Natural selection v Intelligent design

[Jobar]

There were other things that the Judge either ignored or didn't take into consideration such as saying that ID is the same as creationism which is false and was established at the trial but ignored.

If there's any real difference between creationism and ID, it's never been apparent to me, nor was it to Judge Jones; a lot is said on that topic in that video.

I do admit that I haven't kept up with evo/creo debates in the past several years; I thought (and still do think) that the Dover case quashed ID pretty comprehensively, as any sort of respectable scientific theory. But if you want to give me 1 or 2 links which you find the most effective recent arguments for ID, I'll try to check them out when I have time. (And you'll need to do better than the two I read and commented on earlier; if it's something that EvoWiki has already addressed, it won't be much of a challenge.)

 

[stevevw]

If there's any real difference between creationism and ID, it's never been apparent to me, nor was it to Judge Jones; a lot is said on that topic in that video.

I do admit that I haven't kept up with evo/creo debates in the past several years; I thought (and still do think) that the Dover case quashed ID pretty comprehensively, as any sort of respectable scientific theory. But if you want to give me 1 or 2 links which you find the most effective recent arguments for ID, I'll try to check them out when I have time. (And you'll need to do better than the two I read and commented on earlier; if it's something that EvoWiki has already addressed, it won't be much of a challenge.)

Those sites were not to do with any support for scientific evidence for ID. They were just a commentary on the trial from a ID perspective. There's plenty of ID peer reviewed papers out there that give good account for themselves. In fact I think its since we have discovered more detail about the genome, physics and our universe that we are seeing the great design in things. Its getting harder for scientists to say that life and existence created itself somehow and naturalistic processes can account for the great complexity we are finding.

More and more we are seeing how life is coded with a very multi layered language that makes our greatest designed computers look like child's play. We see that our universe is so finely tuned that there are just to many things that would have to fall in the right place at the right time to create life and our planet. Just about everything is working to a law and pattern that is beyond any random chaos which comes from naturalistic processes. Here's a few to start with but there's plenty more if you need them. I've tried to give a cross section covering different areas.
The Coherence Of An Engineered World
http://www.witpress.com/elibrary/wit-transactions-on-ecology-and-the-environment/114/19279
The “Wow! signal” of the terrestrial genetic code
http://www.sciencedirect.com/science/article/pii/S0019103513000791
Self-organization vs. self-ordering events in life-origin models
http://www.sciencedirect.com/science/article/pii/S1571064506000224
The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law.
http://www.ncbi.nlm.nih.gov/pubmed/12419661
Evidence Of Design In Bird Feathers And Avian Respiration
http://www.witpress.com/elibrary/dne-volumes/4/2/399

 

[Archaeopteryx]

What do you mean Koonin speaks about the very things I have been saying. He goes through the different discoveries from Darwin to the modern day discoveries through genetics. The different views which bring into question evolution through adaptation. How HGt can be seen as something that undermines Darwin evolution.

Look at Table 1.

I have included some comments which I have put in blue so they are separated from Koonins comments.

The observations of extensive, ubiquitous and occurring via multiple routes HGT outlined above lead to a fundamental generalization: the genomes of all life forms are collections of genes with diverse evolutionary histories. The corollary of this generalization is that the TOL concept must be substantially revised or abandoned because a single tree topology or even congruent topologies of trees for several highly conserved genes cannot possibly represent the history of all or even the majority of the genes (146–149). Thus, an adequate representation of life's history is a network of genetic exchanges rather than a single tree, and accordingly, the ‘strong’ TOL hypothesis, namely, the existence of a ‘species tree’ for the entire history of cellular life, is falsified by the results of comparative genomics.

Which is what I've been saying, steve. This doesn't put evolution into doubt. It merely shows that the picture is more complicated than a strict version of the TOL implies, with additional sources of genetic variation. Contrary to what creationists claim, this is not a "death blow" to evolution.

At the level of general concepts of evolutionary biology with which I am primarily concerned here, genomic studies on gene duplication lead to, at least, two substantial generalizations. First, the demonstration of the primary evolutionary significance of duplication's including duplication's of large genome regions and whole genomes is a virtual death knell for Darwinian gradualism.

evolution clearly tends to generate new functional devices by tinkering with the old ones after making a backup copy rather than create novelty from scratch.
He is acknowledging here that evolution uses existing genes to make changes rather than create new genetic material.

Hang on, what do you expect evolution to rely on?

On the whole, the theoretical and empirical studies on the evolution of genomic complexity suggest that there is no trend for complexification in the history of life and that, when complexity does substantially increase, this occurs not as an adaptation but as a consequence of weak purifying selection, in itself, paradoxical as this might sound, a telltale sign of evolutionary failure. It appears that these findings are sufficient to put to rest the notion of evolutionary ‘progress’, a suggestion that was made previously on more general grounds.
So it seems he is saying that the evidence from genetics isn't moving towards more complexity for which we would expect from evolution and strong natural selection of more complex info. IE simple life to more complex life. When complexity does occur it is the result of weak selection which seems to be something that would come from selection of existing genetics.

