Some say that scientists are looking at what is happening everywhere and trying to describe it in terms of natural processes. They will prescribe things like laws in an attempt to describe reality. But as we have seen with gravity and Newtons laws it can be wrong and Einstein came up with a better and more complete description with the theory of relativity. But now we are finding that gravity may need a newer understanding from quantum physics. So it seems the laws and descriptions that scientists place on things are an attempt to describe reality but are always incomplete. They are only a description and have no creative ability and they dont explain how these thing came about. This is a world view of existence and maybe it is humans trying to fit what we see to that world view rather than it actually being what it really is.
If God is creator of all things then He is the creator of the quantum world as well. As we know in the quantum world things defy the standard physics that we use to describe the world we see. Yet we know that the quantum world is what is at the beginning of all things and really what gave birth to our reality. But what gave birth to the quantum world. There maybe something that scientists havnt discovered or will never understand that is the driving force for all things. Science through a world view believe they have and will discover the answers to everything. They describe it as a theory of everything. Maybe there are things science will never comprehend. Maybe all science is trying to do is put a natural explanation on Gods creation.
A Prescribed Evolutionary Hypothesis.
http://www.ncbi.nlm.nih.gov/pubmed/15889345
Universal Genome in the Origin of Metazoa: Thoughts About Evolution
(a) the Universal Genome that encodes all major developmental programs essential for various phyla of Metazoa emerged in a unicellular or a primitive multicellular organism shortly before the Cambrian period; (b) The Metazoan phyla, all having similar genomes, are nonetheless so distinct because they utilize specific combinations of developmental programs.
Universal Genome in the Origin of Metazoa: Thoughts About Evolution (PDF Download Available). Available from: http://www.researchgate.net/publication/6177829_Universal_Genome_in_the_Origin_of_Metazoa_Thoughts_About_Evolution [accessed Jan 31, 2016].
You can do one better: If science ever thinks it has found a complete, consistent description of the natural world, it is wrong... provably. This was shown mathematically by Kurt Gödel. I don't know of any scientists who dispute this (which is not to say they don't exist, but if they exist, they are demonstrably wrong).
That said, it might be worth considering the idea of Karl Barth that we ought to find God in what we know, not in what we do not know. If we look for gaps in scientific understanding and try to stick God into those spots, it's possible we're mistaken... historically, we are likely to be shown wrong. "Okay," one will say, "let us be shown wrong when we're shown wrong." So, there is no natural explanation for the quantum world? And there we have found God? And if people find something natural in that place, no matter?
It seems like the method of identifying gaps in our knowledge and putting God into them is a weak tool for attaining knowledge. Let me propose an alternative method: Whatever people find and describe in natural terms, let it be so. It is by faith that we know that God is present in all places at all times, and in all events. Instead of pointing to a gap in knowledge and telling the world, "He is there, to the exclusion of natural causes!" let us say, "Bidden or unbidden, God is present."
I was thinking more on indirect evidence as we will never be able to confirm this through the direct physical evidence. By looking at what is happening now through genomics we can get to know how things work and apply that to the past. There is evidence that complex creatures that require similar genetics to what we see today were around very early on. Even the creatures of the Cambrian period have very complex body parts and show all the modern body plans. We can see that the forms in proteins have universal structures that seem to conform to a natural form like the laws of physics rather than come from a Darwinian evolving process. They have pre set shapes that are beyond the capabilities that Darwinian evolution could create.
Other indirect evidence comes from things like our DNA has less junk and is more functional. Also there is growing evidence for HGT and endosymbiosis and symbiosis. So creatures may be able to share genetic info more freely especially in the beginning when all things were more united under similar genetic makeups. This may also be connected with the environment. Rather than the environment being something that creatures have to conform to it could be that the environment itself is part of creatures being able to share genetic info. This is seen especially in the micro, plant and aquatic worlds. So it may be that there is more capacity within the genome to create new genetic info by tapping into a vast amount of existing info that was there from the beginning.
Darwinian evolution in the light of genomics
Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651812/
The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law.
The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word
http://www.ncbi.nlm.nih.gov/pubmed/12419661
Okay, I misunderstood what was meant by "early." Yes, in one sense that's early. In another sense, it's quite late. The Cambrian was closer in time to today than it was to the first (evidence we have of) life on Earth. Cambrian life is complex because it was the product of billions of years of development. If we're talking about self-replicating molecules, however, there is something much simpler.
We actually don't even need to go to HGT and such to talk about the inter-relations of creatures and their environments. Beavers build dams. We're heating up the environment. That creatures impact their environments was known in Darwin's time. His insight was that environments impact the creatures, too, over generations.
You're right that the Phylogenic Tree is fuzzy where organisms that do HGT are concerned. It's pretty useful for everything that doesn't require a microscope to see, but some tiny organisms freely transfer information. But the real problem here is that the term "species" is very hard to pin down. We have this intuition of what constitutes a species, but no matter how we define it, there are organisms and circumstances that don't quite fit. Natural selection still applies. The frequency of alleles is tied to how beneficial the alleles are in their respective niches.
Your second link is about protein folding. They're talking about understanding what changes are possible based on how proteins are folded. It may sound like they are saying that what species will look like is a foregone conclusion, but they are actually talking about limitations on the kinds of proteins that can evolve.
I think some of the links I posted above will address the ability of natural selection and mutations to produce new complex variations. But here are a couple more that deal with the fitness side of things. It seems that mutations are more detrimental to the fitness of living things rather than a source of better, fitter and more complex life. Afterall they are errors to what is already good and working.
I am not saying that evolution doesn't play some role in the scheme of things. Its just to what extent it may do so. There maybe some natural selection happening but I dont think its the dominate driving force. Mutations dont produce anything like the amount of creative power that evolutionists give it. I think a lot is mistaken for the ability of living things to tap into using existing genetic info. The ability of natural selection and mutations is limited and the evidence we see cannot be explained by Darwinian evolution.
Estimating the prevalence of protein sequences adopting functional enzyme folds.
http://www.ncbi.nlm.nih.gov/pubmed/15321723
The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.4
Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution”
http://www.ncbi.nlm.nih.gov/pubmed/21243963
Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation
http://www.sciencemag.org/content/332/6034/1190.abstract
Be careful about your sources. The second one is an ID journal.
Most mutations are neutral -- they confer neither a benefit or detriment to the organism. Statistically, detrimental is more likely than beneficial. This is where natural selection comes in. A detrimental modification is likely to be selected against, whereas a beneficial one is likely to increase in frequency within a population. It's very intuitive, if you think about it. Interestingly, your third link has nothing to do with that! An important insight (that is less intuitive) is that a loss-of-function mutation is not necessarily a detrimental mutation. In general it is. But if it gets selected for, from the previous point about selection's tendencies, then it conferred a benefit. If you imagine a creature losing its eyesight, for example, it no longer has to produce the proteins necessary for eyesight. Those proteins are expensive. Now, one may observe that it's better to have the eyesight and pay the cost than not to have the eyesight... but what about in a deep-sea fish where eyesight is useless or almost useless? It's a loss-of-function mutation that, overall, confers benefit. In our own evolutionary history, we had nocturnal creatures who lost their ability to differentiate colors. We regained it, and so the genes we have to see color are different from other mammals.
