment shifts. But, this is not the case if we look at genes. Looking at genes shows a regular and slow rate of change, in other words gradualism. In reality, both are useful theories and which one is appropriate depends on the time scale in question.

Quote
Three, he claims there was more oxygen in the atmosphere way back when, and that's why dinosaurs got so big. That sounds very Hovind-esque to me, but I have no idea whether it's true and what the evidence is.
This is a Hovindism and incredibly stupid, in part because there were still very many small animals at the time (including dinosaurs). If this was the case, we'd see a much greater range of sizes for the dinosaurs discovered. This claim is used to suggest dinosaurs were nothing more than big lizards, but this fails even if the oxygen thing was legit. We can look at the anatomy of both dinosaurs and modern lizards (as well as fossilized lizards) and see some major differences. One such difference is their legs and hips. Lizards (http://www.naturephoto-cz.com/photos/sevcik/blue-tailed-lizard--ameiva-auberi.jpg) walk with their legs splayed out past their sides. Dinosaurs (http://www.dimensionsguide.com/wp-content/uploads/2009/12/Dinosaur-Sizes.jpg) walked much more like us with their legs directly underneath their bodies. The pictures I linked to should help illustrate the difference. As a result, the idea is incoherent.
Title: Re: Crash Course in Evolution and What It Is
Post by: Auri-El on January 17, 2012, 11:26:25 am
Awesome, that's very helpful! I love learning new things. I don't know very much about a lot of things, but when someone who's supposed to be a scientist claims that "virus" is a species, I do know that means he's an idiot. I can't believe he said half the things he did. He even pointed out during lecture that dinosaurs are not giant lizards, then he goes and basically says "but they're giant lizards."
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 17, 2012, 11:55:33 am
Anybody who says that "virus" is a species does not know biology. Granted, I'd also say anybody who says evolution is false doesn't know biology.
Title: Re: Crash Course in Evolution and What It Is
Post by: rosenewock21 on January 17, 2012, 12:00:59 pm
Quote
Three, he claims there was more oxygen in the atmosphere way back when, and that's why dinosaurs got so big. That sounds very Hovind-esque to me, but I have no idea whether it's true and what the evidence is.
This is a Hovindism and incredibly stupid, in part because there were still very many small animals at the time (including dinosaurs). If this was the case, we'd see a much greater range of sizes for the dinosaurs discovered. This claim is used to suggest dinosaurs were nothing more than big lizards, but this fails even if the oxygen thing was legit. We can look at the anatomy of both dinosaurs and modern lizards (as well as fossilized lizards) and see some major differences. One such difference is their legs and hips. Lizards (http://www.naturephoto-cz.com/photos/sevcik/blue-tailed-lizard--ameiva-auberi.jpg) walk with their legs splayed out past their sides. Dinosaurs (http://www.dimensionsguide.com/wp-content/uploads/2009/12/Dinosaur-Sizes.jpg) walked much more like us with their legs directly underneath their bodies. The pictures I linked to should help illustrate the difference. As a result, the idea is incoherent.
[/quote]

Indulge me, won't you?

I've seen things on both the History Channel and Animal Planet claiming that higher oxygen levels were responsible for gigantic insects. One was, I believe, about lesser known prehistoric animals and had someone explaining how insects can only grow so large under our current oxygen levels before they can no longer sustain growth.

Any truth to this or is it more pseudo-science from the people who brought us "Jurassic Fight Club" and "Lost Tapes"?
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 17, 2012, 12:19:12 pm
Quote
Three, he claims there was more oxygen in the atmosphere way back when, and that's why dinosaurs got so big. That sounds very Hovind-esque to me, but I have no idea whether it's true and what the evidence is.
This is a Hovindism and incredibly stupid, in part because there were still very many small animals at the time (including dinosaurs). If this was the case, we'd see a much greater range of sizes for the dinosaurs discovered. This claim is used to suggest dinosaurs were nothing more than big lizards, but this fails even if the oxygen thing was legit. We can look at the anatomy of both dinosaurs and modern lizards (as well as fossilized lizards) and see some major differences. One such difference is their legs and hips. Lizards (http://www.naturephoto-cz.com/photos/sevcik/blue-tailed-lizard--ameiva-auberi.jpg) walk with their legs splayed out past their sides. Dinosaurs (http://www.dimensionsguide.com/wp-content/uploads/2009/12/Dinosaur-Sizes.jpg) walked much more like us with their legs directly underneath their bodies. The pictures I linked to should help illustrate the difference. As a result, the idea is incoherent.

