Evolution Pros and Cons

[Galapagos]

Originally Posted by questor

Galapagos, you seem to have difficulty understanding my words. I have never said evolution has not occurred. I said species variation is obvious.

Funny choice of words. The common ancestry of organisms on Earth is regarded as science fact. Do you accept or reject the evidence for this fact? You have been far from clear on this throughout this discussion.

Originally Posted by questor

''Nevertheless, a great deal remains to be determined regarding the ''mechanisms'' that have created (and destroyed) biological diversity since the emergence of life on Earth.''
These mechanisms are what I am talking about.

Mechanisms of evolutionary change would be those such as natural selection , genetic drift, and gene flow.
Evolution 101: Mechanisms of Change

Originally Posted by questor

I am saying we don't know the biochemical mechanism that causes the changes and what motivates the change to occur. If you can explain this, have at it, if you can't , let's close the thread. This is getting tedious.

If you mean the causes of change in nucleotide sequence, or the molecular changes(mutations) that provide the raw material for natural selection to work on, as usual, you could have saved us all time by simply looking at wikipedia:
Mutation - Wikipedia, the free encyclopedia

In biology, mutations are changes to the nucleotide sequence of the genetic material of an organism. Mutations can be caused by copying errors in the genetic material during cell division, by exposure to ultraviolet or ionizing radiation, chemical mutagens, or viruses, or can be induced by the organism, itself, by cellular processes such as hypermutation.

If you mean the way genes are expressed( DNA or gene code to protein product), then again, you should have checked wiki:
Gene expression - Wikipedia, the free encyclopedia

[HydrogenBond]

Maybe we are talking about two different things. I was trying to show that evolution can not involve random mutations. Let me try to explain my logic with a simple experiment. We start with a beaker of bacteria. We separate it into two beakers, so we start with two equal colonies. The first colony will be the control, where we maintain optimized conditions. To the second colony we will add an environmental stress that the bacteria need to overcome through genetic changes and selective advantage.

If mutations were random, since both beakers began exactly the same, both should be throwing the same random dice. Once the beaker with the stress develops the ability to adapt, the control beaker should also have the same ability if the process was done randomly. I am not saying the whole beaker will change but at least some of the bacteria should randomly change. If we then added the stress to the control, both beakers will have the same bacteria with selective advantage, right.

The analogy is two people, each with two dice. It doesn't matter if one goes to the casino and other is at home. Over time the dice will still have the same odds if we assume random throws by each.

The reality of the situation is the bacteria with the environmental stress will evolve the ability to overcome the stress faster than the one that is not seeing the stress. There is something casual about the stress that will cause that bacteria colony to change the odds away from the control colony.

[Galapagos]

Originally Posted by HydrogenBond

Maybe we are talking about two different things. I was trying to show that evolution can not involve random mutations.

Uhh... but it does. Most mutations in experimental or wild populations are very obviously deleterious ones. Read here, in the "harmful mutations section" on wiki, feel free to check the citation[7]:
Mutation - Wikipedia, the free encyclopedia

Most mutations are the result of copying errors and damage from heat or light. Those factors are as random as anything could be.

Originally Posted by HydrogenBond

Let me try to explain my logic with a simple experiment. We start with a beaker of bacteria. We separate it into two beakers, so we start with two equal colonies. The first colony will be the control, where we maintain optimized conditions. To the second colony we will add an environmental stress that the bacteria need to overcome through genetic changes and selective advantage.

If mutations were random, since both beakers began exactly the same, both should be throwing the same random dice. Once the beaker with the stress develops the ability to adapt, the control beaker should also have the same ability if the process was done randomly. I am not saying the whole beaker will change but at least some of the bacteria should randomly change. If we then added the stress to the control, both beakers will have the same bacteria with selective advantage, right.

The analogy is two people, each with two dice. It doesn't matter if one goes to the casino and other is at home. Over time the dice will still have the same odds if we assume random throws by each.

The reality of the situation is the bacteria with the environmental stress will evolve the ability to overcome the stress faster than the one that is not seeing the stress. There is something casual about the stress that will cause that bacteria colony to change the odds away from the control colony.

