questions for science( let's hear your answers)

[Gman]

Respectfully, I disagree. The ToE was fully supported in the 1930's when basic inheritance patterns were understood (or at least rediscovered). It continued to be supported for the next 3 decades when the structure and function of DNA was discovered. And it continues to be supported by recent advances in molecular genetics today. The only thing that happened in the 90's that revolutionized our ability to test the theory was the development of rapid, cheap and efficient means of sequencing DNA enabling the field of molecular phylogenetics to come into its own (this is what I did for my doctoral thesis). As for everyone being convinced that their research "aligns" with the ToE - you seem to hold this theory to a different standard than other theories. A theory is, by definition, an idea that has been thoroughly tested and is true beyond reasonable doubt. At some point, science agrees that the idea is a scientific truth and begin using it for its explanatory power (another hallmark of a theory). So, like any scientific theory, the ToE is used as a lens through which to examine and understand patterns and observations in science. This is not unique to the ToE - again, all theories are treated in the same way. And if patterns or observations can't be explained by evolution - or worse still are inconsistent with it, then it is time to reexamine it.

Respectfully, I disagree with you too… Again, we have barely begun to scratch the surface of genetics. Take GenBank for example.. GenBank, which is a genetic sequence database, is the annotated collection of all publicly available DNA sequences.. If we look at the growth of GenBank, it appears to be doubling every 18 months. This graph alone, starting from 1982 has been virtually dead until we get to the early 90's.. From this graph alone we can clearly see that we have a tremendous amount of collecting available of nucleotide sequences and their protein translations, not to mention the study of the results..



Also, I would argue that the ToE has NOT been tested beyond reasonable doubt… It should be noted that evolution itself has also found it virtually impossible to chemically produce the basic molecules required for any living system as well. Evolution has never been witnessed to chemically produce life either. It claims to have occurred over millions of years in very slow processes which scientist can't replicate. According to evolutionist Dr. Paul Davies, “The origin of life is one of the great outstanding mysteries of science. Nobody knows how a mixture of non-living chemicals can transform itself into a living cell. Because they have almost nothing to go on, scientists differ sharply on how likely such a genesis event (Abiogenesis) might be. Some think it happened only once in the universe - and we are the result. Others believe there is a deep principle built into the laws of nature that prompts life to form readily wherever there are Earth-like conditions.”

Abiogenesis is just one of the many problems DE faces… There are numerous others as well...

Well, I guess we need to define "answers". A scientific theory can provide the "what" or "how" answers, but it usually doesn't provide the "why" ones. Why does gravity behave the way it does? Why do continents float around the surface of the Earth? In a philosophical or metaphysical sense, the ToE can not explain why life evolved - it can simply provide an explanation of how it evolved. For that reason, I believe theology and religion serve a very important function...they fill in gaps not filled or fillable by science.

How? In regards to gravity, I don't think you can compare Darwinian evolution to gravity. When you look at the scientific methods of Copernicus, Galileo, and Newton they made observations plus predictions that anyone could observe… Darwinian evolution is not like that. DE is a different kind of science, it's a historical science that claims what happened in the past, it's not like gravity at all… Gravity can make simple predictions like the gravitational force between the earth and the moon. It's something that can be measured.. Darwin tried to make predictions with populations, such as making statements like “every single organic being around us may be said to be striving to the utmost to increase in numbers.” Ok, let's take a look at humans then… Well, I decided, and I'm sure that there are many others like me, not to increase in numbers. I have no children. How do people like me fit into this equation? Again, this is just one of many predictions that in reality can't really be measured like the force of gravity…

Now, ID does purport to explain the existence of certain structures not explainable by naturalistic explanations, and as I have been careful to point out naturalistic explanations for these questions do seem to exist.

Well I would disagree with that… Evolution is said not to be 100% factual or completely answered when it comes to science. There are theories, yes, but no smoking guns on either side when it comes to the topic of origins. What we have here are only weights of evidence in favor of one view and sometimes neglecting the other. Sometimes even scientists don't always agree on the scientific outcome of the evolutionary or design predictions either as we have witnessed.

Really? This is a huge surprise to me.

That ID proponents do not seek to have ID taught or mandated into the public biology classrooms? Can you show me a court case where they have?

As a high school teacher, I agree that fostering critical thought is important. However, as a biology teacher I am left to wonder what "controversy" there is to teach? There are those who feel the ToE is insufficient in its explanatory power, but have yet to provide examples of structures it can't explain. There are those who oppose the theory based on religious grounds, but this hardly seems reason enough to teach the "controversy" in my classroom. Finally, at what point do we dignify every criticism of an idea in our classrooms? Science is not a democracy of ideas - only those that have been rigorously tested and have passed the testing are accepted. ToE has been tested and has passed on every account. ID has not. Would you advocate teaching the ideas promoted by Holocaust deniers in a history class? This may seem like hyperbole, but is actually an apt comparison.

ToE has NOT been tested and has passed on every account. Again, evolution has never been witnessed to create life either. It claims to have occurred over millions of years in very slow processes which scientist can't replicate… I'll leave our article Religion and Intelligent Design Impede Science and Close Off Inquiry? for the rest…

You seem to be conflating what I have been saying here. I have said twice, that public school teachers may (and in fact do) teach ID together with evolution giving it equal treatment in their classrooms. In their units on evolution, both are taught and the students are left to decide which they accept. This is currently not considered a violation of the Constitution, so there is nothing besides state standards and teacher discretion preventing them from so doing.

No… I don't think you are understanding what I meant. I will guarantee that you will ever find a public class with a text book devoted to ID.. You will never find a public school with ID in their curricula. That is a MAJOR difference in what you are saying…

This seems like a little selective quote mining. The article goes on to state: "Both he and Doolittle are at pains to stress that downgrading the tree of life doesn't mean that the theory of evolution is wrong - just that evolution is not as tidy as we would like to believe. Some evolutionary relationships are tree-like; many others are not." So we know that the trunk of the tree of life is messy which is unsurprising given how often genes may have been exchanged. And yet branching, tree-like relationships are the way most evolutionary relationships can be described - pick up virtually any scientific journal in the biological science and you see phylogenetic trees delineating the ancestor-descendant relationships in groups of organisms. But it seems at the very trunk of the tree, relationships get a bit messy. So really all that the article is saying is that the metaphor works in some cases and not others - not that evolution, per se, is wrong.

Messy?? Well that hardly classifies as being proved beyond a shadow of doubt… Ok, well then let's look at the closing paragraph for a better view…

Quoting Rose…

"The tree of life is being politely buried, we all know that," he says. "What's less accepted is that our whole fundamental view of biology needs to change." Biology is vastly more complex than we thought, he says, and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century. If he is right, the tree concept could become biology's equivalent of Newtonian mechanics: revolutionary and hugely successful in its time, but ultimately too simplistic to deal with the messy real world. "The tree of life was useful," says Bapteste. "It helped us to understand that evolution was real. But now we know more about evolution, it's time to move on."

Again, they are finding that Darwin's tree of life is too simplistic. The real world is really more complicated than that… Now while it may be true that he isn't exactly throwing out evolution, he is taking a different view on it and reconstructing the thoughts that made it up which means that it isn't written in stone (it's structure) as many would propose..

If you can doubt Darwin's tree then how can you compare Darwinism to gravity??? How can you measure a MESSY disappearing tree??

No, not surprised. The courts would tend to stay out of such matters until ideas which may be rooted in religious ideology are promoted in public schools. At this point, the courts will need to assess the ideas and determine whether their promotion violates the constitution.

Really and how is ID rooted in religious ideology?

The question was over how it got labeled. But if it really does have teeth and can cut it in the scientific arena, it will do so.

