Macroevolution - do you believe?

[gashin]

I've been reading creationist books and watching debates and creationists do make good points. While there is a lot of evidence for microevolution, there isn't enough to prove macroevolution (evolution of new species). In addition, macroevolution doesn't fulfill one of the critical steps of the scientific method: repeatable testabilitily. We can't test macroevolution therefore it can never consider it to be a fact, thus even the most ardent scientists cannot claim it is a scientific truth. I am on the border between macroevolution and creationism because coming from an academic background in biology (B.S.), I'm starting to realize more and more that scientists are teaching based on faith just as much as religious preachers but are favored more by our educational systems and the government. In your replies please avoid talking about religion or the origins of life as these are also matters of faith, as the majority of scientists will admit (although not the religious ).

 

[umop apisdn]

Once they find a mule that can reproduce, I'm sure that's all the proof I'd need to believe speciation(is that a word?) exists. We already see evolution in bacteria and viruses (though not exactly experimentally reproducible, there's a lot of evidence to support it).

The problem with proving macroevolution scientifically is that experimental standards change faster than it occurs. Though it is a leap of faith, its existence is one of the strongest logical conclusions to reach with the evidence given.

Now, nothing can disprove (or prove!) intelligent design, and nothing ever will, which gives us a tough decision to make... do we disown religious ideas (which could only be unscientific explanations of natural phenomena and a means of social control, but that's another discussion...) that we've been raised to believe and that have been passed down from generation to generation in favor of science? That's up to the observer.

I can't fully say that both don't coexist. If intelligent design did exist, why would the Creator not allow evolution? Surely he/she/it/they would know that the Earth would evolve and that the species would need to also. Would genetic evolution not solve this problem within the natural laws (that could have been created)? Though I can't fully believe in such a Creator, this pretty much sums my ideas.

 

[Brittany]

I think it is a bit hard to avoid discussing religion with this subject. I'll keep my thoughts to myself, I'm a bit intolerant.

 

[gashin]

Once they find a mule that can reproduce, I'm sure that's all the proof I'd need to believe speciation(is that a word?) exists. We already see evolution in bacteria and viruses (though not exactly experimentally reproducible, there's a lot of evidence to support it).

If this experiment is what you are referring to Macro-evolution observed in the laboratory | Digital Bits Skeptic it isn't an example of bacterial macroevolution as the citrate-tolerant E. coli were still E.coli and not an entirely new species. This experiment could be repeated but it would still only produce E.coli. In addition, bacteria can obtain new traits through transformation and conjugation of dna from the outside environment and other bacteria, respectively - processes multicellular organisms cannot carry out, thus they can obtain new traits without selection. Thus this is not an example of macroevolution by natural selection into a new species as theorized by evolutionists. Viruses reproduce by an entirely different process than other living things (they basically take up dna from hosts randomly and are selected for by natural selection) so they don't really evolve as all they do is reproduce - they have no complex structures and are basically a protein capsule containing dna and this hasn't changed at all.

The problem with proving macroevolution scientifically is that experimental standards change faster than it occurs. Though it is a leap of faith, its existence is one of the strongest logical conclusions to reach with the evidence given.

What changes in standards are you referring to? All a theory needs to be proven as being true scientifically is for an experiment to produce hard results time after time. Logical conclusions based on things such as fossils is not science - it's speculation because it can't be proven by a repeatable experiment nor by direct observation. The existence of fossils of extinct animals is not evidence of macroevolution because there is no evidence that the animal reproduced, while the lack of the rest of the animal only brings even more doubt on speculations of their use as evidence for evolution.

Now, nothing can disprove (or prove!) intelligent design, and nothing ever will, which gives us a tough decision to make... do we disown religious ideas (which could only be unscientific explanations of natural phenomena and a means of social control, but that's another discussion...) that we've been raised to believe and that have been passed down from generation to generation in favor of science? That's up to the observer.