I think you just gave a confused summary of the experiments done by Cairns(and others since). These were a few cases where a response to stress was observed in certain single-celled organisms(Lamarckism has long been discredited for larger organisms) , and even Cairns himself has backed off the Lamarckian explanation:
Lamarckism - Wikipedia, the free encyclopedia

Originally Posted by wiki

In 1988, John Cairns at the Radcliffe Infirmary in Oxford, England, and a group of other scientists renewed the Lamarckian controversy (which by then had been a dead debate for many years).[16] The group took a mutated strain of E. coli that was unable to consume the sugar lactose and placed it in an environment where lactose was the only food source. They observed over time that mutations occurred within the colony at a rate that suggested the bacteria were overcoming their handicap by altering their own genes. Cairns, among others, dubbed the process adaptive mutation.

If bacteria that had overcome their own inability to consume lactose passed on this "learned" trait to future generations, it could be argued as a form of Lamarckism; though Cairns later chose to distance himself from such a position.[17] More typically, it might be viewed as a form of ontogenic evolution.

Phenotypic plasticity - Wikipedia, the free encyclopedia
Baldwin effect - Wikipedia, the free encyclopedia

[questor]

I don't know why this argument continues. most are arguing macro events (mutations and natural selection) and I am asking for answers to micro events (biochemistry) of genetic change. In order for gene replication to take place, the DNA helix needs to unwind and each half must be copied and the helix rewound. All of this takes a large number of biochemical reactions along with the raw materials and energy to carry out the process. What is the motivating factor or force that directs all this to happen? What directs the helix to unwind? What causes the genes and alleles to line up properly so replication can continue? Yes, information and directions are encoded in the genes, but what is its chemistry?

[Galapagos]

Again with the questions questor? Have you still not figured out how to use wikipedia or google?

Originally Posted by questor

I don't know why this argument continues. most are arguing macro events (mutations and natural selection) and I am asking for answers to micro events (biochemistry) of genetic change.

I mentioned mechanisms of evolution such as selection because you misused the term.

You have apparently completely overlooked/ignored the segment that discusses specifically what occurs at the molecular basis during genetic mutations(eg point mutations, duplications, transpositions).

Originally Posted by questor

In order for gene replication to take place, the DNA helix needs to unwind and each half must be copied and the helix rewound. All of this takes a large number of biochemical reactions along with the raw materials and energy to carry out the process.

Google is your friend:
Philosophical Transactions of the Royal Society--- Biochemistry of Meiosis
Biochemistry of meiosis. [Philos Trans R Soc Lond B Biol Sci. 1977] - PubMed Result

Bioessays-- The genetic analysis of mitosis in Aspergillus nidulans
Wiley InterScience :: Session Cookies

Originally Posted by questor

What is the motivating factor or force that directs all this to happen?

Mitogen - Wikipedia, the free encyclopedia

Originally Posted by questor

What directs the helix to unwind?

Helicase - Wikipedia, the free encyclopedia

Originally Posted by questor

What causes the genes and alleles to line up properly so replication can continue?

I think you mean "nucleotide bases". Genes and alleles are the result of nucleotide bases being lined up properly.

http://en.wikipedia.org/wiki/Complem...ecular_biology)
Base pair - Wikipedia, the free encyclopedia



Questor, answer this question: Do you or do you not accept both the overwhelming evidence and scientific consensus on the fact of evolution and common ancestry of the biota on Earth?
Please do not avoid this question again.

[HydrogenBond]

I can see the common biology on the earth. But I can also see paths of life getting more complex in terms of functionality, as time went on. I often mistake evolution with progress, in terms of improving functionality and complexity. But I am getting the impression, even backwards functionality, is still called evolution as long as this means a selective advantage.

A gang of street thugs who are not afraid to use guns will have selective advantage. The smart child who goes to school to learn would then be less evolved because he has no selective advantage among the thugs. This is modern evolution is a nut shell. In my mind, I see the smart kid as more evolved, even if he lacks selective advantage on the streets. This seems logical. But the definition says the lower common denominator can be more evolved.

According to evolutionary theory, if creationism is able to gain selective advantage in the social environment, that would make it more evolved than evolutionary theory. I am not saying this should happen, I am just applying the theory to show how it allows you make stuff up. Real progress is not a necessary requirement evolutionary theory. If we use the idea of evolution meaning real progress apart from aberrations which selective advantage can create, it doesn't matter who has selective advantage. That is what I am fighting for; evolution based on an objective system of increased complexity of affect.

