The Origin of the DNA Code: Did Evolution Occur Between Neighbors?

Jerry writes:

Is there any evidence that these entities arose gradually and what are the intermediaries and how many organisms had these intermediaries or have them now in the world. We would expect thousands at a minimum. Otherwise they might as well have just “poofed” into existence.

You will have to justify expecting “thousands at a minimum”. Given the age of the lineages involved, extinction can be expected to whittle down many of them. It is well-known that older lineages have less species diversity than younger lineages for just that reason. As for your argument from incredulity (given your admitted lack of expertise, one can only say your argument is basically “I can’t imagine how this came about”) consider we do have extant species that are intermediate in nature: some species possess both gills that can function in and out of water, and wings which they do not use for flight, but for other purposes. So we know, developmentally, that these features can coexist in the same individual. And we have the genetic knowledge that all of the features are generated by proteins coded for by very similar genes. An example: Marden JH & MA Thomas (2003). Rowing locomotion by a stonefly that possesses the ancestral pterygote condition of co-occurring wings and abdominal gills. Biological Journal of the Linnean Society 79(2): 341-349

leading hypothesis for the origin of insect wings is that they evolved from thoracic gills that were serial homologues of the abdominal gills present in fossil pterygotes and in the nymphs of some modern mayflies, damselflies and stoneflies. Co-occurrence of thoracic wings and abdominal gills is the primitive condition for fossil pterygote insects, whereas the winged stage of modern insects almost exclusively lacks abdominal gills. Here we examine the locomotor behaviour and gill morphology of a stonefly, Diamphipnopsis samali (Plecoptera), which retains abdominal gills in the winged adult stage. This species can fly, but also uses its forewings as oars to accomplish rowing locomotion along the surface of water. The abdominal gills are in contact with both air and water during rowing, and their elaborately folded surface suggests an ability to contribute to gas-exchange. D. samali nymphs also have behaviours that place them in locations where their gills are exposed to air; they forage at night at the stream margin and within bubble curtains in rapids. These traits may exemplify an early pterygote condition in which gill and protowing function overlapped in an amphibious setting during a transition from aquatic to aerial locomotion and gas exchange. Rowing locomotion provides a novel and mechanically intermediate stage for the wings-from-gills and surface-skimming hypotheses for the origin of insect wings and flight

Dave Wisker

"No, it is just that Carroll, all his colleagues and most other scientists are too stupid to understand what it is all about." You are implying that is we who are stupid but all we ask is that someone explain it to us instead of pointing to some source and say it is there. Why is it for over four years no one is able to explain it to us. You do not seem to be able to do so. All you do is say it is so but can not say why it is so. Give it a shot and see how you do instead of just pointing to others. Tell us what is in Sean Carroll's books that should be considered that we are not already considering. I have his first book and can look at what you consider relevant. Others here also have his books. jerry

Joseph (39), "We IDists say if something looks designed we should be able to check into that possibility." For pete's sake, of course you can! It's a free country. No-one is trying to stop you - in fact we'd be delighted if you tried and then published the results for all to see and analyse. Our beef has always been that ID makes claims and comes up with no evidence for them - it's basically just "if it looks designed then it's reasonable to assume it was designed until proven otherwise", occasionally coupled with incorrect calculations of probability. On that point, Gil Dodgen once mentioned a few weeks back that he started to doubt evolution on the basis of high-school level mathematics; but despite requests from several of us to share the math with us, we've seen nothing. Gaz

No, it is just that Carroll, all his colleagues and most other scientists are too stupid to understand what it is all about. Maybe the effort of the ID movement should be directed at educating scientists instead of being directed at the general public? But isn't that the problem, what is there to teach? I suggest stepping up the work in the ID labs. Cabal

"what about a study of Sean B. Carrol’s Endless Forms?" There is nothing in Sean Carroll's Endless Forms book that is a threat to ID. He is essentially describing the process of gestation and how the very complicated process proceeds through a remarkable unfolding of events that is barely understood and how a series of switches lead to the final organism. At one point he says the code that controls human embryonic development is about 10,000 pages of small print long. One of the best arguments for design I have ever seen. In his latter book which essentially presented no examples that are a threat to ID he again helps the pro ID cause. Thank you Sean Carroll for making the design argument. I know you have to say you are anti ID but keep on writing these pro ID books. Is Sean B. Carroll a stealth ID supporter? jerry

Cabal, I read "Endless Forms..." AND "Making of the Fittest". Carroll doesn't shine any light on the dilemma. The issue here is one of testability. The premise of UCD is useless to science without it. Joseph

Joseph,

Insect wings- Scientists should be able to take developing crustys and modify them to get wings from gills. Heck if they have the genes isolated what is keeping them from this test?

