The Origin of Novelty

I would say this is characteristically wrong. Many proposals of step-by-step processes of novel features have been proposed: mammalian jaws and ear bones, cetaceans, amphibians, the eye, birds, etc. What is meant by a statement like this is that the resolution of such a sequence is not fine enough. The expectation is that we should have a record of every single step in the process. If this process does indeed take millions of years, then such a demand is absolutely ridiculous. If instead, all the extant species of today come from a relatively small number of originally created species less than 6,000 yrs ago, then the demand for this kind of fine resolution would be much more justified. The demand for such a demonstration should be much greater on someone who believes that, for example, the family Muscidae diversified from a single created pair into well over 500 known species in just 6,000 years. If that were truly the case, the resolution of this step-by-step process would have the level of detail that is usually being demanded.But since these processes are thought to take millions of years, we don't expect that level of detail. What we do is study the processes we can see and apply them to historical events. Does this prove anything? No, maybe not. But the attempt is not to prove what happened but to better understand it. The best we can hope to do is gain a better understanding of what has happened in the past.That said, I would like to submit to you the case of Elysia chlorotica. This organism is a sea slug that has the capability to live autotrophically. This slug digests the contents of a unicellular algae but keeps the chloroplasts intact. It then incorporates the chloroplasts into its digestive tissues. The interesting thing is that these plastids can survive and function for an extended time without the original algal nuclear genes. The genes for ancillary proteins needed for plastid function have been incorporated into the the sea slug's nuclear DNA apparently by HGT. The next step for this organism to become a true plant / animal is to transfer the genes from the plastid vertically into the germ line so the chloroplasts can be manufactured during development and no algal cells need be taken up to allow the slug to be autotrophic.So, step-by-step development of a novel feature:1. Slug eats algal cells.
2. Plastids are retained in digestive tract
3. Ancillary genes are incorporated into slug nuclear DNA by HGT.
4. Organism can survive autotrophically
5. Genes for plastid production are transferred to germ line (possible future event?)
6. Elysia chlorotica is a fully functional plant / animalUnfortunately, I don't have the time to fully unpack all the details of this study (I really shouldn't have taken the time to post what I have ...) but here are two papers on the subject. Maybe you could read through these and see if you think ifA. This represents a novel feature? and
B. Does the author present a plausible step-by-step process by which this novel feature has developed? The Making of a Photosynthetic Animal
Sea Slug Kleptoplasty and Plastid Maintenance in a MetazoanHBD

Maybe you don't have pdf capability? full txt versions below The Making of a Photosynthetic Animal
Sea Slug Kleptoplasty and Plastid Maintenance in a MetazoanGive those a go ... I would tend to agree that Neo-Darwinism is insufficient to provide an adequate explanation of evolutionary processes. I think the problem is that it is too simplistic (especially when defined as random mutation + natural selection). I believe the future of Evolutionary Biology must include developmental processes in the mix. Although mutation + selection is generally correct, it cannot adequately explain the process by itself. So in that sense I agree with you.Do you consider HGT to be a mutation? But if you read the paper you can see that it is not the whole story. The algae must be present in the early stage of development for the slug to grow into a mature adult. The presence of the algae affects the developmental process of the slug. However, without the HGT of critical genes, the slug would not be able to utilize the chloroplasts for extended periods of time and they would quickly degenerate when algal nuclear DNA was not present.In the OP you requested: My example should fit the bill. I have given you the benefit of the doubt that you sincerely want to have a discussion and that you would respect responses that were not "quotes from talk-origins" or the like. I put some thought into my post and provided a clear example of what you were asking for. If you have only come to throw around insults then I apologize, but I don't want to play that game.HBD