[Galapagos]

Firstly, here is a better link discussing the rates of mutation and historic experiments done to establish this. It also discusses the experiments by Cairns, and the implications entailed:
Mutation Rates

Originally Posted by HydrogenBond

I can see the common biology on the earth. But I can also see paths of life getting more complex in terms of functionality, as time went on. I often mistake evolution with progress, in terms of improving functionality and complexity. But I am getting the impression, even backwards functionality, is still called evolution as long as this means a selective advantage.

This wiki page explains this common lay person fallacy of "devolution" quite well:
http://en.wikipedia.org/wiki/Devolut...ogical_fallacy)

Originally Posted by wiki

In common parlance, "devolution", or backward evolution is the notion a species may evolve into more "primitive" forms. From a scientific perspective, devolution does not exist.[1][2] Lay people may see evolution as "progress", reflecting the 19th century ideas of Lamarckism and orthogenesis, but modern genetically-based biological evolution theory asserts that evolution occurs by such mechanisms as natural selection, genetic drift, and mutation, and is therefore not directional, forward or backward in time; hence "devolution" is not a valid concept.

Also, read this if you want to understand the history of progress and evolution:
Evolution and Philosophy: Progress and Direction in Evolution

One of the more common misconceptions, with a history long before Darwin, is that evolution is progressive; that things get more complex and perfect in some way. In fact, this view is attributed more to social and religious attitudes of 18th and 19th century European culture than to any evidence. It was a given that things are getting better and better, every way, every day. This persisted until long after Darwinism, until the middle of this century (e.g., Teilhard de Chardin). Even Darwin was ambiguous about it, talking on occasion about 'perfection' as a result of selection.
[....]
Many criticisms of Darwinism rest on a misunderstanding of the nature of teleology. Systems of biology that are end-seeking are thought to be end-directed, something that Darwinism makes no use of in its models. Outside biology - indeed, outside science - you can use external teleology all you like, but it does not work as an explanation of any phenomena other than those that are in fact the outcomes of agents like stock brokers. And even there, teleology is not always useful, for which stock brokers (or cabal of stockbrokers) desired the goal of the 1987 crash, or the 1930 depression? External teleology is useless in science, and any science that attempts to be teleological will shortly become mysticism.

Originally Posted by HydrogenBond

A gang of street thugs who are not afraid to use guns will have selective advantage. The smart child who goes to school to learn would then be less evolved because he has no selective advantage among the thugs. This is modern evolution is a nut shell. In my mind, I see the smart kid as more evolved, even if he lacks selective advantage on the streets. This seems logical. But the definition says the lower common denominator can be more evolved.

... That isn't how evolution works at all? You are also egregiously misusing the word evolve here. And what is all this "more evolved" garbage?

Here, check out this evolution Q&A on pbs.org. I quote #10:
Evolution: Frequently Asked Questions

10. How do organisms evolve?
Individual organisms don't evolve. Populations evolve. Because individuals in a population vary, some in the population are better able to survive and reproduce given a particular set of environmental conditions. These individuals generally survive and produce more offspring, thus passing their advantageous traits on to the next generation. Over time, the population changes.

If there are genes contributing to such behaviors as you mention, and if the genotypes of the population are changing, then the population is evolving. Individuals do not become "more evolved", and the example you gave is a poor one.

Originally Posted by HydrogenBond

According to evolutionary theory, if creationism is able to gain selective advantage in the social environment, that would make it more evolved than evolutionary theory. I am not saying this should happen, I am just applying the theory to show how it allows you make stuff up. Real progress is not a necessary requirement evolutionary theory.

According to who's evolutionary theory? The one you just made up?

What you are saying sounds like it would fall under memetics, and if you understand memetics, you know that a meme spreading around does not mean it is of positive influence on the well-being of the possessor. Memes replicate for their own ends(selfishly, simply to make more copies of themselves) as genes can be said to.
I recommend you read "The Selfish Gene" by Richard Dawkins Hbond. It is a good popular science look at evolution and natural selection, and would clear up many of your misconceptions.

Amazon.com: The Selfish Gene: 30th Anniversary...
Amazon.com: The Selfish Gene: 30th Anniversary...

Originally Posted by HydrogenBond

If we use the idea of evolution meaning progress apart from aberrations which selective advantage can create, it doesn't matter how has selective advantage, real is real. That is what I am fighting for; evolution based on an objective system of increased complexity of affect.