To my understanding, here he is addressing a very specific idea here about evolution, not evolution on the whole.

The apparent universality of these and other central characteristics of genome evolution suggests that relatively simple, non-selective models might be sufficient to form the framework of a general evolutionary theory with respect to which purifying selection would provide boundary conditions (constraints) whereas positive, Darwinian selection (adaptation) would manifest itself as a quantitatively modest, even if functionally crucial modulator of the evolutionary process.
So here it is saying that the main source of evolution may be from non selective sources which are those already mentioned like HGT and existing genetics. Darwinian selection through Adaptation seems to be modest and plays a minor role as I have said before.

How does this cast doubt on evolution?

Comparative genomics revealed a striking diversity of evolutionary processes that was unimaginable in the pre-genomic era. In addition to point mutations that can be equated with Darwin's ‘infinitesimal changes’, genome evolution involves major contributions from gene and whole genome duplication's, large deletions including loss of genes or groups of genes, horizontal transfer of genes and entire genomic regions, various types of genome rearrangements, and interaction between genomes of cellular life forms and diverse selfish genetic elements

I'm not seeing how this casts doubt on evolution.

Evolutionary genomics effectively demolished the straightforward concept of the TOL by revealing the dynamic, reticulated character of evolution where HGT, genome fusion, and interaction between genomes of cellular life forms and diverse selfish genetic elements take the central stage.

Again, how does this cast doubt on evolution?

So the TOL becomes a network, or perhaps, most appropriately, the Forest of Life that consists of trees, bushes, thickets of lianas, and of course, numerous dead trunks and branches. Whether the TOL can be salvaged as central trend in the evolution of multiple conserved genes or this concept should be squarely abandoned for the Forest of Life image remains an open question.

Same question as above. It seems you are saying that because the picture is more nuanced and complex than previously imagined, that evolution is on the verge of being discarded. Yet your own source disagrees with this. He is optimistic that a more sophisticated understanding of evolutionary biology is on the horizon.

 

[Archaeopteryx]

For those who are interested, here are some more papers on HGT and evolution:

From Journal of Biology (2009;8:59):

Background: Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the ‘tree of life’ concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic ‘forest of life’.

Results: A comprehensive comparative analysis of a ‘forest’ of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.

Conclusions: Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.

From Proc. R. Soc. B. (2010;277:819-827):

The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.

Recently, several calls have been put forward for a new evolutionary synthesis (Dean & Thornton 2007; Pigliucci 2007; Carroll 2008; Koonin 2009) that encompasses mechanisms other than mutation, natural selection and drift to explain evolutionary changes, such as developmental constraints and epigenetic modifications among others.

Today it seems evident, from the studies discussed below, that horizontal (or lateral) gene transfer, the direct visualization of which has been achieved recently (Babić et al. 2008), is an important force driving the evolution of Bacteria and Archaea, as well as that of unicellular eukaryotes, and should therefore also be considered as part of the structure of any evolutionary synthesis.

Horizontal gene transfer, ‘the non-genealogical transmission of genetic material from one organism to another’ (Goldenfeld & Woese 2007), is a source of new genes and functions to the recipient of the transferred genetic material. In this sense, it is a mechanism that permits the acquisition of evolutionary novelties. But these acquisitions are primarily non-genealogical, questioning, in my opinion, the neo-Darwinian conception of a gradualist process driving the appearance of novel traits and functions.

In this review, I will discuss how horizontal gene transfer fits in with current evolutionary thinking, as well as the challenges that it proposes for the current evolutionary paradigm.

From Current Opinion in Microbiology (2011;14(5):615-623):

Gene acquisition by lateral gene transfer (LGT) is an important mechanism for natural variation among prokaryotes. Laboratory experiments show that protein-coding genes can be laterally transferred extremely fast among microbial cells, inherited to most of their descendants, and adapt to a new regulatory regime within a short time. Recent advance in the phylogenetic analysis of microbial genomes using networks approach reveals a substantial impact of LGT during microbial genome evolution. Phylogenomic networks of LGT among prokaryotes reconstructed from completely sequenced genomes uncover barriers to LGT in multiple levels. Here we discuss the kinds of barriers to gene acquisition in nature including physical barriers for gene transfer between cells, genomic barriers for the integration of acquired DNA, and functional barriers for the acquisition of new genes.