You are right. I don't see that you have made this claim. Your arguments are typical YEC tactics though. If a hole can be poked into evolutionary theory, then creation becomes true by default. I do realize that there is a growing number of non-creationists that are finding fault with traditional Darwinian mechanisms. However, the difference is that those scientists are proposing alternate ideas and hypotheses not just calling those who except Darwinistic mechanism idiots. IMHO you should switch tactics a bit and propose a better explanation for the observations we have. People are going to cling to the current paradigm until a better explanation comes along. Because RM + NS are largely right, it is just too simplistic. I realized this in my Introductory Botany course when the professor asked "Why do plants produce secondary metabolites?" There is a couple basic ways to answer this. You could say "God made them that way" or you could say "Random mutations and natural selection over millions of years did it." Regardless of the correctness of either answer, I feel they both fail to truly provide an answer. There is a third, perhaps more appropriate answer, IMO. "We don't really know why." But what we can do is discover what advantage these secondary metabolites have for the plant, how they affect interactions with other organisms, and how they are produced and processed by the plant. We can also explore relationships with other plants and get a pretty good idea about how these secondary metabolites came to be.So if you're railing against the simplistic, non-answers then I am right with you. But that does not seem to be the case. You seem to simply find Neo-Darwinism implausible. Perhaps you could clarify this some. You can't possibly mean that there is no good evidence that mutations do occur or that natural selection does not differentiate between those individuals that produce more offspring and those that produce less offspring. So you must mean that there is not good evidence that RM + NS can produce the large scale changes required of evolutionary processes. What is the mechanism that can produce non-random changes? This would be a good place to provide an alternate hypothesis that could replace Darwinistic mechanisms. Are you suggesting that epigenetic changes are non-random?The problem that people have is that there is no known mechanism that can predict environmental factors and direct genetic changes to take advantage of those factors. And there is plenty of evidence that they are controlled by basic, universal principals which for all intents are random with respect to the organism's needs. A mechanism that can direct genetic changes in a non-random, beneficial way would be an incredible discovery. Think of the implications it could have on the fight against cancer or genetic diseases.One final thought here. Neo-Darwinism is kind of an obsolete term. It is still used, but the modern theory is usually referred to as the Modern Synthesis. The Modern Synthesis includes many more factors than just RM + NS.HBD

Or maybe he raises a valid question. Not much in the way of a point, per se. Perhaps it would be more appropriate to ask a question in this way. "Given the evolutionary mechanisms we know of, what types of novel features should we expect to observe in the 200 or so years that we have been studying evolutionary process?" Would we expect eyes or wings or legs to pop up where they previously did not exist in a 200 year time span? Obviously not. There should be no reason to have to explain why we don't see that happening. So what should we reasonably expect? Wouldn't this be the case throughout history though? At any given time, an organism would have been adapted to its environment in such a way as to "have all its bases covered." Sounds kinda teleological Perhaps a different way of looking at this is the environment is quite stable at this point in history. It seems there is a correlation between a stable climate and stasis in the fossil record. Rapid climate change may drive rapid development of novel features. Although, I am not sure how strong this correlation actually is though. We may be in a period of stability and organism stasis. But with the changes coming due to global warming, maybe we'll get to see some rapid development of novel features. IMHO we need to have a much better understanding of evolutionary processes. We certainly have gained a tremendous amount of knowledge in the last 200 years or so but I think this has lead to the attitude that we pretty much have the process of evolution figured out, we just need to tie up a few loose ends. I would suggest we really don't know as much as we think we do. I think we are barely scratching the surface when it comes to our knowledge of biological systems and their evolution. It seems as if what bolder-dash is "bolder-dashing" about is this disparity between how much we think we know and how little we actually do know.When we better understand developmental processes and how the environment interacts with the genome through epigenetics and how mutations can affect both of these processes, then maybe we can have better answers to questions as to how novel features have arisen. For now, we can just do the best we can and offer some well reasoned and informed speculation (about the past).HBD

Hi mindspawn I for one would have a much easier time accepting this type of hypothesis (not willing to call it a theory at this point) if it wasn't constrained to 6,000 years. A creation scenario would be much more plausible if the time frame was say more like (at least) 10,000,000 to 100,000,000 years since the creation event. But since most creationists want to cram all of earth's history into 6,000 years, it becomes a virtual impossibility to reconcile with the available evidence. Do you consider an old earth as a possibility? These statements are simply not true. What you need to keep in mind is that what we "observe" is a snapshot of history. Tiny, tiny pieces of what has happened. We don't expect to see significant changes (on the order of what creationists usually demand) in the comparatively small time period we have been studying evolution. Maybe 150 years seems like a long time, but in the grand scheme of things, its nothing - insignificant.Another thing I have noticed in some of your discussions is that you put too much emphasis on "coding genes." Coding genes get all the glory and recognition but they are only a piece of the whole picture. Theoretically, you could have two organisms with the exact same coding genes, but they express significantly different phenotypes. The major player in phenotype changes is in developmental processes. Developmental processes can use existing genetic materials and reorganize them into completely new structures depending on when and how they are expressed. I would encourage you to do some research into this area of study .. it is fascinating - and enlightening.Ultimately, the issue comes back to time. The earth is old: really, really old (I could accept that the accepted value of ~4.6 billion is off, but not by orders of magnitude). This is the starting point for how we look at the history of biological organisms. When we realize that the earth is indeed old, it changes the constraints we put on biological evolution.HBD