There is evidence for intelligent design in that organisms are far too complex to have happened by chance, but if there is no evidence that supports natural selection, the question becomes proving who the designer is, not if nature was designed.

I can't fully say that both don't coexist. If intelligent design did exist, why would the Creator not allow evolution? Surely he/she/it/they would know that the Earth would evolve and that the species would need to also. Would genetic evolution not solve this problem within the natural laws (that could have been created)? Though I can't fully believe in such a Creator, this pretty much sums my ideas.

I'm wondering that also - but the problem is, macroevolution is a theory based on faith! There is no scientific evidence and no direct observation of macroevolution so it is as much a leap of faith to believe in macroevolution as it is to believe in intelligent design.

 

[gashin]

Hehe I'd like your views - just don't bring in religious texts. I'm a fundamentalist Christian who is struggling with adopting creationism because of my scientific background, but I know that logically, as soon as bring up religious concepts, you're not using scientific logic.

I think it is a bit hard to avoid discussing religion with this subject. I'll keep my thoughts to myself, I'm a bit intolerant.

 

[Brittany]

Well, I'm an atheist. That should pretty much explain my views.

I hope you're able to reconcile your faith and knowledge, I just couldn't. There is too much cold, hard PROOF out there. I admit I'm no scientist, but it definitely makes more sense that life evolved, and didn't drop from the sky perfectly formed.

 

[gashin]

I was an Atheist for 6 years - until I saw God, twice. But there is no scientific evidence for macroevolution. There is no "cold, hard PROOF out there." Microevolution does occur and this is supported by enough evidence and repeatable experiments to confirm it as being a fact. There is no evidence for macroevolution on the other hand. If there is no evidence that new species were produced by natural selection, it is just as much a leap of faith as believing in an intelligent designer to believe in macroevolution. The problem I see with this whole debate is that we've been raised on the assumption that macroevolution is a fact supported by scientific evidence, which it is not.

Well, I'm an atheist. That should pretty much explain my views.

I hope you're able to reconcile your faith and knowledge, I just couldn't. There is too much cold, hard PROOF out there. I admit I'm no scientist, but it definitely makes more sense that life evolved, and didn't drop from the sky perfectly formed.

 

[gatsby]

AH heck no. I don't think I will be participating beyond what I am sure will be a Quixotic attempt start things off on the right foot by clearing up two issues. These are only important if you really want to discuss the topic rather than rehash an old set of arguments, which is really what is happening when these two issues are brought up in this way (Old creationist tricks unfortunately).

1.) There is no natural distinction between micro and macro evolution. The mechanisms are and have always been proposed to be the same in a theory of Natural Selection. When a biologist(or anyone else who studies evolution) mentions this it is a distinction of levels of analysis not nature. In addition this is a pretty rare subject in biology. If someone studies macro-evolution, they are studying the evolution (via natural selection on the same scale as microevolution) of a large or significant trait over time. An example might be researching the opposable thumb in primates. This is a trait tha defines the order which is why sometimes it is talked about as being above the species level, but its origin would not have a different mechanism than any other trait. To do this you might compare all the different primate thumbs looking for similar structure and propose that this is a trait in the original primate humb, blah blah blah. That is all that distinction means outside of the Craionism/ID/Natural Selection debate.

2.) Second point (obviously) is that there is some disagreement as to whether speciation exists. There are different species so it has to exist. Some species are new. FOr example in the last 70 years HIV differentiated itself from SIV and there are now 2 species of HIV. That happened. The only argument would be how did that happen? Was it via natural selection or was this the design of some supernatural designer (I agree that is a lousy way to put that but some force other than natural selection). Basically, other species exist, they have 'appeared' at different times. The argument is how that happened. natural selection does a very nice job of explaining this in simple terms but if people have a better explanation they should propose it and collect the data. There is a third option which has no evidence supporting it and all the evidence against it, that all species were created at the same TIME and have just died out. This third one would be strict creationism and supporting that is like supporting the idea the Earth is 6000 years old and the center of the universe. You can try, but that a tough row to hoe.