Like how Darwinian evolution does? I thought you said earlier that it doesn't have all the answers…

So this is a metaphor you're going with? That scientists are like shoe salesmen? I understand the comparison you are making between the ToE and ID, but do you really feel that scientists are paid to preserve their ideas at the exclusion of all others? Do you really believe this, or are you just using your metaphor to make a point?

What I mean is that we are only looking at one product.. A Nike salesman would be a fool to sell a different product than his own… They are paid by the Nike Corporation… Science was meant to be debated and when the debate is taken away from it, people may learn about evolutionary theory but in the end they don't always believe in it because they were never allowed to debate it, or try a different shoe...

Cheers,
G -

[ARWallace]

Gman -

>>Respectfully, I disagree with you too… Again, we have barely begun to scratch the surface of genetics. Take GenBank for example.. GenBank, which is a genetic sequence database, is the annotated collection of all publicly available DNA sequences.. If we look at the growth of GenBank, it appears to be doubling every 18 months. This graph alone, starting from 1982 has been virtually dead until we get to the early 90's.. From this graph alone we can clearly see that we have a tremendous amount of collecting available of nucleotide sequences and their protein translations, not to mention the study of the results..

Respectfully, I disagree with your disagreement! I know what GenBank is - I have deposited sequences there myself. And your graph confirms what I said earlier - that with recent advances in molecular techniques, the availability of DNA and protein sequences has risen astronomically. However, there are two important points here: first, the ToE has been tested and used as a theory to explain observations in our natural universe for far longer than this. The marriage of mathematics, genetics and evolution in the 1930's gave rise to population genetics which explains and predicts patterns of gene frequency changes. Barbara McClintock's discovery of transposable elements in the 40's and 50's helped explain precisely the sort of mess that you feel can't be explained with respect to the trunk of the tree of life. Lynn Margulis resurrected and popularized the theoru of serial endosymbiosis in the 80's, and it is a remarkably powerful and well supported explanation of eukaryotes could have evolved from prokaryotes. Discoveries in paleontology have supported the ToE for a century and a half. The list goes on. Now, the second point is that many of these DNA and protein sequences have been used for molecular phylogenetic analyses, and time and time again these analyses are wonderfully consistent with patterns predicted by evolution, and by patterns found using other comparisons. So the ToE has been tested and developed for 150 years, just as I claimed originally (and ID remains the new kid on the block). And it has withstood scrutiny extremely well over this time.

>>Also, I would argue that the ToE has NOT been tested beyond reasonable doubt… It should be noted that evolution itself has also found it virtually impossible to chemically produce the basic molecules required for any living system as well.

Um, I think this is untrue. While we may never know the exact steps leading to life from nonlife, numerous experiments have demonstrated that all of the steps necessary to go from inorganic molecules to short, variable sequence of replicating molecules upon which selection could act are possible under natural conditions. And I am not sure what quote mining accomplishes; you quote a scientist who simply admits that science may not be able to fully resolve a question about an event that occurred 4 billion years ago without leaving fossil evidence but yet are able to demonstrate the steps are theoretically possible as a failure for evolution?

>>When you look at the scientific methods of Copernicus, Galileo, and Newton they made observations plus predictions that anyone could observe… Darwinian evolution is not like that.

Actually, it is. There are patterns in DNA, morphology, behavior, fossils, plate tectonics, biogeography and so on and so on that all must be consistent with the idea for it to be true. It is every bit as testable as gravity, and the comparison is apt.

>>DE is a different kind of science, it's a historical science that claims what happened in the past

I know what historical sciences are - and they are used in other fields of science besides evolution. Geology, physics and astronomy all use the hypothetic-deductive approach to answering questions about events that happened in the past or are too difficult or impossible to test directly in lab settings. We use this approach in courtrooms every day and sentence men to death based on hypothetico-deductive methods of inquiry of events that occurred without eye witnesses. This is a rather unfair criticism of science.

>>“every single organic being around us may be said to be striving to the utmost to increase in numbers.” Ok, let's take a look at humans then… Well, I decided, and I'm sure that there are many others like me, not to increase in numbers. I have no children. How do people like me fit into this equation?

Well, if there is a genetic basis to such a decision, your fitness becomes zero while those with genes that tend to propagate, will. It's simple, really and totallly consistent with what Darwin said.

I have to run - class is about to start...sorry for the incomplete response.

Cheers
Al

[ARWallace]

Couple of thoughts between classes...

>>No… I don't think you are understanding what I meant. I will guarantee that you will ever find a public class with a text book devoted to ID.. You will never find a public school with ID in their curricula. That is a MAJOR difference in what you are saying…

I understand totally what you are saying - I agreed that there aren't classes devoted to ID in public schools. And there aren't classes on evolution either. Evolution is taught as units in a biology class or referenced where relevant (e.g. the evolution eukaryotes). So why should we have a whole class devoted to ID when we don't have them devoted so ToE? What I am saying is that many teachers teach ID along with evolution - "let the students decide" sort of thing. And as per my earlier comments, The ToE has been around for 150 years and is a well established scientific theory. Why should we let an idea that is new and relatively untested in - particularly when it seems to fail the tests that have been done. I come back to my question about Holocaust deniers having a voice in history classes.

Now, since ID is new, there has not been much of an opportunity for it to mandated into curricula by school boards, but I'll bet the farm that it is in the future. Do you disagree that attempts to implement ID into public schools will be made in the future, and that variants of biology texts will be encouraged if not mandated to be adopted together with mainstream biology texts (much like they were in Dover)?

>>Really and how is ID rooted in religious ideology?

Careful, now. That's not what I said. I said that if ID is implemented into science curricula that I guarantee that it will wind up in courts where judges will decide whether it is religious ideology or not...just as they did with YEC.

>>What I mean is that we are only looking at one product.. A Nike salesman would be a fool to sell a different product than his own… They are paid by the Nike Corporation… Science was meant to be debated and when the debate is taken away from it, people may learn about evolutionary theory but in the end they don't always believe in it because they were never allowed to debate it, or try a different shoe..

First of all, debate does exist. We're having one right now. Moreover, healthy debate is exceedingly abundant in the scientific community - just pick up a scientific journal. Second of all, I continue to reject your metaphor as unfairly portraying evolutionary biologists (after all, how many do you know personally and have worked with intimately enough to know that they are secretly or overtly protecting an idea they know to be false?) and continue to hold them and their theory to a different standard than other scientists. Finally, science is not a democracy of ideas - quite the opposite. Only those that show any real promise as being true or productive are advanced. But that doesn't mean that debate over the ideas doesn't exist - but if the ideas do not show any real promise, they are quickly rejected by the scientific community. ID has not, as yet, shown to be a productive or viable field of research (its possible theistic or questionable origins notwithstanding). Regardless of whether the idea was developed and advanced by the Pope himself for the greater glory of the Vatican is not relevant if the idea itself is scientific AND has the promise of being a viable scientific theory. So let ID stand or fall on its own merits - it's still young and under development, so who knows what will happen in the next few decades...

Cheers
Al

[robyn hill]

I suppose one could chase its tail all day trying to prove one theory over another. I don't disagree with science,I just don't agree that in order for something to exist,it has to pass scientific criteria.I don't think the following statement is logical:

Scientists have a set of criteria to decide if a theory is solid and is proven as a truth. If theories can't pass under this criteria-they can't be solid theory. There are things that can't be tested, things outside of our universe, things beneath the view of the microscope,so theories as to their existence can't be true.