From Trends in Genetics (2011;27(4):157-163):

Horizontal gene transfer is increasingly described between bacteria and animals. Such transfers that are vertically inherited have the potential to influence the evolution of animals. One classic example is the transfer of DNA from mitochondria and chloroplasts to the nucleus after the acquisition of these organelles by eukaryotes. Even today, many of the described instances of bacteria-to-animal transfer occur as part of intimate relationships such as those of endosymbionts and their invertebrate hosts, particularly insects and nematodes, while numerous transfers are also found in asexual animals. Both of these observations are consistent with modern evolutionary theory, in particular the serial endosymbiotic theory and Muller's ratchet. Although it is tempting to suggest that these particular lifestyles promote horizontal gene transfer, it is difficult to ascertain given the nonrandom sampling of animal genome sequencing projects and the lack of a systematic analysis of animal genomes for such transfers.

From Front Cell Infect Microbiol. (2012;2:119):

When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain “ribosomal Tree of Life” that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: (1) pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept, (2) Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and (3) evolution of evolvability, i.e., dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary biology.

From PNAS (2012;109(13):4962-4967):

Lateral gene transfer (LGT), the acquisition of genes from other species, is a major evolutionary force. However, its success as an adaptive process makes the reconstruction of the history of life an intricate puzzle: If no gene has remained unaffected during the course of life's evolution, how can one rely on molecular markers to reconstruct the relationships among species? Here, we take a completely different look at LGT and its impact for the reconstruction of the history of life. Rather than trying to remove the effect of LGT in phylogenies, and ignoring as a result most of the information of gene histories, we use an explicit phylogenetic model of gene transfer to reconcile gene histories with the tree of species. We studied 16 bacterial and archaeal phyla, representing a dataset of 12,000 gene families distributed in 336 genomes. Our results show that, in most phyla, LGT provides an abundant phylogenetic signal on the pattern of species diversification and that this signal is robust to the choice of gene families under study. We also find that LGT brings an abundant signal on the location of the root of species trees, which has been previously overlooked. Our results quantify the great variety of gene transfer rates among lineages of the tree of life and provide strong support for the “complexity hypothesis,” which states that genes whose products participate to macromolecular protein complexes are relatively resistant to transfer.

From PNAS (2012;109(43):17513-17518):

The timing of the evolution of microbial life has largely remained elusive due to the scarcity of prokaryotic fossil record and the confounding effects of the exchange of genes among possibly distant species. The history of gene transfer events, however, is not a series of individual oddities; it records which lineages were concurrent and thus provides information on the timing of species diversification. Here, we use a probabilistic model of genome evolution that accounts for differences between gene phylogenies and the species tree as series of duplication, transfer, and loss events to reconstruct chronologically ordered species phylogenies. Using simulations we show that we can robustly recover accurate chronologically ordered species phylogenies in the presence of gene tree reconstruction errors and realistic rates of duplication, transfer, and loss. Using genomic data we demonstrate that we can infer rooted species phylogenies using homologous gene families from complete genomes of 10 bacterial and archaeal groups. Focusing on cyanobacteria, distinguished among prokaryotes by a relative abundance of fossils, we infer the maximum likelihood chronologically ordered species phylogeny based on 36 genomes with 8,332 homologous gene families. We find the order of speciation events to be in full agreement with the fossil record and the inferred phylogeny of cyanobacteria to be consistent with the phylogeny recovered from established phylogenomics methods. Our results demonstrate that lateral gene transfers, detected by probabilistic models of genome evolution, can be used as a source of information on the timing of evolution, providing a valuable complement to the limited prokaryotic fossil record.

From Annual Review of Genetics (2012;46:341-358):

The flow of genes between different species represents a form of genetic variation whose implications have not been fully appreciated. Here I examine some key findings on the extent of horizontal gene transfer (HGT) revealed by comparative genome analysis and their theoretical implications. In theoretical terms, HGT affects ideas pertaining to the tree of life, the notion of a last universal common ancestor, and the biological unities, as well as the rules of taxonomic nomenclature. This review discusses the emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions. I also discuss the bacterial pangenome, which provides an important case study on the permeability of species boundaries. An interesting observation about bdelloid rotifers and their reversion to asexual reproduction as it pertains to HGT is included.

From Trends in Genetics (2013;29(3):170-175):

Many bacterial and archaeal lineages have a history of extensive and ongoing horizontal gene transfer and loss, as evidenced by the large differences in genome content even among otherwise closely related isolates. How ecologically cohesive populations might evolve and be maintained under such conditions of rapid gene turnover has remained controversial. Here we synthesize recent literature demonstrating the importance of habitat and niche in structuring horizontal gene transfer. This leads to a model of ecological speciation via gradual genetic isolation triggered by differential habitat-association of nascent populations. Further, we hypothesize that subpopulations can evolve through local gene-exchange networks by tapping into a gene pool that is adaptive towards local, continuously changing organismic interactions and is, to a large degree, responsible for the observed rapid gene turnover. Overall, these insights help to explain how bacteria and archaea form populations that display both ecological cohesion and high genomic diversity.