Indulge me, won't you?

I've seen things on both the History Channel and Animal Planet claiming that higher oxygen levels were responsible for gigantic insects. One was, I believe, about lesser known prehistoric animals and had someone explaining how insects can only grow so large under our current oxygen levels before they can no longer sustain growth.

Any truth to this or is it more pseudo-science from the people who brought us "Jurassic Fight Club" and "Lost Tapes"?
There does seem to be some truth with insects, at least.
http://www.eurekalert.org/pub_releases/2006-10/aps-gim100706.php (http://www.eurekalert.org/pub_releases/2006-10/aps-gim100706.php)

But, insect physiology is very much different than vertebrate physiology and while oxygen may be limiting for them, I'm not sure that it is limiting for reptiles. Either way, people like Hovind use it to claim that dinosaurs are just really big lizards and to deny dinosaur biodiversity. It's much easier to convince people that the brachiosaurus fossil is just a really, really big lizard than to tell them the fossil isn't real.
Title: Re: Crash Course in Evolution and What It Is
Post by: rosenewock21 on January 17, 2012, 12:36:50 pm
Much thanks, Vene.

Hovind amuses me to no end. My seven year old will tell you that most dinosaurs were around the size of a pony and that a T-Rex is closer to a chicken than a komodo dragon. If a seven year old can do that, you'd think any adult with limited internet access could do the same.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 17, 2012, 09:18:10 pm
I'm not sure about oxygen, but reptiles (which dinosaurs were not) are limited by the amount of heat they can get. Prime example, snakes get bigger the closer you get to the equator. The reason I say I'm not sure about oxygen is because the equator is also rich in that, so it could very well be a factor. It's why you get larger insects near the equator, that's for sure. I mention this because there WERE legitimate giant reptiles back then, so that's not TOTAL bullshit, the problem is that not EVERYTHING back then was a giant reptile.

I'm not exactly sure why megafauna declined, but the ones we have left could be good examples. Elephants are going extinct due to habitat destruction & poaching. If a lot of forest died as a result of the mass extinction, then the large grazing dinosaurs would have went with it, if they went with it, so would the larger carnivores
Title: Re: Crash Course in Evolution and What It Is
Post by: The Right Honourable Mlle Antéchrist on January 17, 2012, 10:22:25 pm
but reptiles (which dinosaurs were not)

Dinosaurs are classed as reptiles. The misconception is that they were lizards, mostly stemming from the etymology behind the order's name (Dinosaur means "Terrible Lizard") and outdated hypotheses.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 17, 2012, 10:33:31 pm
Fair enough. What I'm really trying to get at here is that they're very close to birds & probably warm blooded. So if you think of "modern reptiles," IE snakes, lizards, turtles, etc., dinosaurs are not going to follow most of those rules. Which explains why I keep forgetting they're technically considered reptiles, but in any case, it's highly unlikely they'd be misidentified lizards. If anything, the lizard label would be the more likely misidentification, as it was when Iquanadon was first discovered.
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 17, 2012, 10:41:32 pm
Birds are totally reptiles now.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 17, 2012, 10:51:08 pm
Are they, or are you just messing with me?
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 17, 2012, 11:23:55 pm
To some extent, it still depends on who you ask, but the only way to make the reptiles monophyletic is to include birds.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 17, 2012, 11:36:16 pm
Wouldn't you also have to include mammals? Monophyletic is "all descendents of a common ancestor," correct? And aren't mammals descended from reptiles (http://www.reptileevolution.com/reptile-tree2.htm)?
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 18, 2012, 12:03:38 am
If we look at the phylogeny we see we don't need to include mammals.
(http://kentsimmons.uwinnipeg.ca/16cm05/1116/34-20-AmniotePhylogeny-L.gif)
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 18, 2012, 12:14:26 am
I don't follow. Clearly mammals aren't closely related to birds, dinosaurs, & "modern reptiles," but there are also a number of much older animals, in the Carboniferous & Permian eras, that are classified as reptiles.
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 18, 2012, 12:26:44 am
Lithp, synapsida is mammals, and anapdsia and diapsida are reptiles. You can easily make mammals monophyletic while keeping them separate from reptiles and have reptiles also be a monophyletic group.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 18, 2012, 12:58:00 am
So, what about this (http://www.reptileevolution.com/paleothyris.htm)? If the page is to be believed, its ancestors include synapsida & diapsida, & it is still considered a reptile.
Title: Re: Crash Course in Evolution and What It Is
Post by: Jack Mann on January 18, 2012, 01:18:17 am
For its ancestors to include both synapsida and diapsida, it would require interbreeding between wildly different species.  Rather, it shares a common ancestor with both synapsida and diapsida.