This could be a fun argument if people kept within those realities, but they don't and it turns into political/cultural twaddle and makes everyone mad.

 

[gatsby]

I was an Atheist for 6 years - until I saw God, twice.

BTW, I do want to point out that I think it is wicked cool that you have seen God and feel that connection. I just don't think God and science are in any conflict. I have said it before and I will say it again. Science is a method that helps you understand the world you live in and faith helps you live in that world.

 

[gashin]

AH heck no. I don't think I will be participating beyond what I am sure will be a Quixotic attempt start things off on the right foot by clearing up two issues. These are only important if you really want to discuss the topic rather than rehash an old set of arguments, which is really what is happening when these two issues are brought up in this way (Old creationist tricks unfortunately).

1.) There is no natural distinction between micro and macro evolution. The mechanisms are and have always been proposed to be the same in a theory of Natural Selection. When a biologist(or anyone else who studies evolution) mentions this it is a distinction of levels of analysis not nature. In addition this is a pretty rare subject in biology. If someone studies macro-evolution, they are studying the evolution (via natural selection on the same scale as microevolution) of a large or significant trait over time. An example might be researching the opposable thumb in primates. This is a trait tha defines the order which is why sometimes it is talked about as being above the species level, but its origin would not have a different mechanism than any other trait. To do this you might compare all the different primate thumbs looking for similar structure and propose that this is a trait in the original primate humb, blah blah blah. That is all that distinction means outside of the Craionism/ID/Natural Selection debate.

2.) Second point (obviously) is that there is some disagreement as to whether speciation exists. There are different species so it has to exist. Some species are new. FOr example in the last 70 years HIV differentiated itself from SIV and there are now 2 species of HIV. That happened. The only argument would be how did that happen? Was it via natural selection or was this the design of some supernatural designer (I agree that is a lousy way to put that but some force other than natural selection). Basically, other species exist, they have 'appeared' at different times. The argument is how that happened. natural selection does a very nice job of explaining this in simple terms but if people have a better explanation they should propose it and collect the data. There is a third option which has no evidence supporting it and all the evidence against it, that all species were created at the same TIME and have just died out. This third one would be strict creationism and supporting that is like supporting the idea the Earth is 6000 years old and the center of the universe. You can try, but that a tough row to hoe.

I understand your point, but there is no scientific evidence of new species evolving from older ones. Scientific evidence is something that can be proved time and time again in repeatable experiments and the evolution of new species simply isn't supported by science. Again, you can't USE VIRUSES at all in a discussion of evolution! They're just protein capsules that contain DNA - DNA which changes all the time RANDOMLY as viral reproduction is a sloppy business. When a Virus attaches to a host, it inserts its DNA into the host genome to manipulate the host DNA and protein production centers into producing copies of viral DNA and the protein capsule to enclose the DNA. It isn't a clear cut mechanism - practically all cycles of viral reproduction result in the viral offspring containing DNA of the host. Thus new Viral strains can arise WITHOUT natural selection and they don't evolve new structures and become a new species. Even evolutionary scientists will NEVER use a virus model to study evolution because of these very reasons!

One final point - Natural Selection is a design mechanism that modifies organisms according to environmental and social pressures. However, there is no scientific evidence that Natural Selection can design new species so it is as much a leap of faith to believe in evolution as the source of new species as to claim that there is an Intelligent Designer. This the leap of faith I'm getting at.

This could be a fun argument if people kept within those realities, but they don't and it turns into political/cultural twaddle and makes everyone mad.

The problem with a debate such as this is that people have been raised believing that the existence of new species is the result of evolution - even though this is a scientifically unproven claim preached as being truth by scientists.