Hi Faith, Are you sure about this? If the only way to get from a wolf to a chihuahua or from a wolf to a Great Dane is by eliminating alleles, wouldn't that suggest that all those alleles exist in the original population - the wolf? So, every allele that is needed for the hundreds of dog breeds exists in the original wolf population and breeders simply eliminate unwanted alleles? And since each individual wolf has only 2 alleles at each loci,wouldn't it be theoretically possible for just the right combination of alleles to come together during recombination so that a wolf would give birth to a chihuahua or a Great Dane or a maybe labradoodle?And wouldn't it also be possible to arrange dog breeds in a hierarchical system so that the dog breed with the most alleles was the basal group and breeds with fewer and fewer alleles branch out?Do you think maybe something more than just reducing genetic diversity by eliminating alleles is going on here?HBD

I did not say that artificial breeding does not reduce genetic variability. It does and in that she was largely correct. But what she seemed to imply was that breeding is accomplished by eliminating genetic diversity alone. The implication is that all the characteristics we find in dog breeds were originally in the wolf; they were just so well mixed that the phenotype that is expressed is ... a wolf. It just can't be that simple. The alleles that originally existed in the wolf population must have changed sometime during the selection process.Your position is that these alleles did change but that all such changes were actually diseases that humans thought were neat so they breed for that disease. Is that accurate?The problem is that when you try to oversimplify a situation like this it just gets reduced to silliness. Greyhounds were bred for speed, they are the second fastest animal on earth. Do you consider that a loss of function as compared to the wolf? It is not. But while breeders are selecting for this gain in function (increased speed) they are inadvertently selecting for less desirable traits like lack of body fat and thin, fragile skin and long, thin bones. Breeders did not intentionally select specifically for these traits, they were by products of the desirable trait - speed.The thing I wanted Faith to think about was that there is more going on that just allele frequency or eliminating Great Dane alleles to breed Chihuahuas.But I am sure you already know all this ... I guess if you define anything that is different from the original to be a disease ... then sure. Like little Buster who was born 20% larger than all his siblings and no one would play with him because he so was deformed ... its really sad when you think about it. But his human owners felt sorry for him so they found another reject puppy that was also freakishly large and introduced the two. They had puppies that grew up to be abnormally large, so they didn't feel so out of place. But no one wanted to own such a freakishly large dog - I mean who wants a deformed, diseased dog? So the whole family was euthanize and that put an end to freakishly large, diseased dogs. It just too bad that no one can find any dogs with any novel features - now there would be a market for that!HBD

Faith, how is it that you define "novel"? Because I don't think you argue that nothing has changed since the beginning of creation. Do you think that organisms have only experienced degradation since the creation? What happens when an organism adapts to a different environment? Do they have a function or a characteristic that gives them an advantage in that new environment or are they simply one step closer to extinction because they are in a state of degradation and since the conditions have changed, and they also change to suit the new environment - which means they have degraded.I just don't understand how you see this issue. What it seems to me that people here are saying is that a mutation may be deleterious in one environment but not in another. For example, there are two populations of foxes. One population lives in the Arctic and one population lives in Florida. Each gets the same mutation for white fur (which you may argue is a loss of function but it may actually be a gain in function since on a molecular level, the mutation may involve a protein that can now function to block the pigment production pathway. So while pigment production may be lost, the loss may actually be caused by a new enzymatic function). The mutation will be deleterious in Florida but advantageous in the Arctic. Same mutation ... same "deformation" ... different effect on fitness.I don't think anyone, but Bolder-dash, is suggesting that a gross mutation such as a cleft palette would be a beneficial mutation. That is merely reducto absurdum. What they are saying is that whether a mutation is harmful, beneficial or advantageous is not a simple, straight forward idea. Some things that may seem harmful at first glance may in fact, prove to be beneficial.Defining novel is an important part of the discussion. In the fox example I gave, I suspect that you would not consider white fur to be a novel feature. But why? Because there is no longer pigment being produced? But it could very well be that there is no pigment being produced because of a new function of a enzyme. It seems that opponents of evolution expect too much from the idea of novel.HBD