I do not understand this part at all.

Originally Posted by HydrogenBond

Rational science is more evolved than empiricism, in the sense of being more advanced, since the alchemist were empiricists before the age of reason. But empirical has the selective advantage since there is more of that.

Again, using the word "evolved" like this is unhelpful and confusing.

Originally Posted by HydrogenBond

If you try to add logic to evolution you get squashed since selective advantage goes to the older method of science because it is more evolved.

Clarify this please. It sounds to me like you're making the same old ID/creationist argument that non-science, religious ideas of divine intervention in biology, or mystical concepts of progress or teleology are not accepted by professional biologists.
See here, specifically these topics:
CA320: Scientists challenging established dogma
CA230.1: Preconceptions affecting conclusions.
CA325: Creationists publishing
CA012: Snobbery

[questor]

Galapagos, you asked:
''Questor, answer this question: Do you or do you not accept both the overwhelming evidence and scientific consensus on the fact of evolution and common ancestry of the biota on Earth?
Please do not avoid this question again.'
I do indeed accept that the great majority of scientists have reached a consensus
on this issue. I do agree there is abundant evidence for variation in species due to mutations or environmental conditions. I do not neccessarily agree that all life started with one single cell organism, since there could have been numbers of cells formed in the same environment for the same reasons. The multiplicity of species would lead me to believe there was more than one original progenitor. It also troubles me that the fossil inventory does not show a smooth continuum of evolution and some species seemed to appear relatively quickly from questionable
ancestors. ( eg.human beings) I realize that millions of years have passed, but these same years passed for chimps and after millions of years they are still chimps. If you read my first post of this thread, I did not deny the tenets of evolution, but I have some questions about the package.
Now, you answer this question. Comparing life to an orchestra, with the instruments being the genes and the players being the biochemical enzymes and the music being the product; who is the conductor, and who wrote the music?

[Galapagos]

Originally Posted by questor

Galapagos, you asked:
''Questor, answer this question: Do you or do you not accept both the overwhelming evidence and scientific consensus on the fact of evolution and common ancestry of the biota on Earth?
Please do not avoid this question again.'
I do indeed accept that the great majority of scientists have reached a consensus
on this issue. I do agree there is abundant evidence for variation in species due to mutations or environmental conditions.

" Do you or do you not accept both the overwhelming evidence"
You missed this part(again). You accept the consensus, or you accept all of the evidence for this science fact?

Originally Posted by questor

I do not neccessarily agree that all life started with one single cell organism, since there could have been numbers of cells formed in the same environment for the same reasons. The multiplicity of species would lead me to believe there was more than one original progenitor.

At the level of the first replicating entiteis or primitive/proto life forms, there may have been more than one. This is covered on the abiogenesis wiki page:
Abiogenesis--Multiple Genesis - Wikipedia, the free encyclopedia

The Last Universal Common Ancestor is an ongoing subject of research in biology:

Originally Posted by wiki

The last universal ancestor (LUA), also called the last universal common ancestor (LUCA), the cenancestor or "number one" in slang, is the hypothetical latest living organism from which all organisms now living on Earth descend. Thus it is the most recent common ancestor of all current life on Earth. It is estimated to have lived some 3.5 to 3.8 billion years ago (sometime between the Basin Groups and Paleoarchean eras)[1] .

Originally Posted by questor

It also troubles me that the fossil inventory does not show a smooth continuum of evolution and some species seemed to appear relatively quickly from questionable
ancestors. ( eg.human beings) I realize that millions of years have passed, but these same years passed for chimps and after millions of years they are still chimps. If you read my first post of this thread, I did not deny the tenets of evolution, but I have some questions about the package.

This can be answered by any of the following FAQ pages on creationist claims(even though you aren't a stealth creationist , just someone asking questions)
CC300: Cambrian Explosion
CC301: Cambrian Explosion and Evolutionary Branching
CC201: Phyletic gradualism
CC050: Hominid transition
CC202: Transitional fossils and direct ancestry

Originally Posted by questor

Now, you answer this question. Comparing life to an orchestra, with the instruments being the genes and the players being the biochemical enzymes and the music being the product; who is the conductor, and who wrote the music?

Oh, I know this one! A magical disembodied cosmic personality appeared from out of nowhere and designed all life on Earth!!!!!