From Science (2013;339(6124):1207-1210):

Some microbial eukaryotes, such as the extremophilic red alga Galdieria sulphuraria, live in hot, toxic metal-rich, acidic environments. To elucidate the underlying molecular mechanisms of adaptation, we sequenced the 13.7-megabase genome of G. sulphuraria. This alga shows an enormous metabolic flexibility, growing either photoautotrophically or heterotrophically on more than 50 carbon sources. Environmental adaptation seems to have been facilitated by horizontal gene transfer from various bacteria and archaea, often followed by gene family expansion. At least 5% of protein-coding genes of G. sulphuraria were probably acquired horizontally. These proteins are involved in ecologically important processes ranging from heavy-metal detoxification to glycerol uptake and metabolism. Thus, our findings show that a pan-domain gene pool has facilitated environmental adaptation in this unicellular eukaryote.

From Nature Reviews Genetics (2015;16:472-482):

Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent–offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.

 

[Archaeopteryx]

Those sites were not to do with any support for scientific evidence for ID. They were just a commentary on the trial from a ID perspective. There's plenty of ID peer reviewed papers out there that give good account for themselves. In fact I think its since we have discovered more detail about the genome, physics and our universe that we are seeing the great design in things. Its getting harder for scientists to say that life and existence created itself somehow and naturalistic processes can account for the great complexity we are finding.

No... that doesn't appear to be happening. ID is not in the midst of some grand resurgence.

 

[stevevw]

Look at Table 1.

Which is what I've been saying, steve. This doesn't put evolution into doubt. It merely shows that the picture is more complicated than a strict version of the TOL implies, with additional sources of genetic variation. Contrary to what creationists claim, this is not a "death blow" to evolution.

Yes it does and you must be reading something different.[/quote]

Hang on, what do you expect evolution to rely on?

To my understanding, here he is addressing a very specific idea here about evolution, not evolution on the whole.

How does this cast doubt on evolution?

I'm not seeing how this casts doubt on evolution.

Again, how does this cast doubt on evolution?

Same question as above. It seems you are saying that because the picture is more nuanced and complex than previously imagined, that evolution is on the verge of being discarded. Yet your own source disagrees with this. He is optimistic that a more sophisticated understanding of evolutionary biology is on the horizon.

I don't want to get into a debate about another person and what their true intentions are and what they meant by what they said. I didn't post the link for Koonin as proof that evolution is false. I posted it to show the variety of things that are questioning the Darwinian version of evolution. Most people agree that there is a form of evolution happening so I don't even say that evolution is completely false anyway. Its the extent of what some say evolution is capable of is the question and I posted Koonin appraisal of the many different areas that are questioning the the classic version. That version is being dismantled bit by bit with new discoveries.

What Koonin personally believes is another thing and not necessarily true. What he personally thinks is not why I posted that link. The fact is the evidence from other scientists he mentioned does question evolution to thee point that it most likely is not the main cause for change in animals. Even Koonin acknowledges those conclusions. But if you cant see that the article that is written by Koonin isn't at the very least showing that Darwinian evolution through mutations and natural selection and adaption is being challenged even to the point of playing much of a role at all in how creates change then you are not going to agree with what he is saying no matter what.

Its OK to say that this evidence only changes the fringe of evolution and the main core of it is still in tact. But that's is just not the case. Its the other way around. The main core of how mutations can evolve complex new abilities by creating new genes that were not there has very little evidence. Its the acquisition of new genetic abilities from other sources which are not Darwinian evolution that is said to be the main source which makes evolution a minor player if at all.

But what you are doing is only seeing one of my links and casting aside all the others. Look at this in terms of all the support I posted. Go in and check out the rest of the support and see if that states the same as you think. The main part of the support comes from the actual testing of whether mutations have the ability to evolve new complex abilities and that's where the best support is.

Koonin paper is only an additional source to show where the changes can come from because the tests have already shown that its not the cause for change in living things. So look at Koonins paper as a small part of all the support I posted and see it in that context rather than trying to single it out in isolation. Koonins personal opinion doesn't hold as much weight as the actual papers that show the tests done to disprove evolution.

But here is another statement from Koonin anyway. He definitely questions evolution and states that the one Darwin came up with is just about dead and buried and its time for a new version. But he doesn't know what that is at the moment. But its not from the type of evolution that Darwin states. The thing is you cant have your cake and eat it too. These articles are saying that other sources for the changes in creatures is the majority reason for how they change and Darwinian evolution is a minor reason.

So even if we say that there is some evolution happening its role isn't significant enough to account for everything that has and is being attributed to it by most scientists now. Its role isn't big enough to confidently say that It can crate something like a bird wing through random mutations and adaptations. Because if it could do that then its role would need to be dominate and strong and the evidence I posted shows its not.

The Origin at 150: is a new evolutionary synthesis in sight?
The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the Tree of Life as we knew it but also another central tenet of the Modern Synthesis inherited from Darwin, gradualism. In a world dominated by HGT, gene duplication, gene loss, and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.