 

[gashin]

Thanks - I was an anti-theist for a long time and God revealed himself in such an obvious way that I had to do a 180. I don't think this is an issue between religion and science, however. It's an issue of scientists making the claim that new species can arise from evolution without scientific evidence. Scientific truth changes all the time according to new evidence which contrasts with the faith scientists have of evolution of new species being a fact without any scientific evidence.

BTW, I do want to point out that I think it is wicked cool that you have seen God and feel that connection. I just don't think God and science are in any conflict. I have said it before and I will say it again. Science is a method that helps you understand the world you live in and faith helps you live in that world.

 

[gatsby]

So a virus doesn't count? How are we classifying viruses then? Not life? They are actually a pretty clean example because they mutate at such a high rate. They are almost all mutation and selection. What you are describing is why they mutate at a very high level and doesn't really have anything to do with the selection part. As an example, I just took a peek in a grad level Mechanisms of Evolution text book and one of the very first examples is about viruses. Its a great example because there are so few other factors getting in the way.

So, if you agree there are different species and I have noticed that you don't suggest that all species were created at the same time, where do these new species come from? Notice we are no longer discussing whether speciation happens, but rather what is the mechanism.

 

[gashin]

Scientists do not consider viruses to be a form of life as they do not exhibit the basic characteristics of life such as the cell structure, metabolism, and the complex biochemical pathways, structures, and development. Scientists do not consider Viruses to undergo evolution in the same way as life as they do not mutate new structures - only their DNA/RNA changes and this occurs the majority of the time through the random incorporation of host DNA during the replication of viral DNA. Thus, they gain new genomic sequences WITHOUT natural selection. In addition, when a new viral strain is produced - it is still identified as being the same species. You can't use it as an example of the formation of new species for life because they aren't examples of life and no new virus species have ever been found to have evolved from another species (a strain is a member of the species with a novelty characteristic - they are still the same species)! Their methods of reproduction and survival are so far off from those of life-forms that it cannot be used as evidence for the evolution of life as they do not evolve into new species and because they have no complex structures that have evolved because of microevolution. The fact that new strains develop is due to the random uptake of DNA and the sloppy replication mechanisms of viruses - replication mechanisms that do not seem to be evolving. In addition, there is no evidence of viruses before they were first observed in the late 19th century as they were too small to be maintained in any fossil record.

This is the question I am trying to get at - why do we assume that evolution can produce new species when there is no scientific evidence to support it? It is as huge a leap of faith to claim that evolution produced new species as it is to claim that an Intelligent Designer was the source.

So a virus doesn't count? How are we classifying viruses then? Not life? They are actually a pretty clean example because they mutate at such a high rate. They are almost all mutation and selection. What you are describing is why they mutate at a very high level and doesn't really have anything to do with the selection part. As an example, I just took a peek in a grad level Mechanisms of Evolution text book and one of the very first examples is about viruses. Its a great example because there are so few other factors getting in the way.

So, if you agree there are different species and I have noticed that you don't suggest that all species were created at the same time, where do these new species come from? Notice we are no longer discussing whether speciation happens, but rather what is the mechanism.

 

[gatsby]

This is the question I am trying to get at - why do we assume that evolution can produce new species when there is no scientific evidence to support it? It is as huge a leap of faith to claim that evolution produced new species as it is to claim that an Intelligent Designer was the source.

I certainly don't want to get side tracked on viruses, but the example I mentioned is not simply an issue of different strains (can't readily infect the same hosts, attach the cells via different mechanisms and sites wihin the cell...) and we do know a fair amount of the history of HIV.