As ridiculous as this statement appears, as it is logically incorrect, this is what I hear atheists claim all the time. When a theory doesn't pass science standards, it must not be true. I find people ignorant when they claim science as the ultimate judge on what passes as truth or theory. It is one set of criteria. In western society, some have accepted science as the measure of all truth. I agree with many scientific theories, that is to go without saying, what I don't agree with is that all truth must be accepted by scientific criteria.There are so many events that occur that sceince can't explain, that doesn't mean they don't exist!If truth can't exist outside of a scientific crierea based funnel, then science becomes an elitist club where others aren't allowed in if they don't agree to the club's criteria. I don't blame science for this, I think this is a narrow minded way to view science and our existence. Scientific criteria, created by man, becomes God, all knowing, when we view possibility -only-through its lens. And, after all, I think we can ALL agree to this statement, that man, to this day, has never been proven to be all-knowing, I don't think we need any evidence to see this as true .

[zoegirl]

I suppose one could chase its tail all day trying to prove one theory over another. I don't disagree with science,I just don't agree that in order for something to exist,it has to pass scientific criteria.I don't think the following statement is logical:

Scientists have a set of criteria to decide if a theory is solid and is proven as a truth. If theories can't pass under this criteria-they can't be solid theory. There are things that can't be tested, things outside of our universe, things beneath the view of the microscope,so theories as to their existence can't be true.

As ridiculous as this statement appears, as it is logically incorrect, this is what I hear atheists claim all the time. When a theory doesn't pass science standards, it must not be true.

Who made that statement? If a theory doesn't pass science standards, it just simply can't be held to be proven by scietific standards. Sicence is greatly limited. It can only be applied to bservalbe, measureable, and controllable events. As such, phenomena outside the physcial realm is outside of the observational methods of science. Doesn't mean that other means of study can't be applied, just that science can't be used.

And there lies the great power and the great limitation of science. ANd those who want to use science to disprove God are overapplying its use.

I find people ignorant when they claim science as the ultimate judge on what passes as truth or theory. It is one set of criteria. In western society, some have accepted science as the measure of all truth. I agree with many scientific theories, that is to go without saying, what I don't agree with is that all truth must be accepted by scientific criteria.There are so many events that occur that sceince can't explain, that doesn't mean they don't exist!If truth can't exist outside of a scientific crierea based funnel, then science becomes an elitist club where others aren't allowed in if they don't agree to the club's criteria. I don't blame science for this, I think this is a narrow minded way to view science and our existence. Scientific criteria, created by man, becomes God, all knowing, when we view possibility -only-through its lens. And, after all, I think we can ALL agree to this statement, that man, to this day, has never been proven to be all-knowing, I don't think we need any evidence to see this as true .

No problems here...agreed

[David Blacklock]

Hi Robyn - There is certainly more to life than science and science shouldn't claim dominion over every form of human belief and experience. On the other hand, science (simply put) consists of observing and describing how the universe works. As time has passed, the observational techniques used by science have become more and more complicated and refined, but science is still deriving theorums based on ingenious methods used to observe the natural earth and universe in action. The technologies that have resulted have completely changed our lives - and that's not even what scientists set out to do. They started out driven by curiosity as to how things work - and for a lot of scientists, that is still the only driving force. For almost all of them, it is still a major driving force. Except for those of us who live like Mennonites or are on boy scout camp-outs (and these groups use science-derived technology too) every aspect of the typical day in the US is loaded with science-derived assistance, to the extent that in the US, we each have the equivalent of 50-100 slave hours of help per day (if we used slaves to get as much done as the typical person gets done). From getting up in the morning (electric alarm clock, comfortable room temp), shaving (electricity, modern razors packaged with polymers, special foams accelerated out of special propulsive devices), showering (calibrated and reliable water pressure with treated water), toaster (not wood burning) with bread you didn't have to make, sausage screened for parasites...every second of your day is reliant on science instead of superstition - which was relied on during all human history other than the last couple of hundred years - and life was tough. Now, thanks to science, life is considerably easier (as a norm). For those wise enough to get a good education and have reasonably good health, life can be about as easy as you want to make it. If the powers of observation by those who have made it a career to study it end up with theories that are inconvenient, so be it. In a hundred years, today's mainstream science will be added to and some of it will be changed, but at any given time, my money is on mainstream science as the collection of data most likely to be true and reliable - for those areas scientists observe and study. Of course, that excludes theology and many other areas of endeavor.

DB

[robyn hill]

hi David,

I said,
I don't disagree with science,I just don't agree that in order for something to exist,it has to pass scientific criteria.

you said,
There is certainly more to life than science and science shouldn't claim dominion over every form of human belief and experience.

I think we agreed on this point. I am exceedingly grateful to science, and that goes without saying, after all we wouldn't be having this conversation, but when people hold science to be the only truth and absolute, I think we are narrowing the parameters of our intellect.

[ARWallace]

G'man -

I never got around to responding to your concerns about the tree of life problem. You say "Messy?? Well that hardly classifies as being proved beyond a shadow of doubt…"

Let's start with what the ToE is - it is basically a series of statements about how organisms with heritable and variable characteristics change over time. Specifically, alleles for traits that confer a survival or reproductive advantage will enjoy differential success over time compared to those for traits for lower survival or reproductive rates. The outcomes of this process over long periods of time are macroevolution, speciation, adaptation and/or extinction. Now, in general, when you examine this process over long periods of time, you tend to see patterns that are consistent with branches of a tree - species emerge, split from common ancestors, thrive and split more, or often just go extinct. So the metaphor of a tree of life tends to work quite well when applied to evolutionary change. Indeed, phylogenetic analyses of groups of species, or genera, or families do show patterns of change that - when shown topographically - resemble a tree.

Now, the genetic changes that are produced over long periods of time in most speciation events are small and subtle - a mutation here, insertion there, maybe a gene duplication event now and then. And when you examine the DNA of groups of organisms, you can use these changes as roadmaps to delineate the events that occur during their diversification. However, there are occasionally changes that occur that produce new types of organisms that make things a little more difficult in terms of recreating the events that took place. For example, the changes that gave rise to eukaryotes from prokaryotes were not of the small, incremental changes in DNA that produce a new species of bee from another (for example). Rather, it appears that mitochondria and chloroplasts were once free-living bacteria which were engulfed by another organism, and rather than being digested, became incorporated into the cell and all of its descendants. This is not uncommon in nature - it's how we have come to depend on bacteria in our guts for assistance in digestion, or protists in the guts of termites. It's called endosymbiosis.

This does not mean that evolution had no hand in this - presumably this ancestral proto-eukaryote had some advantage over those without their new symbiont. And so selection favored this new form of life. So we're not violating any laws of nature; just discovering a new way to change living organisms that is a little different than the processes usually leading to new species. But here's the kicker - if these events really did occur, then there must be things that are true today that we can use to decipher the events from the past. It's the dreaded historical science you dislike so much - but it is exactly how we know what happened billions of years ago. Mitochondria and chloroplasts are of about the same size as bacteria. They possess their own DNA. They can replicate by binary fission (like bacteria) autonomous of the cells in which they reside. They possess 2 layers of membrane - just what you'd expect from something with its own membrane engulfed by another membrane-bound organism. Their inner membrane is more chemically similar to eubacterial membranes than eukaryotic membranes. Like bacteria, their DNA is circular and not linear, and it does not have introns or histone proteins (like eukaryotes). The first amino acid of mitochondrial and plastic transcripts is equivalent to that of eubacteria, and different from that of eukaryotes. Mitochondria and chloroplasts produced their own ribosomes, which have 30S and 50S subunits (like bacteria), and not the 40S and 60S subunits of the eukaryotic cells in which they occur. Many antibiotics that kill eubacteria also affect the mitochondria and chloroplasts. The list goes on - and what's more, we have a good idea of why the association of mitochondria would be favored: for billions of years, photosynthetic bacteria had been producing O2 gradually changing the composition of the Earth's atmosphere. Geologists can track the changes by how oxidized iron formations are in various rock-strata. An anaerobic bacteria that engulfed an aerobic one would have an advantage (as would the symbiont - a safe place with access to the cell's energy and nutrients). Quite simply, the evidence are all there at fit remarkably well - and we have reconstructed an evolutionary event that happened billions of years ago using evidences left behind for us to work with.