However, it's true that it probably shouldn't be considered a reptile unless mammals are.  Really, what we consider "reptiles" should probably be split into several different groups (testudines, squamates [possibly further split into squamates and sphenodonts], crocodilians, and dinosaurs [including birds]).
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 18, 2012, 01:26:49 am
No, I meant to say that its successors include those groups, sorry, I was rushing around with chemistry, & I'm already something like 3 hours late for bed.
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 18, 2012, 10:34:24 am
Lithp, here's a phylogeny of that organism:
(http://sysbio.oxfordjournals.org/content/54/4/530/F3.medium.gif)
http://sysbio.oxfordjournals.org/content/54/4/530.full (http://sysbio.oxfordjournals.org/content/54/4/530.full)

Paleothyris acadiana is still on a completely different lineage than synapsida.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 18, 2012, 10:01:06 pm
Then I guess this:


Quote
Paleothyris is at the base of a large clade, the Protosynapsida, defined as Paleothyris, Passer, their last common ancestor and all of its decendants. Casineria and the microsaurs are outgroups. The Protosynapsida includes the Synapsida and the Diapsida.

...must be incorrect. All I know is that I keep hearing that mammals evolved from reptiles in the Permian Era. Hence, the conclusion I keep coming to is that either all of those things are wrong, or mammals are descended from animals classed as reptiles.

I wish I had a scanner so I could show you exactly what I'm looking at, but I don't.
Title: Re: Crash Course in Evolution and What It Is
Post by: Jack Mann on January 19, 2012, 08:27:17 pm
Mammals evolved from a common ancestor to reptiles, one which resembled modern reptiles more than modern mammals.  Because of earlier scientific understanding, they were classified as reptiles, leading to a paraphyletic designation (that is, the descendants of a reptile should likewise be called reptiles).  The common ancestor should be called something other than reptile under monophyletic definitions.  I also think that reptilia should be split up.  Right now, reptiles basically consist of everything in amniota left over after mammals and birds are taken out.  The wastebin of amniotes.
Title: Re: Crash Course in Evolution and What It Is
Post by: D Laurier on January 26, 2012, 03:04:34 pm
Tending to agree that "reptiles" is a bogus class. More a "wastebin" than a meaningfull grouping.
Title: Re: Crash Course in Evolution and What It Is
Post by: Vene on January 26, 2012, 05:27:17 pm
Tending to agree that "reptiles" is a bogus class. More a "wastebin" than a meaningfull grouping.
If you want to see a real wastebin look up protista.
Title: Re: Crash Course in Evolution and What It Is
Post by: D Laurier on January 26, 2012, 07:17:27 pm
Tending to agree that "reptiles" is a bogus class. More a "wastebin" than a meaningfull grouping.
If you want to see a real wastebin look up protista.
No thankyou. I'm gonna take your word for it.
I'll just pour myself another margarita instead. It's less frustrating.

Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 26, 2012, 08:47:14 pm
Protists are a fucking mess.
Title: Re: Crash Course in Evolution and What It Is
Post by: Auri-El on January 28, 2012, 07:41:49 pm
Well, in case anyone's interested, my complaint didn't seem to do much. The division chair talked to the professor, who "seemed concerned that a student was having difficulty comprehending the class". Yeah, I smell bullshit. However, this frees me to challenge the professor's claims in class, provided I feel confident enough in my knowledge. Which isn't likely to happen; I did some online research of the guy, and he's done lectures for ICR and is a big friend of the "leading creationists." Meaning he knows his stuff. But I'm going to try, anyway.