That said be careful not to confuse evolution with natural selection and vice versa. Natural Selection is not the first theory of evolution and ID as it is proposed (if you take it on face value rather than a political trick to sneak creationism into high schools) attempts to be a competing theory of evolution. Like I said other than suggesting that all species were created at the same time we are talking about different theories to explain the data. The data is that there are different species and those species 'appear' at different times. Natural selection is a Theory about the mechanism that explains this and as a Theory it has been very successful at predicting and explaining the data in biology, archeology, anthropology, genetics, psychology... for over 100 years. 150 years ago there was not the same sample of fossils we have now and they keep falling into place, there wasn't even a real idea of genes or population genetics but that fits. Heck 150 years ago there was barely an idea that viruses existed and yet they appear to be subject to natural selection too. it does not all hinge on observing speciation. We have a pretty good idea that speciation exists the issue is the mechanism and natural selection fits the model there. If there is a competing Theory for a mechanism other than natural selection it has to be stated, and researched in a way that can generate competing hypotheses that can be tested with data. You can't just choose ID or creationism as the default because that is what you believe. It needs to be presented as a viable mechanism and positive support for the alternative provided. I am cool with people trying to do just that, but that is how it has to be done to be a proper competing scientific theory. When natural selection was proposed it did a very good job of describing the available data and since then hypotheses generated by natural selection have been supported and the data continues to fit better than any other Theory. In addition, no one has produced a competing theory that makes any predictions in contrast to natural selection and supported it with positive support. This is why people who have studied the field get frustrated. Propose the alternative and support it and people will have to pay attention. It really is that simple. That goes well beyond a matter of faith no matter how much you want to believe that it does.

 

[Rhetoric Camel]

One of my favorite Folk Guitar players/singers/songwriters
The Origin of Species - By Chris Smither

YouTube - Chris Smither - "Origin Of Species" - from "One More Night" performance DVD

Well, Eve told Adam
Snakes? I've had 'em!
Let's get outta here!
Go raise this family someplace outta town.

They left the garden just in time
With the landlord cussin' right behind.
They headed East,
and they finally settled down.

One thing led to another:
A bunch of sons,
One killed his brother
And they kicked him out with nothin' but his clothes.

And the human race survived
'Cause all those brothers found wives
But where they came from
Ain't nobody knows.

Then came the flood
Go figure...
Just like New Orleans only bigger.
No one who couldn't swim would make it through.

The lucky ones were on a boat
Think "circus"
And then make it float
I hope nobody pulls the plug on you!

How they fed that crowd is a mystery.
It ain't down in the history,
but it's a cinch they didn't
live on cakes and jam.

Lions don't eat cabbage
And in spite of that old adage,
I ain't never seen one
Lie down with a lamb.

Well, Charlie Darwin looked so far
Into the way things are.
He caught a glimpse of God's
unfolding plan.

God said: "I'll make some DNA"
They can use it any way they want
From paramecium
Right up to man."

"They'll have sex
And mix up sections of their code
They'll have mutations...
The whole thing works like clockwork over time."

"I'll just sit back in the shade
While everyone gets laid.
That's what I call
Intelligent design."

Yeah, you and your cat named Felix,
Both wrapped up in that double helix,
Is what we call
Intelligent design.

 

[gashin]

I'm not rejecting natural selection or evolution as the best fit model - I just think it is wrong to claim it is the truth for he origin of species as there are no examples of new species having evolved - even Darwin brought doubt on his own theory in his book, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. Fossil records and the like are extremely flawed because scientists make claims of genetic relationships based on anatomy - while analogy in structure can be seen in nature without homology in genetic code. Since there are huge gaps in the fossil record, and very little to no accurate sequencing of ancient DNA, to make the claim that evolution is the source of new species is purely speculation. The fact is that despite this lack of scientific evidence, the majority of the scientific community has accepted this to be true and this is taught as true in educational systems throughout the world. It is thus a matter of scientific faith and not scientific truth - this is what is troubling me.

I certainly don't want to get side tracked on viruses, but the example I mentioned is not simply an issue of different strains (can't readily infect the same hosts, attach the cells via different mechanisms and sites wihin the cell...) and we do know a fair amount of the history of HIV.