Equally outdated is the (neo)Darwinian notion of the adaptive nature of evolution: clearly, genomes show very little if any signs of optimal design, and random drift constrained by purifying in all likelihood contributes (much) more to genome evolution than Darwinian selection 16, 17. And, with pan-adaptationism, gone forever is the notion of evolutionary progress that undoubtedly is central to the traditional evolutionary thinking, even if this is not always made explicit.

The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784144/

So clearly he is saying that Darwinian evolution as stated in the classic theory is gone, finished dead and buried. He is not saying that the main tenets of the theory are still there and just need adjustment. He is saying they are finished and need to be replaced by something else. That something else was discussed in his paper and they were not the type or mechanism that evolution is based on. They were non adaptive and selective processes and evolution's main tenet is Natural selection.

 

[stevevw]

No... that doesn't appear to be happening. ID is not in the midst of some grand resurgence.

Its not about a resurgence and I didn't think ID was really on the table anyway at any stage. Its just that as we see the finer details of life and existence it is showing more complexity than we ever imagined. That makes it harder to explain how that complexity could have come about by accident. The difficulties that science has has for a long time and as some say will always have is that they cant explain why some things are the way they are. Things like the finely tuned universe for life, how gravity can keep everything in its place ect and what they have discovered from quantum physics. All this is pointing to some sort of design and not just a random accident. But they didnt see this until they got to this point in their discoveries.

 

[Loudmouth]

Yes it does and you must be reading something different.

No it doesn't. The authors that you are referencing are saying that these other mechanisms should be a part of the theory of evolution.

I didn't post the link for Koonin as proof that evolution is false. I posted it to show the variety of things that are questioning the Darwinian version of evolution.

What Koonin is arguing for is a non-Darwinian theory of evolution, not a disproof of evolution. All of the mechanisms you are referring to are natural processes of mutation that are random with respect to fitness, and cause change over time in organisms. They are evolutionary mechanisms.

Its the extent of what some say evolution is capable of is the question and I posted Koonin appraisal of the many different areas that are questioning the the classic version. That version is being dismantled bit by bit with new discoveries.

You might as well be arguing that gravity is under question because Newton's Laws are not fully accurate.

 

[Archaeopteryx]

I don't want to get into a debate about another person and what they true intentions are and what they meant by what they said. I didn't post the link for Koonin as proof that evolution is false. I posted it to show the variety of things that are questioning the Darwinian version of evolution. Most people agree that there is a form of evolution happening so I don't even say that evolution is completely false anyway. Its the extent of what some say evolution is capable of is the question and I posted Koonin appraisal of the many different areas that are questioning the the classic version. That version is being dismantled bit by bit with new discoveries.

If your only point was that our understanding of evolutionary biology is advanced by new discoveries in comparative genomics, then I struggle to see the relevance this has to the overarching theme of the thread, which is titled "Natural selection v Intelligent design." How does this relate to intelligent design?

What Koonin personally believes is another thing and not necessarily true. What he personally thinks is not why I posted that link. The fact is the evidence from other scientists he mentioned does question evolution to thee point that it most likely is not the main cause for change in animals. Even Koonin acknowledges those conclusions. But if you cant see that the article that is written by Koonin isn't at the very least showing that Darwinian evolution through mutations and natural selection and adaption is being challenged even to the point of playing much of a role at all in how creates change then you are not going to agree with what he is saying no matter what.

That doesn't appear to be what Koonin is saying. He states, "Darwin's paramount insight on the interplay between chance and order (introduced by natural selection) survived, even if in a new, much more complex and nuanced form, with specific contributions of different types of random processes and distinct types of selection revealed." He goes into detail in Table 1, which examines "The status of the central propositions of Darwinism-Modern Synthesis in the light of evolutionary genomics."

Its OK to say that this evidence only changes the fringe of evolution and the main core of it is still in tact. But thats is just not the case. Its the other way around. The main core of how mutations can evolve complex new abilities by creating new genes that were not there has very little evidence. Its the acquisition of new genetic abilities from other sources which are not Darwinian evolution that is said to be the main source which makes evolution a minor player if at all.

Look at Table 1! It explicitly contradicts what you are claiming here.

But what you are doing is side tracking again and trying to salvage a bit of support for evolution from one of my links and cast aside all the others again. Look at this in terms of all the support I posted.

Why should I go through every single link you post when, in almost every single instance in which I have done so, I have found that the authors' don't agree with what you're claiming?

Go in and check out the rest of the support and see if that states the same as you think. The main part of the support comes from the actual testing of whether mutations have the ability to evolve new complex abilities and that's where the best support is. Koonin paper is only an additional source to show where the changes can come from because evolution by mutations and natural selection has been disproves in the papers I have linked for the actual tests done. So look at Koonins paper as a small part of all the support I posted and see it in that context rather than trying to single it out and take everything out of context.