So getting back to the tree of life; at the trunk of the tree of life, events get a little messy (yes, messy). Rather than one, single prokaryote that roots the entire tree and is the ancestor to all living organisms, it appears that there may be several trunks to the tree of life. We have not violated evolution here, we have simply deconstructed a metaphor that works very well for most other speciation events in most other oprganisms. Bacteria routinely exchange DNA, or take bits of DNA up from their environment, and it is not the least bit surprising that at some point in the 3 billion years that bacteria were the sole inhabitants of this planet, that some species of bacteria used a mechanism other than simple mutation and subsequent differential success to differentiate. And there is invariably evidences that were left behind as a result for us in examine and piece together the events that occurred.

In short, it is my position that a messy trunk to the tree of life if not a problem for evolution. And in all likelihood we will piece together the events that occurred and I'll bet the farm that they are not inconsistent with the ToE. And not because scientists are behaving like shoe salesmen.

Cheers
Al

[Gman]

Respectfully, I disagree with your disagreement! I know what GenBank is - I have deposited sequences there myself. And your graph confirms what I said earlier - that with recent advances in molecular techniques, the availability of DNA and protein sequences has risen astronomically. However, there are two important points here: first, the ToE has been tested and used as a theory to explain observations in our natural universe for far longer than this. The marriage of mathematics, genetics and evolution in the 1930's gave rise to population genetics which explains and predicts patterns of gene frequency changes. Barbara McClintock's discovery of transposable elements in the 40's and 50's helped explain precisely the sort of mess that you feel can't be explained with respect to the trunk of the tree of life. Lynn Margulis resurrected and popularized the theoru of serial endosymbiosis in the 80's, and it is a remarkably powerful and well supported explanation of eukaryotes could have evolved from prokaryotes. Discoveries in paleontology have supported the ToE for a century and a half. The list goes on. Now, the second point is that many of these DNA and protein sequences have been used for molecular phylogenetic analyses, and time and time again these analyses are wonderfully consistent with patterns predicted by evolution, and by patterns found using other comparisons. So the ToE has been tested and developed for 150 years, just as I claimed originally (and ID remains the new kid on the block). And it has withstood scrutiny extremely well over this time.

Looks like we respectively disagree with each other… In regards to Genbank, it is the repository that keeps track of all the genes that have been sequenced. If you sequence a gene you can submit it to GenBank (which is publicly available to anyone) so that other investigators can look at that gene sequence. Basically the data in GenBank has been doubling in data every 18 months… Why? Because gene sequencing has been automated via computers.. We have just begun to collect the data.. We still have to analyze the data being collected. And, contrary to what you propose, the analysis are NOT wonderfully consistent with patterns predicted by evolution, and by patterns found using other comparisons… It is not a slam dunk for ToE by any means… One of the things scientists are finding with these DNA sequences is the puzzle of “ORFan genes” (Open Reading Frame genes) the sequence of DNA that codes for protein. By comparing the genes they are looking for a match, but in the case of ORFan genes, however, they are not finding matches.. Ordinary the sequences come back with matches, except for the ORFan genes. Of course scientists may theorize where they came from, but nothing is for certain.. Let's look what the scientists (who are not creationists) are saying about this…

Russell Doolittle, from the article “Microbial genomes multiply.”

“In every genome examined so far, at least a quarter of the genes remain 'hypothetical', in that no function can be ascribed. After such a long history of biochemical and genetic examination, how could there be so much in the way of unknown equipment?... there are large numbers of unidentified genes in a variety of organisms that look conventional in every way. Where these unique sequences are coming from and what they do remain baffling mysteries.”

Or Daniel Fischer and Ben Guion “Analysis of Singleton ORFan in fully Sequenced Microbial Genomes”

“…each ORFan represents a mystery awaiting interpretation … For example, how have their sequences diverged to such an extent that no similar sequences are detected today? If evolution works through descent with modification then why is it that no similar sequences are found in other organisms? Why is it that we do not find today any of the necessary “intermediate” sequences that must have given rise to these ORFans?”

It just all goes back to what I was saying before that sometimes scientists don't always agree on the scientific outcome of the evolutionary predictions.. They can be questioned…. It's not always written in stone.

Um, I think this is untrue. While we may never know the exact steps leading to life from nonlife, numerous experiments have demonstrated that all of the steps necessary to go from inorganic molecules to short, variable sequence of replicating molecules upon which selection could act are possible under natural conditions. And I am not sure what quote mining accomplishes; you quote a scientist who simply admits that science may not be able to fully resolve a question about an event that occurred 4 billion years ago without leaving fossil evidence but yet are able to demonstrate the steps are theoretically possible as a failure for evolution?

This actually goes back to what I was saying before, that evolution claims to have occurred over millions of years in very slow processes which scientist can't replicate. Ok, so you can create life from nonlife? If so, please show us your work… Oh, there are many, many ideas on how life may have occurred but nothing is solid yet at all… If you want, please look at some of the problems abiogenesis faces on our Is the Chemical Origin of Life (Abiogenesis) a Realistic Scenario? page.

Actually, it is. There are patterns in DNA, morphology, behavior, fossils, plate tectonics, biogeography and so on and so on that all must be consistent with the idea for it to be true. It is every bit as testable as gravity, and the comparison is apt.

I know what historical sciences are - and they are used in other fields of science besides evolution. Geology, physics and astronomy all use the hypothetic-deductive approach to answering questions about events that happened in the past or are too difficult or impossible to test directly in lab settings. We use this approach in courtrooms every day and sentence men to death based on hypothetico-deductive methods of inquiry of events that occurred without eye witnesses. This is a rather unfair criticism of science.

And what science are we talking about? From all I know, we were talking about Darwinian evolution. Are we going off on other subjects now? You can't take Darwinism and formulate it to an equation like F=MA the force of gravity. Dawinism is NOT a law, you can't measure it.. You might be able to do that with areas of microevolution but not with macroevolution.. It's all just speculation… And if you believed that life arose by chance processes, you have to believe that millions of years ago life arouse from non-life, from matter, and this violates the law of biogeneis. No scientist has ever showed this law could ever be violated.

Well, if there is a genetic basis to such a decision, your fitness becomes zero while those with genes that tend to propagate, will. It's simple, really and totallly consistent with what Darwin said.

Well it contradicts what Darwin said.. He said, ”every single organic being around us” it's a statement that just isn't true…

I understand totally what you are saying - I agreed that there aren't classes devoted to ID in public schools. And there aren't classes on evolution either. Evolution is taught as units in a biology class or referenced where relevant (e.g. the evolution eukaryotes). So why should we have a whole class devoted to ID when we don't have them devoted so ToE? What I am saying is that many teachers teach ID along with evolution - "let the students decide" sort of thing. And as per my earlier comments, The ToE has been around for 150 years and is a well established scientific theory. Why should we let an idea that is new and relatively untested in - particularly when it seems to fail the tests that have been done. I come back to my question about Holocaust deniers having a voice in history classes.

This statement is simply NOT true….. Evolution is the “supposed” glue or philosophy around practically all the sciences.. It is totally engrained into Biology, Astronomy, Physics, Anthropology etc…. I can show you parts of my Biology book devoted to DE if you don't believe me… I don't think you understand what I'm saying… From what you have been saying, ID doesn't qualify as science… So of course you can say you teach ID along with DE… And from what you are teaching is that ID is NOT science. That is the legal approach.. What you are not saying is that DE is not really science either…. Again, the theoretical process thought to produce relatively large evolutionary change within biological organisms is completely speculation… It has never been witnessed and this has been confirmed by science…

As far as ToE being around for 150 years, the Roman empire was around for even longer and it eventually fell too..