That's a question I am not qualified to answer, but there may perhaps be some problems involved with replicating a process of I don't know how many steps? If it were as easy as your questions implies, I am certain it would already have been done. But, if you are so interested in the subject, what about a study of Sean B. Carrol's Endless Forms? Cabal

Evolution isn’t being debated. ID is not anti-evolution. camanintx:

They why are so many posts and comments here anti-Darwin?

Darwinism is a specific form of evolution- one that mandates non-telic processes.

If ID is about the origin of life and not how one species evolves into another, shouldn’t you be trying to refute the work of Alexander Oparin instead?

IDists understand that if living organisms did not arise from non-living matter via non-telic processes there is no reason to infer non-telic processes are solely responsible for its diversity. The debate is all about the mechanisms- direceted (ID) vs undirected. Joseph

David Wisker, These are interesting articles but I do not see how they support Darwinian evolution. I believe the insect wing evolution is very speculative and any progress on the way to a fully functioning wing should have left many alternatives to live on into the future. There are a whole lot of wingless insects that exist today so why didn't the winged intermediaries make it through. Both the insect wings and the multi chambered heart seem to depend upon the finding of proteins used in the embryonic development of each entity. One would expect to find several proteins used to regulate the development of each so the finding of them is nothing unusual. Using these proteins to somehow stimulate an altered entity is also nothing new and what one would expect. However, the move from one form to a much more complex form requires more than just the expression or lack of expression of a couple of genes. It requires the coordination of a host of mechanism of which I would guess they do not yet know much about. And all of these intermediary steps had to be viable and many should have persisted. Is there any evidence that these entities arose gradually and what are the intermediaries and how many organisms had these intermediaries or have them now in the world. We would expect thousands at a minimum. Otherwise they might as well have just "poofed" into existence. I am far from an expert on these subjects and would welcome any insight you might have as to how these entities arose in the specific organisms. I can understand how natural selection would favor a wing or a four chambered heart but how did these complex systems arise to be selected? One cannot just say gills grew and then they eventually became wings. Or how did all the ancillary systems or parts arise for the four chambered heart. I don't believe a four chambered heart is just an extra chamber or is it? All the extra plumbing and systems need an explanation or examples too. And where are they in today's world or the fossil world? As I said these appear to be interesting articles but it seems to me they beg the explanation (question). They all assume evolution by gradual means and then gear the discussion into this scenario with little evidence it actually happened this way. jerry

camanintx:

They why are so many posts and comments here anti-Darwin? If ID is about the origin of life and not how one species evolves into another, shouldn’t you be trying to refute the work of Alexander Oparin instead?

Many of the posts are anti-Darwin because our beef is with the universality of the Darwinian model, not necessarily the universality of common ancestry (commonly defined as "the fact of evolution). There is a vast chasm between the OOL question and the question of speciation. If natural speciation were proved it would hardly affect any of IDs core arguments. ID's position (though that's a bit of a broad statement because all telic non-Darwinians are IDers though we don't all view ID the same) is that some phenomena of nature are not evolvable via the Darwinian mechanism, and that the only known mechanism that can evolve such things is "intelligence". Further on the OOL issue, there is a vast chasm between the hoped "because of such and such conditions in the prebiotic earth, a simple replicator started" to the simplest known form of life. That vast chasm is the proper study of evolutionary science, not OOL science. bFast

Joseph, #39

Evolution isn’t being debated. ID is not anti-evolution.

They why are so many posts and comments here anti-Darwin? If ID is about the origin of life and not how one species evolves into another, shouldn't you be trying to refute the work of Alexander Oparin instead? camanintx

Insect wings- Scientists should be able to take developing crustys and modify them to get wings from gills. Heck if they have the genes isolated what is keeping them from this test? But the real question is: What is the non-telic explanation for regulatory sequences? Is there any science behind it? Joseph

“Is that why biologists have to keep reminding temselves tat what they are looking at is not designed?” Gaz:

That’s your fantasy.

Crick said it. Dawkins also said something very similar. Also ID isn't a dead end because once design is determined we still have to study it so that we can understand it. I said: “2- Yes the design inference opens up new questions- those new questions are separate from the design inference (just as the OoL is held separate from evolution)” And you responded with:

Nonsense.