In what way have I taken Koonin's paper out of context? You presented it as evidence and I showed you that the author doesn't seem to agree with what you're claiming.

But here is another statement from Koonin anyway. He definitely questions evolution and states that the one Darwin came up with is just about dead and buried and its time for a new version. But he doesn't know what that is at the moment. But its not from the type of evolution that Darwin states. The thing is you cant have your cake and eat it too. These articles are saying that other sources for the changes in creatures is the majority reason for how they change and Darwinian evolution is a minor reason.

No, steve. Don't misrepresent what Koonin is claiming.

The Origin at 150: is a new evolutionary synthesis in sight?
The discovery of pervasive HGT and the overall dynamics of the genetic universe destroys not only the Tree of Life as we knew it but also another central tenet of the Modern Synthesis inherited from Darwin, gradualism. In a world dominated by HGT, gene duplication, gene loss, and such momentous events as endosymbiosis, the idea of evolution being driven primarily by infinitesimal heritable changes in the Darwinian tradition has become untenable.

Equally outdated is the (neo)Darwinian notion of the adaptive nature of evolution: clearly, genomes show very little if any signs of optimal design, and random drift constrained by purifying in all likelihood contributes (much) more to genome evolution than Darwinian selection 16, 17. And, with pan-adaptationism, gone forever is the notion of evolutionary progress that undoubtedly is central to the traditional evolutionary thinking, even if this is not always made explicit.

The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking: in the post-genomic era, all major tenets of the Modern Synthesis are, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the Modern Synthesis is gone.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784144/

Yes, and Koonin goes on to say:

What’s next? The answer that seems to be suggested by the Darwinian discourse of 2009: a postmodern state not so far a postmodern synthesis. Above all, such a state is characterized by the pluralism of processes and patterns in evolution that defies any straightforward generalization 18 19.

Are there any glimpses of a new synthesis on the horizon? At the distinct risk of overestimating the promise of the current advances, I will mention two candidates. The first one is the population-genetic theory of the evolution of genomic architecture according to which evolving complexity is a side product of non-adaptive evolutionary processes occurring in small populations where the constraints of purifying selection are weak 16. The second area with a potential for major unification could be the study of universal patterns of evolution such as the distribution of evolutionary rates of orthologous genes which is nearly the same in organisms from bacteria to mammals 20 or the equally universal anticorrelation between the rate of evolution and the expression level of a gene 21. The existence of these universals suggests that simple theory of the kind used in statistical physics might explain some crucial aspects of evolution.

Whether or not the directions mentioned above and others can be combined in a new evolutionary synthesis in the foreseeable future, is too early to tell. I will venture one confident prediction, though: those celebrating the 200th anniversary of the Origin will see a vastly different landscape of evolutionary biology.

This paper also includes a table that examines "The fate of the central tenets of (neo)Darwinism in the post-genomic era," which is well worth reading.

 

[Archaeopteryx]

Its not about a resurgence and I didn't think ID was really on the table anyway at any stage. Its just that as we see the finer details of life and existence it is showing more complexity than we ever imagined. That makes it harder to explain how that complexity could have come about by accident.
The difficulties that science has has for a long time and as some say will always have is that they cant explain why some things are the way they are. Things like the finely tuned universe for life, how gravity can keep everything in its place ect and what they have discovered from quantum physics. All this is pointing to some sort of design and not just a random accident. But they didnt see this until they got to this point in their discoveries.

Who said that it came about "by random accident"? You still think that's all evolution is?

 

[pshun2404]

Who said that it came about "by random accident"? You still think that's all evolution is?

IYO, was purpose, plan, or intent inherent when inanimate matter/energy became the building blocks for life? Did the information for how or governing how this would occur exist prior to this formation process, or was it by chance (when just the right molecules, in just the right environment, at the right moment, with the correct and necessary forces all in place...etc...)????

 

[Loudmouth]

IYO, was purpose, plan, or intent inherent when inanimate matter/energy became the building blocks for life?

No scientist is claiming that humans were produced by inanimate matter becoming the building blocks of life.

Also, if you claim that there is a purpose, plan, or intent behind the origin of life, then it is up to you to prove it. We don't have to disprove that which is unevidenced.

Did the information for how or governing how this would occur exist prior to this formation process, or was it by chance (when just the right molecules, in just the right environment, at the right moment, with the correct and necessary forces all in place...etc...)????

The laws of chemistry predate life, if that is what you are asking.

 

[FrumiousBandersnatch]

We would expect to see similarities in the genetics of similar looking creatures.