Now, since ID is new, there has not been much of an opportunity for it to mandated into curricula by school boards, but I'll bet the farm that it is in the future. Do you disagree that attempts to implement ID into public schools will be made in the future, and that variants of biology texts will be encouraged if not mandated to be adopted together with mainstream biology texts (much like they were in Dover)?

While I may not think ID is ready for prime time ID will most likely naturally arise in biology classrooms whether design is mandated or not since the evolutionary theory was born in the theological cradle as it did with Darwin. Darwin as well on various occasions posed theological and philosophical questions on evolution (or to a creator) in his book, “The Origin of Species.” As an example he wrote, “To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes.” Statements like this should probably belong in philosophy classes. In fact Neil Shanks, a professor of philosophy of science, claimed that many of Darwin's books have been eliminated from certain scientific classroom discussions due to their theological content. Is this being fair to science?

Careful, now. That's not what I said. I said that if ID is implemented into science curricula that I guarantee that it will wind up in courts where judges will decide whether it is religious ideology or not...just as they did with YEC.

And how do you define a religious ideology? Why isn't atheism a religion or belief system?

First of all, debate does exist. We're having one right now. Moreover, healthy debate is exceedingly abundant in the scientific community - just pick up a scientific journal. Second of all, I continue to reject your metaphor as unfairly portraying evolutionary biologists (after all, how many do you know personally and have worked with intimately enough to know that they are secretly or overtly protecting an idea they know to be false?) and continue to hold them and their theory to a different standard than other scientists. Finally, science is not a democracy of ideas - quite the opposite. Only those that show any real promise as being true or productive are advanced. But that doesn't mean that debate over the ideas doesn't exist - but if the ideas do not show any real promise, they are quickly rejected by the scientific community. ID has not, as yet, shown to be a productive or viable field of research (its possible theistic or questionable origins notwithstanding). Regardless of whether the idea was developed and advanced by the Pope himself for the greater glory of the Vatican is not relevant if the idea itself is scientific AND has the promise of being a viable scientific theory.

Well it looks like you have already made your mind up… Umm.. No…. The debate does NOT exist in the public classrooms… Ok, can you show me where? Again The U.S. Supreme Court ruled in the 1987 case of Edwards v. Aguillard that any form of design is another form of creationism and that it violates the Establishment Clause, which prohibits state funds to religion.. You cannot show up to a fight, jump into the ring, do your victory dance and declare victory… You have to ALLOW the other fighter to fight also. Again, ID might be able to explain things where evolution can't… And if you think ID is anti science.. You might want to read our article, Religion and Intelligent Design Impede Science and Close Off Inquiry?

By Rich,ID is Anti-Science?

“Many members of the anti-intelligent design lobby claim that the goals of intelligent design are to introduce religious teaching into the schools in the guise of science. Accordingly, ID proponents just want to say "God did it," and stifle any future scientific research. However, this claim is just a red herring thrown out to garner support against the "evils" of intelligent design.”

So let ID stand or fall on its own merits - it's still young and under development, so who knows what will happen in the next few decades...

I agree… So why not let it? By the way you are talking, it sure seems to me that your mind is already made up on the issue, not to let it in... It seem that this debate is fruitless..

[Gman]

never got around to responding to your concerns about the tree of life problem. You say "Messy?? Well that hardly classifies as being proved beyond a shadow of doubt…"

Let's start with what the ToE is - it is basically a series of statements about how organisms with heritable and variable characteristics change over time. Specifically, alleles for traits that confer a survival or reproductive advantage will enjoy differential success over time compared to those for traits for lower survival or reproductive rates. The outcomes of this process over long periods of time are macroevolution, speciation, adaptation and/or extinction. Now, in general, when you examine this process over long periods of time, you tend to see patterns that are consistent with branches of a tree - species emerge, split from common ancestors, thrive and split more, or often just go extinct. So the metaphor of a tree of life tends to work quite well when applied to evolutionary change. Indeed, phylogenetic analyses of groups of species, or genera, or families do show patterns of change that - when shown topographically - resemble a tree.

Now, the genetic changes that are produced over long periods of time in most speciation events are small and subtle - a mutation here, insertion there, maybe a gene duplication event now and then. And when you examine the DNA of groups of organisms, you can use these changes as roadmaps to delineate the events that occur during their diversification. However, there are occasionally changes that occur that produce new types of organisms that make things a little more difficult in terms of recreating the events that took place. For example, the changes that gave rise to eukaryotes from prokaryotes were not of the small, incremental changes in DNA that produce a new species of bee from another (for example). Rather, it appears that mitochondria and chloroplasts were once free-living bacteria which were engulfed by another organism, and rather than being digested, became incorporated into the cell and all of its descendants. This is not uncommon in nature - it's how we have come to depend on bacteria in our guts for assistance in digestion, or protists in the guts of termites. It's called endosymbiosis.

This does not mean that evolution had no hand in this - presumably this ancestral proto-eukaryote had some advantage over those without their new symbiont. And so selection favored this new form of life. So we're not violating any laws of nature; just discovering a new way to change living organisms that is a little different than the processes usually leading to new species. But here's the kicker - if these events really did occur, then there must be things that are true today that we can use to decipher the events from the past. It's the dreaded historical science you dislike so much - but it is exactly how we know what happened billions of years ago. Mitochondria and chloroplasts are of about the same size as bacteria. They possess their own DNA. They can replicate by binary fission (like bacteria) autonomous of the cells in which they reside. They possess 2 layers of membrane - just what you'd expect from something with its own membrane engulfed by another membrane-bound organism. Their inner membrane is more chemically similar to eubacterial membranes than eukaryotic membranes. Like bacteria, their DNA is circular and not linear, and it does not have introns or histone proteins (like eukaryotes). The first amino acid of mitochondrial and plastic transcripts is equivalent to that of eubacteria, and different from that of eukaryotes. Mitochondria and chloroplasts produced their own ribosomes, which have 30S and 50S subunits (like bacteria), and not the 40S and 60S subunits of the eukaryotic cells in which they occur. Many antibiotics that kill eubacteria also affect the mitochondria and chloroplasts. The list goes on - and what's more, we have a good idea of why the association of mitochondria would be favored: for billions of years, photosynthetic bacteria had been producing O2 gradually changing the composition of the Earth's atmosphere. Geologists can track the changes by how oxidized iron formations are in various rock-strata. An anaerobic bacteria that engulfed an aerobic one would have an advantage (as would the symbiont - a safe place with access to the cell's energy and nutrients). Quite simply, the evidence are all there at fit remarkably well - and we have reconstructed an evolutionary event that happened billions of years ago using evidences left behind for us to work with.

So getting back to the tree of life; at the trunk of the tree of life, events get a little messy (yes, messy). Rather than one, single prokaryote that roots the entire tree and is the ancestor to all living organisms, it appears that there may be several trunks to the tree of life. We have not violated evolution here, we have simply deconstructed a metaphor that works very well for most other speciation events in most other oprganisms. Bacteria routinely exchange DNA, or take bits of DNA up from their environment, and it is not the least bit surprising that at some point in the 3 billion years that bacteria were the sole inhabitants of this planet, that some species of bacteria used a mechanism other than simple mutation and subsequent differential success to differentiate. And there is invariably evidences that were left behind as a result for us in examine and piece together the events that occurred.

In short, it is my position that a messy trunk to the tree of life if not a problem for evolution. And in all likelihood we will piece together the events that occurred and I'll bet the farm that they are not inconsistent with the ToE. And not because scientists are behaving like shoe salesmen.

When you say ToE what exactly are you referring to? It's too general. Do you mean mircoevolution or macroevolution? I don't think you can separate the two like what you are saying...