That said be careful not to confuse evolution with natural selection and vice versa. Natural Selection is not the first theory of evolution and ID as it is proposed (if you take it on face value rather than a political trick to sneak creationism into high schools) attempts to be a competing theory of evolution. Like I said other than suggesting that all species were created at the same time we are talking about different theories to explain the data. The data is that there are different species and those species 'appear' at different times. Natural selection is a Theory about the mechanism that explains this and as a Theory it has been very successful at predicting and explaining the data in biology, archeology, anthropology, genetics, psychology... for over 100 years. 150 years ago there was not the same sample of fossils we have now and they keep falling into place, there wasn't even a real idea of genes or population genetics but that fits. Heck 150 years ago there was barely an idea that viruses existed and yet they appear to be subject to natural selection too. it does not all hinge on observing speciation. We have a pretty good idea that speciation exists the issue is the mechanism and natural selection fits the model there. If there is a competing Theory for a mechanism other than natural selection it has to be stated, and researched in a way that can generate competing hypotheses that can be tested with data. You can't just choose ID or creationism as the default because that is what you believe. It needs to be presented as a viable mechanism and positive support for the alternative provided. I am cool with people trying to do just that, but that is how it has to be done to be a proper competing scientific theory. When natural selection was proposed it did a very good job of describing the available data and since then hypotheses generated by natural selection have been supported and the data continues to fit better than any other Theory. In addition, no one has produced a competing theory that makes any predictions in contrast to natural selection and supported it with positive support. This is why people who have studied the field get frustrated. Propose the alternative and support it and people will have to pay attention. It really is that simple. That goes well beyond a matter of faith no matter how much you want to believe that it does.

 

[gatsby]

I guess I am not really seeing your issue here. Of course there is some doubt. Doubt drives science. So if you see natural selection as the best fit and don't see a better model whats the issue? Do you think people are trying to replace a faith in God with a faith in science? I would suggest that the vast majority of people working in the field do not even think in these terms and would rather the people take the argument elsewhere. In fact, the person who was most influential in my education concerning evolution was an extremely religious person who held his faith in extremely high regard.

The model of natural selection has been well tested and is everyday. Its not just the fossil record which is by its nature always going to be spotty. A nice example is that around one fifth of the mammal species are bats, but they are poorly represented in the fossil record because they don't fossilize well. People are doing a pretty good job of extracting ancient DNA (within reason the stuff is fragile). I worked for a couple of years with some of the folks extracting Neanderthal DNA (I wasn't part of that so please don't ask me anything about it. I just drank beer with them after work). Personally,I spent a large part of my career working with adaptationist hypotheses about behavior and natural selection was a great model there. It is a great working Theory. Parts have changed. No one goes back to the 5th part of Darwins theory which is the use/disuse suggestion. It was tried and fond lacking. There is now alot more discussion of mutation than in the past (to the detriment of the field IMO since recombination does a lot of work). So far the alternative has yet to be presented that can even promise to replace all that and until it does and starts to get even a fraction of the positive empirical support natural selection gets everyone will keep plugging away using what has been working.

I'm not rejecting natural selection or evolution as the best fit model - I just think it is wrong to claim it is the truth for he origin of species as there are no examples of new species having evolved - even Darwin brought doubt on his own theory in his book, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. Fossil records and the like are extremely flawed because scientists make claims of genetic relationships based on anatomy - while analogy in structure can be seen in nature without homology in genetic code. Since there are huge gaps in the fossil record, and very little to no accurate sequencing of ancient DNA, to make the claim that evolution is the source of new species is purely speculation. The fact is that despite this lack of scientific evidence, the majority of the scientific community has accepted this to be true and this is taught as true in educational systems throughout the world. It is thus a matter of scientific faith and not scientific truth - this is what is troubling me.

 

[Raenon]

One of the most ridiculous arguments against macroevolution is that once something is a new species, it supposedly cannot produce viable offspring with the original, or other species. Worse, this is based on early scientific beliefs that have been carried over long after it was shown incomplete.