Ah, no. Although there are fundamental similarities in the genetics of all creatures, those that look similar, or have similar features, are not necessarily closely related. When an different (e.g. isolated) ecosystems provide similar niches for exploitation, similar looking creatures with similar lifestyles may evolve independently. For example, the marsupial mammals of Australia; as well as unique marsupials like wallabies & kangaroos, there are (or were) marsupial dogs, cats, rats, etc., that looked and behaved similarly and occupied similar niches to non-marsupial dogs, cats, rats, etc., in other ecosystems. Also, some physical solutions are particularly well-suited for their job - like camera eyes, or flippers. It's called convergent evolution.

Like I said there have been many incidences where fossils have been said to be one thing only to be found out later that they were wrong. Similar looking fossils found in the wrong place are then made into new species because they couldn't have been the same creature in that particular time zone. Even though they virtually look the same. The thing about the line of ape skulls is that they can find a perfect line of transitions for this but never for much else. If there were so many transitions for all life then there would be millions everywhere.

The transitions aren't 'perfect' because you only ever get occasional snapshots with fossilization, and paleontologists working with very limited data will inevitably get some things wrong until more data becomes available; genetic information has been a great help. However, pruning or re-arranging a few branches on the tree doesn't make it any less a tree.

There are cases of animals that are closely related through their genetics that don't look like they have morphed from each other as well.

That can happen too, though it's unusual among complex animals. Which ones do you find troubling?

So because of all this it makes you wonder if the picture isn't being selectively picked to build it that way.

Bear in mind that paleontology is a particularly competitive field because of the scope for major discoveries and career-making. This means that scepticism and challenge is the default approach to new claims and finds, and so frauds and errors are usually found out fairly quickly (particularly after some of the infamous attempts of earlier times), and there is huge incentive to overturn existing paradigms.

But I come back to the best evidence and that's the test done to actually verify random mutations being able to create new functions and complexity. And from what I understand they don't show any evidence that mutations can do this. If anything its the opposite and they cause more harm than any good.

Please provide the relevant references or links to these tests.

Even if a very rare mutation that incurred some benefit could happen it has to keep on happening.

What makes you think so? If the originator of that mutation has viable offspring - and by definition, it has a better than average chance because of the mutation - it will propagate through them. That's a gross over-simplification, but the principle applies.

And in between that happening there would be many sick creatures that didn't make the grade all over the place.

That's partly how evolution works; the badly maladapted ones die without reproducing. Do remember that ALL creatures eventually die - and nearly all get sick. 99% of all species are now extinct.

Test have shown to just make two steps with point mutations in complex organism by first inactivating a binding cite that controls how a gene is expressed and then create a new binding cite in its place. This would convert gene regulation from one type to another but it doesn't actually change the gene.

I'm afraid that's too garbled to make sense of.

OK, having watched the video (8 wasted minutes of my life I won't get back), I see what you're talking about. They're implicitly assuming that all genetic evolutionary change depends on a kind of two-point mutation they say is rare; a claim that needs support - even assuming their calculations are correct - and for which no evidence is supplied.

The rest of the video is one long argument from incredulity, and the whole thing ignores all the painstaking lab studies that have traced mutations through breeding experiments, and through comparative examinations of genomes in the wild - many chains of mutations that have caused phenotypic variations have been traced.

We may not understand all the complexities of gene regulation and expression, but it's clear that if the claim about the point mutation mechanism described in the video is correct (although I've seen no evidence to support that), then changes due to mutations in the real world occur via different mechanisms. In other words, empirical evidence suggests that either they're wrong, or they've shown that the two-point mutation they describe is not the only mechanism for genetic evolution - and frankly I doubt anyone else thought it was.

 

[FrumiousBandersnatch]

Its just that as we see the finer details of life and existence it is showing more complexity than we ever imagined. That makes it harder to explain how that complexity could have come about by accident.

No it doesn't. For example, complexity is associated with non-linear dynamic systems (e.g. chaotic systems and systems involving self-organized criticality). Biological systems from individual cells to whole ecosystems have fractal & chaotic features and evidence of self-organized criticality, and there's a good case to be made that the processes underlying evolution are another example of that.

For an entertaining example of the fractal complexity of non-linear dynamic systems arising from trivially simple formulas, check out the Mandelbrot set.

 

[Archaeopteryx]

IYO, was purpose, plan, or intent inherent when inanimate matter/energy became the building blocks for life? Did the information for how or governing how this would occur exist prior to this formation process, or was it by chance (when just the right molecules, in just the right environment, at the right moment, with the correct and necessary forces all in place...etc...)????

This false dichotomy is typical of creationist thinking.

 

[Jobar]

Its not about a resurgence and I didn't think ID was really on the table anyway at any stage. Its just that as we see the finer details of life and existence it is showing more complexity than we ever imagined. That makes it harder to explain how that complexity could have come about by accident. The difficulties that science has has for a long time and as some say will always have is that they cant explain why some things are the way they are.

If we ever get to the point of explaining everything, and knowing why all things are the way they are, then science will be done. I think we can all agree that we're a long way from the end of that road, even presuming we can get there!