Darwin's tree of life is probably headed for the dust bin.. Darwinian evolution hinges on common ancestry.. The first thing you learn about DE is that all living things are related into one great tree... It's the founding proposition... If you are questioning the tree then technically you are also questioning common descent. Now if scientists are still writing articles in 2009 from "New Scientist Magazine" stating Why Darwin was wrong about the tree of life then this raises a red flag not only for the tree but also common descent.. They go hand in hand... This is a logical problem for Darwinism. As an example, if it were the case that X, then we would know common descent is false... Or the fact that the theory of Common Descent is tested by the "Principle of Continuity.. The problem being that common descent and the Principle of Continuity are not maintained on anything like a level playing field in evolutionary reasoning.. You can't effectively test it....

[ARWallace]

Gman -

I'll respond to your other post later - you do not make it easy to respond with 1 sentence answers...

>>When you say ToE what exactly are you referring to? It's too general. Do you mean mircoevolution or macroevolution? I don't think you can separate the two like what you are saying...

I am referring to the theory of evolution. Micro and macroevolution are totally subjective descriptions of the outcome of selection. Perhaps you could tell me at what point microevolution stops and macroevolution begins? When a new gene develops? When populations differentiate? If so, at what level? When reproductive isolation develops? What about introgressive hybridization? No, macroevolution is simply the logical and inevitable outcome of microevolution and time. And when one stops and the other starts is totally subjective (which is why most evolutionists do not use the terms - they are of little heuristic value).

>>Darwin's tree of life is probably headed for the dust bin.. Darwinian evolution hinges on common ancestry..

Respectfully, I disagree. Life is bounded by common ancestry. These patterns are observed and described abundantly in the scientific literature. If it weren't, phylogenetic analyses would fail entirely. But as the article you cited points out, there are mechanisms that produce variation upon which selection can act besides mutation and recombination. But this in no way violates the concept of descent with modification and in no way violate evolution. Once again, evolution is process that distinguishes between heritable characters that are better suited for an environment. The beauty of molecular genetics is that it allows us to describe the processes that generate this diversity. In my example of endosymbiosis - the original prokaryotes involved in the association were descended from other prokaryotes and they went on to give rise to another line of organisms because the association was favored by evolution. But in this case, the variation upon which selection acted was not a small, subtle genetic change but rather, a chimera. We have not violated evolution here and we still have descent with modification. But in this case (as with HGT) it is a branch of the tree that is the result of two branches combining, not the bifurcation you would see in the usual speciation events. So let's say you're right and we abandon the tree metaphor (at least at the level of single celled organisms) - how does this violate the ToE and how is it inconsistent with descent with modification?

And of course I return to the evidences I presented linking chloroplasts and mitochondria linking them to prokaryotic origins. The historical sciences worked marvelously well enabling us to reconstruct the events that happened in the past. So if HGT and endosymbiosis did give rise to new lineages - this does not mean that the ToE cannot account for these events, only that reconstructing may be more difficult.

Cheers
Al

[ARWallace]

Gman -

>>Looks like we respectively disagree with each other… In regards to Genbank, it is the repository that keeps track of all the genes that have been sequenced.

Again, I know what GenBank is and I am aware of the growth in molecular data it contains. I offered an explanation to explain its growth. On this point we seem to be in abundant agreement.

>>We have just begun to collect the data.. We still have to analyze the data being collected. And, contrary to what you propose, the analysis are NOT wonderfully consistent with patterns predicted by evolution, and by patterns found using other comparisons… It is not a slam dunk for ToE by any means… One of the things scientists are finding with these DNA sequences is the puzzle of “ORFan genes” (Open Reading Frame genes)

Well, it actually is wonderfully consistent - the twin nested heirarchy of life is one of the strongest evidences for evolution, and study after study confirms this. However, you raise the question of orphan genes. I admit that I had not kept up with the scientific literature, and had to do a little digging on these. Turns out that a lot has been done since the 2002 Fischer/Guoin quote you cited. Indeed, a few papers from last year provide a function for these genes (providing species specific differences between closely related organisms http://www.sciencedaily.com/releases/20 ... 203837.htm), their possible origins (transposable elements http://mbe.oxfordjournals.org/cgi/conte ... t/26/3/603) and the notion that many of these are the product of incomplete sequencing (http://www.springerlink.com/content/y743675815171358/). It's amazing what science can do in just a few short years.

>>This actually goes back to what I was saying before, that evolution claims to have occurred over millions of years in very slow processes which scientist can't replicate. Ok, so you can create life from nonlife? If so, please show us your work…

First of all, I did not say that life was created from nonlife in a lab. Never. Please be careful not to misrepresent me. What I did say was that the various stages leading from inorganic material to variable, heritable organic molecules (RNA) capable of being acted on by evolution under conditions believed to have existed on ancient Earth have been demonstrated in lab conditions. Whether they are the exact steps is a matter of some debate, but this does not mean the steps are not theoretically possible. Second, none of these steps violate the ToE in any way; presumably these steps (if, in fact, they were the ones that occurred) did occur very slowly over millions of years with differential survival and reproductive success along the way. It is totally and utterly consistent with the ToE.

>>And what science are we talking about? From all I know, we were talking about Darwinian evolution. Are we going off on other subjects now? You can't take Darwinism and formulate it to an equation like F=MA the force of gravity. Dawinism is NOT a law, you can't measure it..

No, I am not going off topic. Evolution is a scientific theory - all of it. You seem to be confusing some concepts here - a law is a statement intended to describe some actions, and can often be defined in terms of mathematics. It tells you how and not why something occurs in the natural universe. A theory is an explanation of related observations or events. A law tends to describe a single event whereas theories describe many events and their causation. We do not have a law of plate tectonics, or a law of germs and disease or cell law or big bang law. All of these are theories, and all explain phenomena and can be empirically tested. And again, you seem to hold evolution to a different standard than other historical sciences, and hold the theories generated by the historical sciences to a different standard than other scientific theories. This is an unfair mischaracterization, although not the first time the charge has been leveled (http://spot.colorado.edu/~cleland/artic ... eology.pdf ).

>>Well it contradicts what Darwin said.. He said, ”every single organic being around us” it's a statement that just isn't true…

So you're going to hang your hat on one piece of prose gleaned from one sentence from one source and use it to define evolution and how it acts? Really?

>>This statement is simply NOT true….. Evolution is the “supposed” glue or philosophy around practically all the sciences.. It is totally engrained into Biology, Astronomy, Physics, Anthropology etc…. I can show you parts of my Biology book devoted to DE if you don't believe me…

Testament to the success of the theory. That it has been tested by so many scientists in so many disciplines and not only stands up to the scrutiny, but shows how pervasive its explanatory system across discplies is testament to it success. This is exactly what we would expect from a successful scientific theory - one that failed tests after repeated testing and had little explanatory power would not be very useful and not proliferate. You don't need to show me a textbook - I know. I teach biology.

>>From what you have been saying, ID doesn't qualify as science…

Again, this is not what I said. I said that if it does not qualify as a science and/or does not produce any viable predictions, then it has no place next to an idea that does. And if the idea turns out to be a veiled religious idea, then the courts will rule that it can not be legally taught in public schools. Right now, this is not the case and we have teachers teaching ID on an ad hoc basis.

>>What you are not saying is that DE is not really science either….

Really? Did I really say this? Because I thought I had been arguing exactly the opposite.

>>As far as ToE being around for 150 years, the Roman empire was around for even longer and it eventually fell too..

I never said it was absolute. Theories can be falsified and rejected - if they can't, they aren't really theories (e.g. that's why we don't call it Young Earth Theory). The ToE may, at some point, be shown to be wrong. And when and if it is, I'll happily stand up and accept its scientific replacement. But I find your use of metaphors to be interesting.

>>And how do you define a religious ideology? Why isn't atheism a religion or belief system?

As it pertains to our discussion, it is an idea that makes appeals to supernatural or divine intervention as part of its explanatory system.