So, he keeps saying that the primary reason for his disbelief in the dinosaurs-into-birds theory is because there were bird fossils found below where the "earliest" proto-bird should be. (his emphasis, not mine). On the other hand, he does say that it was hard to find evidence against some of the theories that he doesn't agree with; next time he says that I'll point out that lack of evidence is actually pretty good evidence that it's not true. Ahem, sorry to get sidetracked. About the bird: he is horrible at both spelling and biology, and he speaks very quietly so I can never catch the names of species he throws out, so I don't know what this "proto-bird" he claims is too early is called in order to look it up.
Title: Re: Crash Course in Evolution and What It Is
Post by: Lithp on January 30, 2012, 10:23:18 pm
You need to have another meeting with the division chair. Calmly explain to him that you aren't paying tuition to learn voodoo & dousing rods. Then hit him upside the head, to make sure it sinks in.

Seriously, if I were you, I'd be pretty pissed off.
Title: Re: Crash Course in Evolution and What It Is
Post by: Random Dinosaur on January 30, 2012, 10:40:48 pm
Well, in case anyone's interested, my complaint didn't seem to do much. The division chair talked to the professor, who "seemed concerned that a student was having difficulty comprehending the class". Yeah, I smell bullshit. However, this frees me to challenge the professor's claims in class, provided I feel confident enough in my knowledge. Which isn't likely to happen; I did some online research of the guy, and he's done lectures for ICR and is a big friend of the "leading creationists." Meaning he knows his stuff. But I'm going to try, anyway.

So, he keeps saying that the primary reason for his disbelief in the dinosaurs-into-birds theory is because there were bird fossils found below where the "earliest" proto-bird should be. (his emphasis, not mine). On the other hand, he does say that it was hard to find evidence against some of the theories that he doesn't agree with; next time he says that I'll point out that lack of evidence is actually pretty good evidence that it's not true. Ahem, sorry to get sidetracked. About the bird: he is horrible at both spelling and biology, and he speaks very quietly so I can never catch the names of species he throws out, so I don't know what this "proto-bird" he claims is too early is called in order to look it up.

He's probably talking about Protoavis (http://en.wikipedia.org/wiki/Protoavis), a collection of small bones found in a Late Triassic flash flood deposit in Texas. The fossil was claimed to show avian features by its describer, but further analyses showed that the bones were badly preserved and probably belonged to several different animals. The skull, which supposedly contained the most birdlike features, turned out not to be as birdlike as originally claimed and was more like that of a traditional dinosaur.

There's also the argument that most of the "dinobirds" found in China are younger than the "First Bird" Archaeopteryx, but recent finds like Anchiornis (http://en.wikipedia.org/wiki/Anchiornis) do predate Archaeopteryx, which itself may be more like a common ancestor of birds and "raptor" dinosaurs than a highly derived bird.
Title: Re: Crash Course in Evolution and What It Is
Post by: Kristine on August 12, 2012, 12:19:55 pm
AAARRRRGGGG!!!!
http://www.political.com/ThankYou.aspx?g=5e3962899a17431e9ef48a932ff2f7a8&ust=4a8ea92702e44106b44aabdf21552308&se=54
Title: Re: Crash Course in Evolution and What It Is
Post by: Svata on June 04, 2014, 01:04:00 pm
Tending to agree that "reptiles" is a bogus class. More a "wastebin" than a meaningfull grouping.
If you want to see a real wastebin look up protista.

I mean seriously.

*Scientist discovers organism with traits of two or more kingdoms* (single-celled, self propelling photosynthesizer, for example) "Ummm.... Fuck it! Protist!"
Title: Re: Crash Course in Evolution and What It Is
Post by: Random Dinosaur on June 07, 2014, 11:46:31 am
The entire Linnean ranking system is crap left over from when science was still in its creationist infancy and needs to be thrown out entirely. Cladistics is the proper approach now.