Here you go questor, this is what your real problem has been with evolution all along. Intelligent Design is creationism, which is religion, and religions are not science.
Here is an index of responses to any of the silly "design" claims you can come up with
List of Intelligent Design claims
Specific claims regarding your question:
CB180: DNA as language
CI101: Complexity and design
CI410: Design/Designer
CI120: Purpose and design


http://en.wikipedia.org/wiki/Intelligent_design

Originally Posted by wiki

Intelligent design is the assertion that "certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."[1][2] It is a modern form of the traditional teleological argument for the existence of God, modified to avoid specifying the nature or identity of the designer.[3] The idea was developed by a group of American creationists who reformulated their argument in the creation-evolution controversy to circumvent court rulings that prohibit the teaching of creationism as science.[4][5][6] Intelligent design's leading proponents, all of whom are associated with the Discovery Institute, a politically conservative think tank,[7][8] believe the designer to be the God of Christianity.[9][10] Advocates of intelligent design argue that it is a scientific theory,[11] and seek to fundamentally redefine science to accept supernatural explanations.[12]

The consensus in the scientific community is that intelligent design is not science.[13][14][15][16] The U.S. National Academy of Sciences has stated that "creationism, intelligent design, and other claims of supernatural intervention in the origin of life or of species are not science because they are not testable by the methods of science."[17] The US National Science Teachers Association and the American Association for the Advancement of Science have termed it pseudoscience.[18] Others in the scientific community have concurred, and some have called it junk science.[19][20]

[Moontanman]

[quote]

Originally Posted by questor

Galapagos, you asked:
''Questor, answer this question: Do you or do you not accept both the overwhelming evidence and scientific consensus on the fact of evolution and common ancestry of the biota on Earth?
Please do not avoid this question again.'
I do indeed accept that the great majority of scientists have reached a consensus
on this issue. I do agree there is abundant evidence for variation in species due to mutations or environmental conditions. I do not neccessarily agree that all life started with one single cell organism, since there could have been numbers of cells formed in the same environment for the same reasons. The multiplicity of species would lead me to believe there was more than one original progenitor.

It's not accurate to say all life on the earth started with one single cell and progressed from that point, At the time that cells were forming there were many different type of cells some were better adapted than other to using different energy sources and had many different patterns of survival. These organisms were not a single species nor were they really separate species the idea of species didn't really apply, These first very primitive organisms swapped genes regularly, the species barrier didn't really exist. Even today with what we call "species" bacteria still gene swap and often single celled creatures that seem to be totally unrelated can and do swap genes. To say at some point there was a single cell that out competed all the others and swept the planet to be the winner is simply not true. It's a simplified way to talk about a very complex process, the last common ancestor was really many different life forms that had gene swapped until they were all related.

It also troubles me that the fossil inventory does not show a smooth continuum of evolution and some species seemed to appear relatively quickly from questionable
ancestors. ( eg.human beings) I realize that millions of years have passed, but these same years passed for chimps and after millions of years they are still chimps. If you read my first post of this thread, I did not deny the tenets of evolution, but I have some questions about the package.
Now, you answer this question. Comparing life to an orchestra, with the instruments being the genes and the players being the biochemical enzymes and the music being the product; who is the conductor, and who wrote the music?

Again you imply a disparity where non really exists, 10 million years ago there were no chimps, 5 million years ago when the hominid line and the ape line diverged there were no chimps or humans. Both developed slowly over time, chimps are chimps because the evolved into chimps not because they haven't evolved. Chimps might stay in their current form for 100 million more years or they might change into several different species and the chimps might still be around or they might become extinct. Evolution don't alwasy happen just because time has passed, some animals change very little if any once a form has been reached. Do not think that just because humans and chimps descended from a common ancestor that humans have evolved but chimps have not. what you are alluding to is a common question often asked by creationists, if humans evolved from chimps (or apes) why are there still apes around. there is not evolutionary ladder, chimps didn't directly evolve into anything but chimps. There are two species of chimp. There could have been several more at one time or maybe not and chimps have recently evolved into two species of chimp. At one time there were several species of hominids alive on the earth. Now there is just one but that is mostly because we pretty much eliminated the competition either by simply pushing them into extinction by grabbing all the good habitats or by killing them out right. (some think that some hominids may have been absorbed into our genome by hybridization) When some one asks if apes were our ancestors why are there still apes. It's like saying if Europeans were your ancestors why are their still Europeans.