>>Well it looks like you have already made your mind up… Umm.. No…. The debate does NOT exist in the public classrooms…

Why should debate exist in the classroom? We're going to let a bunch of 9th graders decide what ideas should be promoted by the scientific community? Debate should exist among scientists, a philosophers of science. I keep returning to my Holocaust denier - should we teach both sides and let the students decide? Should we teach astronomy and astrology? Flat earth and regular geology? I'm not sure what could be clearer - we don't promote and teach every idea that exists. For one thing, there isn't time. Second of all, at some point it simply serves to confuse students. Third of all, we have groups of experts who can wade through the morass and decide what ideas have made it in science and what ideas have not. There is no sane reason whatsoever that we should teach idea X just because group of people Y and Z find it fanciful - especially if the idea has not yet bore fruit in the discipline to which it belongs. So yes, to the extent that I consider ID to be currently fruitless, I feel it has no place alongside a valid scientific theory. Who know? Maybe Behe et al. really will discover some IC structures and maybe ID will provide us with fruitful avenues of research. Until then, it stays out of my science classroom.

>>Again The U.S. Supreme Court ruled in the 1987 case of Edwards v. Aguillard that any form of design is another form of creationism and that it violates the Establishment Clause, which prohibits state funds to religion..

Really? Can you point me to the place in the decision where that statement was made? I searched (albeit quickly) and could not find any language to that end. I'm not being combative; it's just that I always thought that decision was about creationism and not ID. In fact, I thought it was after that court ruling the the word "Creator" was replaced by "intelligent designer" in most mainstream text. And if it was about ID, why was it not used as a legal precedent in the Dover trial (or was it, and I just missed that too?)

>>You cannot show up to a fight, jump into the ring, do your victory dance and declare victory… You have to ALLOW the other fighter to fight also.

Again, a bad metaphor. You can if the other fighter is doing something illegal or if the fighter is a light flyweight trying to box a heavyweight...

>>I agree… So why not let it? By the way you are talking, it sure seems to me that your mind is already made up on the issue, not to let it in... It seem that this debate is fruitless..

I hope you see why I believe it should not be let in. I have suspicions about its religious ties, but as I said in my last post, none of that matters if the idea IS genuinely scientific and does produce viable explanations and research.

Cheers
Al

[robyn hill]

Al, you said,
Why should debate exist in the classroom? We're going to let a bunch of 9th graders decide what ideas should be promoted by the scientific community? Debate should exist among scientists, a philosophers of science. I keep returning to my Holocaust denier - should we teach both sides and let the students decide? Should we teach astronomy and astrology? Flat earth and regular geology? I'm not sure what could be clearer - we don't promote and teach every idea that exists. For one thing, there isn't time. Second of all, at some point it simply serves to confuse students. Third of all, we have groups of experts who can wade through the morass and decide what ideas have made it in science and what ideas have not. There is no sane reason whatsoever that we should teach idea X just because group of people Y and Z find it fanciful - especially if the idea has not yet bore fruit in the discipline to which it belongs. So yes, to the extent that I consider ID to be currently fruitless, I feel it has no place alongside a valid scientific theory. Who know? Maybe Behe et al. really will discover some IC structures and maybe ID will provide us with fruitful avenues of research. Until then, it stays out of my science classroom.

My thoughts,
In respect to the holocaust, astrology and flat vs.round earth, we do teach those ideas. We teach them in history classes or at least we should be. We learn from the mistakes of history. Those have all been theories which have been proven to either not work or proven false. As far as intelligent design, when students ask how our earth is the only planet with so many systems that happen to provide exactly what is needed to sustain life, science hasn't provided an exact answer- except theories. Intelligent design is one such theory and since so many people accept this as a possible theory, and it hasn't been disproven, students should be taught it exists,if not for any other reason, because It is prevelant today. That doesn't mean we teach that it is right, that is when science is overstepping its boundaries and I suspect many classrooms do that today with certain theories that have also not been proven, but it should be introduced as one theory that is discussed in science today. It is being discussed ,I presume, or I doubt this conversation would've lasted this long.

[Gman]

Well, it actually is wonderfully consistent - the twin nested heirarchy of life is one of the strongest evidences for evolution, and study after study confirms this. However, you raise the question of orphan genes. I admit that I had not kept up with the scientific literature, and had to do a little digging on these. Turns out that a lot has been done since the 2002 Fischer/Guoin quote you cited. Indeed, a few papers from last year provide a function for these genes (providing species specific differences between closely related organisms http://www.sciencedaily.com/releases/20 ... 203837.htm), their possible origins (transposable elements http://mbe.oxfordjournals.org/cgi/conte ... t/26/3/603) and the notion that many of these are the product of incomplete sequencing (http://www.springerlink.com/content/y743675815171358/). It's amazing what science can do in just a few short years.

I looked at your articles (some that I have read before) and they pretty much confirm what I stated earlier. Again scientists may theorize how ORFans relate, but nothing is for certain (as the documents suggest). In fact in one of them they state, "The origin of many such "orphan" genes remains unknown." Of course there are endless possibilities, notions, ideas, etc. for their relations… As an example, I can go around and label parts of my car too, but that doesn't necessarily mean I know how all the parts came together, unless of course I talked to the auto mechanic of course... Who knows?

Let's get back to Genbank… ORFan genes are puzzles because they don't come back with matches.. Ordinarily when a sequence of genes is submitted to GenBank, a lot will come back with matches and we understand their meanings. Except for the ORFans.. That is why they are called ORFans or orphans.. If scientists knew their parents then they wouldn't be calling them ORFans. Do you get it now? Why are they still calling them ORFans then in those documents?

As an example.. The parasite that causes malaria, plasmodium, has a remarkably high number of ORFan sequences. They don't have any matches… This has become a real puzzle for evolutionists as many other viruses do too.. According to Wilson et al… 2005, “The abundance of orphan genes, or genes without known homologues, is amongst the greatest surprises uncovered by the sequencing of a large number of eukaryotic and bacterial genomes.. It is therefore important to determine how the number of orphan genes will change as we sample new genomes… And…The number of these orphan bacterial genes is continuing to rise in a roughly linear fashion despite the large number of genomes sequenced, and this trend shows no signs of levelling off.”

Source: http://mic.sgmjournals.org/cgi/content/full/151/8/2499

Again, scientists may theorize where they came from, but nothing is written in stone here..

First of all, I did not say that life was created from nonlife in a lab. Never. Please be careful not to misrepresent me. What I did say was that the various stages leading from inorganic material to variable, heritable organic molecules (RNA) capable of being acted on by evolution under conditions believed to have existed on ancient Earth have been demonstrated in lab conditions. Whether they are the exact steps is a matter of some debate, but this does not mean the steps are not theoretically possible. Second, none of these steps violate the ToE in any way; presumably these steps (if, in fact, they were the ones that occurred) did occur very slowly over millions of years with differential survival and reproductive success along the way. It is totally and utterly consistent with the ToE.

Ok, fine.. You say, capable of being acted on by evolution? You say, “Whether they are the exact steps is a matter of some debate.”? Well sure anything could be theoretically possible… Maybe it was the marx brothers too… That is the point I have been trying to make with you. These are simply assumptions… They are arguments… Of course they go with ToE, because that is the "legal" interpretation of the facts…

No, I am not going off topic. Evolution is a scientific theory - all of it. You seem to be confusing some concepts here - a law is a statement intended to describe some actions, and can often be defined in terms of mathematics. It tells you how and not why something occurs in the natural universe. A theory is an explanation of related observations or events. A law tends to describe a single event whereas theories describe many events and their causation. We do not have a law of plate tectonics, or a law of germs and disease or cell law or big bang law. All of these are theories, and all explain phenomena and can be empirically tested. And again, you seem to hold evolution to a different standard than other historical sciences, and hold the theories generated by the historical sciences to a different standard than other scientific theories. This is an unfair mischaracterization, although not the first time the charge has been leveled (http://spot.colorado.edu/~cleland/artic ... eology.pdf ).