The problem with this assumption is that human beings, in all their flawed understanding of the world, decide what is and is not a new species.
When a creature has made that leap is a huge, blurry gray area, not a night and day occurance.
A dinosaur did not lay a chicken egg, a chicken did not hatch from a dinosaur egg. This was a long drawn out process full of tiny variations.

If you want to see a great example of different "species" interbreeding successfully, look at dogs and wolves. A chihuahua and a timberwolf can produce viable offspring, even with the obvious physical difficulties involved

 

[gashin]

"The dog (Canis lupus familiaris,[2] pronounced /ˈkeɪ.nɪs ˈluːpəs fʌˈmɪliɛərɪs/) is a domesticated form of the Wolf, a member of the Canidae family of the order Carnivora.:

Dog - Wikipedia, the free encyclopedia

They are the same species - can you give an example of two animal species that can interbreed and produce fertile offspring? There are a few plants that can but their reproduction cycle allows such mutants. The ability to produce fertile offspring is part of the definition of a species - at least this is what I was taught at the 10th ranked Biology program in the U.S.

One of the most ridiculous arguments against macroevolution is that once something is a new species, it supposedly cannot produce viable offspring with the original, or other species. Worse, this is based on early scientific beliefs that have been carried over long after it was shown incomplete.

The problem with this assumption is that human beings, in all their flawed understanding of the world, decide what is and is not a new species.
When a creature has made that leap is a huge, blurry gray area, not a night and day occurance.
A dinosaur did not lay a chicken egg, a chicken did not hatch from a dinosaur egg. This was a long drawn out process full of tiny variations.

If you want to see a great example of different "species" interbreeding successfully, look at dogs and wolves. A chihuahua and a timberwolf can produce viable offspring, even with the obvious physical difficulties involved

 

[gashin]

The problem is that there is no evidence that evolution can produce new species. It's not about faith vs science - it's about scientists making a baseless claim! The fact that the scientific community makes this leap of faith doesn't make it a fact and the reality that scientists in the natural scientists allow a huge amount of error in their standards of evidence onl brings their conclusions under greater suspicion. Evolution and its processes are a viable explanation for the different species - but it's not an explanation supported by any hard evidence. The problem is that when scientists see even any sort of similarity in the genetic code they use that as evidence of common ancestry - this is an assumption not a fact. The only way evolution can be shown to produce new species is if we actuallly observe that it does - there is no evidence of this type yet.

I guess I am not really seeing your issue here. Of course there is some doubt. Doubt drives science. So if you see natural selection as the best fit and don't see a better model whats the issue? Do you think people are trying to replace a faith in God with a faith in science? I would suggest that the vast majority of people working in the field do not even think in these terms and would rather the people take the argument elsewhere. In fact, the person who was most influential in my education concerning evolution was an extremely religious person who held his faith in extremely high regard.

The model of natural selection has been well tested and is everyday. Its not just the fossil record which is by its nature always going to be spotty. A nice example is that around one fifth of the mammal species are bats, but they are poorly represented in the fossil record because they don't fossilize well. People are doing a pretty good job of extracting ancient DNA (within reason the stuff is fragile). I worked for a couple of years with some of the folks extracting Neanderthal DNA (I wasn't part of that so please don't ask me anything about it. I just drank beer with them after work). Personally,I spent a large part of my career working with adaptationist hypotheses about behavior and natural selection was a great model there. It is a great working Theory. Parts have changed. No one goes back to the 5th part of Darwins theory which is the use/disuse suggestion. It was tried and fond lacking. There is now alot more discussion of mutation than in the past (to the detriment of the field IMO since recombination does a lot of work). So far the alternative has yet to be presented that can even promise to replace all that and until it does and starts to get even a fraction of the positive empirical support natural selection gets everyone will keep plugging away using what has been working.