Sir Arthur Eddington said "Not only is the universe stranger than we imagine, it is stranger than we can imagine." Perhaps that's true; but the place of science is to continue to strive to not just imagine how the universe is, and works- but to understand it as well.

The trouble with creationism in any of its forms is that it would have us end that striving. Just saying 'goddidit' doesn't really answer any of our questions. I quite agree with you that the closer we look at life, and at the universe as a whole, the more complexity we see- but that just makes it more fascinating, doesn't it?

 

[stevevw]

If we ever get to the point of explaining everything, and knowing why all things are the way they are, then science will be done. I think we can all agree that we're a long way from the end of that road, even presuming we can get there!

Sir Arthur Eddington said "Not only is the universe stranger than we imagine, it is stranger than we can imagine." Perhaps that's true; but the place of science is to continue to strive to not just imagine how the universe is, and works- but to understand it as well.

The trouble with creationism in any of its forms is that it would have us end that striving. Just saying 'goddidit' doesn't really answer any of our questions. I quite agree with you that the closer we look at life, and at the universe as a whole, the more complexity we see- but that just makes it more fascinating, doesn't it?

I agree that science has helped us understand the world around us. If it wasn't for science we wouldn't have a lot of things. In fact it was the early who promoted scientific thought and many scientific advancements come from religious people. in early history.
http://blogs.nature.com/soapboxscie...much-to-both-christianity-and-the-middle-ages

WE can come a long way since then and accumulated knowledge has got us quickly to the point of the quantum world and sequencing DNA. We are peering deep into the universe and discovering many great mysteries. WE are now looking into things that are showing another strange world which is almost at the point of where something comes into existence from nothing. But any person religious or not is interested in discovering things. I think for religion it is interesting because this can help us see Gods creation and reveal His great design.

But I am not talking about creationism that some are mentioning here which can be a religion in itself. This can be blinkered to a doctrine of limited understanding and dogmatic beliefs. I dont have any particular beliefs but like to investigate things no matter what the outcomes may be. If anything I probably lean towards ID which is based on the science. But still I am not an avid supporter of the ID philosophy. I like science and investigating things as well. But science or at least humans can make science a religion as well and hold onto certain beliefs that are not necessarily true. The frame of thinking that everything has to to completely verified before you can trust in it can hold you back from discovering some things that may give you an insight into other dimensions of life.

 

[stevevw]

No it doesn't. For example, complexity is associated with non-linear dynamic systems (e.g. chaotic systems and systems involving self-organized criticality). Biological systems from individual cells to whole ecosystems have fractal & chaotic features and evidence of self-organized criticality, and there's a good case to be made that the processes underlying evolution are another example of that.

For an entertaining example of the fractal complexity of non-linear dynamic systems arising from trivially simple formulas, check out the Mandelbrot set.

I am not sure of that. It seems the evidence points to certain laws and codes that were in place from an early time in history that everything works to. It may appear that it is self creating but it still draws on those laws as the basic driving force which allows everything to bloom out from this. The evidence for evolution show that mutations are primarily a cost and loss of info and not a creator of more complex systems and functional ability. This is the opposite of evolution.

The evidence for what we see in the universe and existence itself shows order and precision which doesn't come from a random naturalistic process. Inorganic matter is just that and has no creative ability at all. Yet we are told to believe that matter can just about create itself just like life almost into a more complex well orchestrated existence. If anything everything is heading in the opposite direction through entropy. Even our genomes.

 

[pshun2404]

No scientist is claiming that humans were produced by inanimate matter becoming the building blocks of life.

Also, if you claim that there is a purpose, plan, or intent behind the origin of life, then it is up to you to prove it. We don't have to disprove that which is unevidenced.



The laws of chemistry predate life, if that is what you are asking.

Yes already extant laws governed these processes, thank you...I agree...

Where did these laws come from or how did these pre-developmental laws come to be (that matter/energy adheres to)? Any thoughts?

Also I was addressing Arche's post by that question (and typically, rather than taking a stand pulled the wishy washy false dichotomy argument....while I know neither side has time or space to post the vast library of all possibility and fact as to what is involved). I asked him if he thought or considered plan or purpose to the formation of living form. I did not assert it WAS so (though that's what I see as proper interpretation of the evidence we do have)...but the obvious similarity of form and function, and the lawful predictability of process and change, CAN BE seen in this way. And I do not care if all see it this way or not because many are interpreting to deny such a possibility.

Questioning is what leads to progress...

Paul

 

[Loudmouth]

Yes already extant laws governed these processes, thank you...I agree...

Where did these laws come from or how did these pre-developmental laws come to be (that matter/energy adheres to)?

Do you apply the same conditions to all of the scientific theories you accept? Do we have to evidence the origin of the universe in order to accept the Germ Theory of Disease?