No… You said that I gave an unfair criticism of science… I then asked what science you were talking about… All you have demonstrated (very clearly) is that macroevolution is a possibility… It does NOT have all the answers.. It has NEVER been witnessed with our eyes, it is a historical assumption based on what happened in the past.. You are simply mixing your philosophy into your science.. That is all..

So you're going to hang your hat on one piece of prose gleaned from one sentence from one source and use it to define evolution and how it acts? Really?

Ya really… Many scientists make predictions using Darwinian evolution all the time. http://www.darwinspredictions.com/ That is only one case...

Testament to the success of the theory. That it has been tested by so many scientists in so many disciplines and not only stands up to the scrutiny, but shows how pervasive its explanatory system across discplies is testament to it success. This is exactly what we would expect from a successful scientific theory - one that failed tests after repeated testing and had little explanatory power would not be very useful and not proliferate. You don't need to show me a textbook - I know. I teach biology.

This does NOT address what you stated earlier… You said, “So why should we have a whole class devoted to ID when we don't have them devoted so ToE?” You are wrong… Again, DE is totally engrained into science.. I have total chapters devoted only to Darwin in my biology book.. Not ID… It is a philosophy. It's ENTIRE faith or belief system rests on Darwinism and it is not the only one explanation…

Again, this is not what I said. I said that if it does not qualify as a science and/or does not produce any viable predictions, then it has no place next to an idea that does. And if the idea turns out to be a veiled religious idea, then the courts will rule that it can not be legally taught in public schools. Right now, this is not the case and we have teachers teaching ID on an ad hoc basis.

Ad hoc? In a public setting?? Ok, why are they teaching then that ID could also be a valuable solution for science? Could it be that they don't agree with ToE?? Why?? Again, how are you determining what is religious? Also can evolution be falsifiable also? If a scientist performed that same test using gradual evolutionary standards perhaps it would be even harder to falsify since natural selection requires a much longer time or a greater population base of parts to produce life… You might want to read our article Can Intelligent Design (ID) be a Testable, Scientific Theory?

Really? Did I really say this? Because I thought I had been arguing exactly the opposite.

Again you are teaching that DE is the ONLY answer…. It's what you are programmed or have programmed yourself to do.

I never said it was absolute. Theories can be falsified and rejected - if they can't, they aren't really theories (e.g. that's why we don't call it Young Earth Theory). The ToE may, at some point, be shown to be wrong. And when and if it is, I'll happily stand up and accept its scientific replacement. But I find your use of metaphors to be interesting.

Happy? It sure doesn't appear that way to me… You don't appear to be asking questions... It's more of a dictation to me like your mind is already made up..

What we have here are only weights of evidence in favor of one view and sometimes neglecting the other and for the most part that evidence has primarily only been focused on evolution since the separation of church and state many years ago.

As it pertains to our discussion, it is an idea that makes appeals to supernatural or divine intervention as part of its explanatory system.

Atheism can also be a belief system or a religion as well… Maybe not divine, but a belief system in itself..

Why should debate exist in the classroom? We're going to let a bunch of 9th graders decide what ideas should be promoted by the scientific community? Debate should exist among scientists, a philosophers of science. I keep returning to my Holocaust denier - should we teach both sides and let the students decide? Should we teach astronomy and astrology? Flat earth and regular geology? I'm not sure what could be clearer - we don't promote and teach every idea that exists. For one thing, there isn't time. Second of all, at some point it simply serves to confuse students. Third of all, we have groups of experts who can wade through the morass and decide what ideas have made it in science and what ideas have not. There is no sane reason whatsoever that we should teach idea X just because group of people Y and Z find it fanciful - especially if the idea has not yet bore fruit in the discipline to which it belongs. So yes, to the extent that I consider ID to be currently fruitless, I feel it has no place alongside a valid scientific theory. Who know? Maybe Behe et al. really will discover some IC structures and maybe ID will provide us with fruitful avenues of research. Until then, it stays out of my science classroom.

Why shouldn't it?? All you have been saying are predictions and assumptions… Nothing solid at all.. And what about the supposed junk DNA? Contrary to statements by the evolutionary theory it isn't exactly useless but is actually required for genomic functionality, therefore providing more evidence of intelligent design. In fact, a recent study in 2007 at the Stanford University School of Medicine has shown that eukaryotic “junk” DNA is functional as a structural element in the nucleus. Their claim being, "large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections."

Source: http://www.godandscience.org/evolution/junkdna.html

Really? Can you point me to the place in the decision where that statement was made? I searched (albeit quickly) and could not find any language to that end. I'm not being combative; it's just that I always thought that decision was about creationism and not ID. In fact, I thought it was after that court ruling the the word "Creator" was replaced by "intelligent designer" in most mainstream text. And if it was about ID, why was it not used as a legal precedent in the Dover trial (or was it, and I just missed that too?)

In the Dover trail they simply reiterated what happened in the 1987 case of Edwards v. Aguillard… It might not have come under the name of ID, but saying creator, ID, designer, etc., has always been said to be a form of Biblical creationism…

Again, a bad metaphor. You can if the other fighter is doing something illegal or if the fighter is a light flyweight trying to box a heavyweight...

No… You don't understand.. It's about ALLOWING the other fighter into the ring… You haven't done that so of course it is illegal to claim victory. The fight is rigged..

I hope you see why I believe it should not be let in. I have suspicions about its religious ties, but as I said in my last post, none of that matters if the idea IS genuinely scientific and does produce viable explanations and research.

Cells and eyes are not religious texts or objects.. Science should remain as science regardless of the presuppositions or conclusions of the investigator. Science should also be debatable and not be held accountable to one view if there is lacking evidence. Moreover, ID does not seek to identify the designer. It is only concerned with finding any evidence of design.. Design does not require that the designer be a supernatural God either. A number of scientists have already accepted that the existence of intelligent life could exist elsewhere in the universe and that life could be the result of “seeding” by aliens known as the “panspermia” hypothesis. Also ID is not another form of creationism. ID can take no position on religious texts and can make its arguments using purely scientific and observational data also.... Just like DE...

http://www.godandscience.org/evolution/ ... esign.html

[Gman]

I am referring to the theory of evolution. Micro and macroevolution are totally subjective descriptions of the outcome of selection. Perhaps you could tell me at what point microevolution stops and macroevolution begins? When a new gene develops? When populations differentiate? If so, at what level? When reproductive isolation develops? What about introgressive hybridization? No, macroevolution is simply the logical and inevitable outcome of microevolution and time. And when one stops and the other starts is totally subjective (which is why most evolutionists do not use the terms - they are of little heuristic value).

Actually, those questions are more of a hindrance for you more than for me… That is exactly what I stated before…. I said that scientists claim evolution occurred over millions of years in very slow processes which scientist can't replicate… So what do they do? They take microevolution and ASSUME it will eventually lead to macroevolution… I'm sorry, you just can't do that…

Again the problem is that the tree is intertwined into common ancserty. Evolution asserts that the pattern of similarity by which all known organisms may be linked is the natural outcome of some process of genealogy… In other words, all organisms are related..

In short, it is my position that a messy trunk to the tree of life if not a problem for evolution. And in all likelihood we will piece together the events that occurred and I'll bet the farm that they are not inconsistent with the ToE. And not because scientists are behaving like shoe salesmen.

Again... Not only is it messy but it is probably going to get chopped down and disappear.. Until you take the legality out of it, the outcome will always be skewed and equal to the philosophy of the one gathering the information.. That is the problem with common descent and the tree.. If you can take away the tree you can also take away the common ancestor idea...

I'll explain more later...