How is that nonsense? Reality dictates that in the absence of direct observation or designer input the ONLY possible way to make any scientific determination about the designer(s), process(es) used, when, etc., is by studying the design in question. So the correct order goes: 1- Determine design is present (or not) 2- Investigate accordingly so that we may answer any questions about it. “3- No one is preventing anyone from trying to answer those new questions”

No IDist is doing the work either.

How do you know what IDists are and are not working on? I would say with the very limited resources IDists are doing a good job at what they are doing. “4- Also reality tells us it matters a great deal to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely.”

Why?

Because one can only understand something in light of how it arose. Do you think geologists would understand Stonehenge? Or is it better for archaeologists to examine it?

The evidnece for evolution is widely – essentially, universally – accepted in the scientific community.

Evolution isn't being debated. ID is not anti-evolution. Nice try.

You IDists are the ones whoi have to come up with the evidence for your position. You haven’t (other than “it looks like its been designed so it’s reasonable to say it was designed”)

We IDists say if something looks designed we should be able to check into that possibility. You and your ilk refuse to allow the design inference no matter what. Also I understand the modern synthesis. My question was: “What was the methodology used to make the determination that chance and necessity can account for all we observe?” Joseph

camaintx:

Phylogenetic reconstructions demonstrate perfectly how the genetic diversity we find today can arise from a common ancestor.

Phylogenetic reconstructions do not tell us anything about the physiological and anatomical differences observed. Also they can be used as evidence for a common design and/ or convergence.

It is even able to predict where missing intermediates should be which is how Tiktaalik roseae was discovered.

I am reading the book "Your Inner Fish" by Shubin. Tiki was a vague prediction based on common descent. However there still isn't any genetic data which demonstrates the transformations required are even possible. We should be able to take fish emryos, toy with them during deveoplment, and see if we can get a robust bone structure in the fins. From there we can tinker away to see if we can get an air-breather- or go for air-breathing first. But I bet we will find what Dr Denton already reported:

“Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes in Weismann’s “unambiguous bearers of information” or to view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a very small fraction of all known genes, such as developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene.” Michael John Denton page 172 of Uncommon Dissent

Joseph

jerry, You declare these as being incoherent. Incoherent in what way? Both examples show relatively simple genetic pathways to complex adaptations, requiring little extensive genetic changes (i.e, requiring little additional information). Since you insist on an iconoclastic definition of macroevolution as simply the development of complex adaptations, then both examples fit that criteria, and support a Darwinian view. Your asking for additional information is fine, but to say nobody here has presented evidence that supports the Darwinian position and falling under your unique definition of macroevolution is both disingenuous and tiresome. Dave Wisker

Dave Wisker, Tell me why these are not "just so" stories with a little bit of science to support it. These are not coherent defenses of Darwinian macro evolution but mainly speculation. If you disagree then lay out your rationale. As I said before you tend to point to some study and that is it. Lay it out for us. If you cannot then we have to assume something. Have to run for a day or so. jerry

Joseph (26), "Is that why biologists have to keep reminding temselves tat what they are looking at is not designed?" That's your fantasy. In reality, none of the biologists I know do that at all. That's because they understand they have evolved. "What was the methodology used to make the determination that chance and necessity can account for all we observe?" Actually, one could argue that it doesn't - see here: http://en.wikipedia.org/wiki/Modern_evolutionary_synthesis (I wrote) "Additionally, inferring design is a dead end. What research can be done after that? You can’t (according to ID theology) infer who the designer is, or when they did the design, or pretty much anything at all." (You wrote) "1- ID is only abouyt the DESIGN" Exactly - a total dead end. Not science. Doesn't even look at WHEN things might have been designed, despite the fact that the fossil record is there and they ought to be able to trace a design back to a particular geological time. "2- Yes the design inference opens up new questions- those new questions are separate from the design inference (just as the OoL is held separate from evolution)" Nonsense. If you infer design you can work out WHEN it was designed by looking through the fossil record to see when it was first designed. Just as evolutionists look through the geological record to see when a species first appeared. Why doesn't ID do that? Because it doesn't want to offend the fundamentalist Creationist element? "3- No one is preventing anyone from trying to answer those new questions" No IDist is doing the work either. "4- Also reality tells us it matters a great deal to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely." Why? "But you are right. No one has to listen to the design inference. But it is worth noting those who don’t can’t substantiate the claims of their position." The evidnece for evolution is widely - essentially, universally - accepted in the scientific community. You IDists are the ones whoi have to come up with the evidence for your position. You haven't (other than "it looks like its been designed so it's reasonable to say it was designed") "If they could ID would go away." It never will. There will always be a religious core that needs it. Gaz

jerry writes:

If I am wrong then when is someone going to throw out some information or results or studies or findings that support Darwin? When will anyone be able to defend Darwinian macro evolution? The answer it seems is never. But they are wrongfully abused by us. Poor dears. Those who are so easily wronged make our case so easy by their silence on what really counts, science. So keep up the good work.

One wonders why some of us even post anything here. When jerry specifically brought up the origins of complex adaptations like wings or multichambered hearts, I addressed both. I will address both again, just in case new readers think jerry's lament is accurate: Insect wings: Averof M and SM Cohen (1997). Evolutionary origin of insect wings from ancestral gills. Nature 385: 627-630. From the abstract:

Two hypotheses have been proposed for the origin of insect wings. One holds that wings evolved by modification of limb branches that were already present in multibranched ancestral appendages and probably functioned as gills. The second proses that wings arose as novel outgrowths of the body wall, not directly related to any pre-existing limbs. If wings arose from dorsal structures of multibranched appendages, we expect that some of their distinctive features will have been built on genetic functions that were already present in the structural progenitors of insect wings, and in homologous structures of other arthropod limbs. We have isolated crustacean homologues of two genes that have wing –specific functions in insects, pdm (nubbin) and apterous. Their expression patterns support the hypothesis that insect wings evolved from gill-like appendages that were already present in the aquatic ancestors of both crustaceans and insects.

Not only that, but other complex systems (like the insect tracheal breathing system and spider's spinnarets may also be descended from the gill: Damen WGM, T Saradiki and M Averof (2002). Diverse adaptations of an ancestral gill: a common evolutionary origin for wings, breathing organs, and spinnerets. Current Biology12 :1711-1716

Changing conditions of life impose new requirements on the morphology and physiology of an organism. One of these changes is the evolutionary transition from aquatic to terrestrial life, leading to adaptations in locomotion, breathing, reproduction, and mechanisms for food capture. We have shown previously that insects' wings most likely originated from one of the gills of ancestral aquatic arthropods during their transition to life on land [[1]]. Here we investigate the fate of these ancestral gills during the evolution of another major arthropod group, the chelicerates. We examine the expression of two developmental genes, pdm/nubbin and apterous, that participate in the specification of insects' wings and are expressed in particular crustacean epipods/gills. In the horseshoe crab, a primitively aquatic chelicerate, pdm/nubbin is specifically expressed in opisthosomal appendages that give rise to respiratory organs called book gills. In spiders (terrestrial chelicerates), pdm/nubbin and apterous are expressed in successive segmental primordia that give rise to book lungs, lateral tubular tracheae, and spinnerets, novel structures that are used by spiders to breathe on land and to spin their webs [[2]]. Combined with morphological and palaeontological evidence [3-9]], these observations suggest that fundamentally different new organs (wings, air-breathing organs, and spinnerets) evolved from the same ancestral structure (gills) in parallel instances of terrestrialization.

Multichambered hearts: The fact is, we know empirically that subtle modifications of embryonic genes can result in novel traits. Is it hard to imagine the evolution of the multichambered vertebrate heart from a simple one-chamber precursor? Researchers have shown that a simple regulatory change (well within the power of a simple random mutation) during development can result in “an unexpected phenotype: transformation of a single-compartment heart into a functional multicompartment organ.” in the invertebrate tunicate Ciona intestinalis. See: Davidson B, WSJ Beh, L Christiaen, and M Levine (2006). FGF signaling delineates the cardiac progenitor field in the simple chordate. Ciona intestinalis. Genes and Development. 20: 27287-2738 . Dave Wisker

Joseph, #28

Cabal said that universal common descent is still going strong. How can that be when there isn’t any genetic data which demonstrates the transformations required are even possible?

Phylogenetic reconstructions demonstrate perfectly how the genetic diversity we find today can arise from a common ancestor. It is even able to predict where missing intermediates should be which is how Tiktaalik roseae was discovered. camanintx

Cabal:

Can you identify another mechanism which has more influence on which organisms survive to reproduce?

Natural selection in a nutshell- whatever survives, survives.

Are you suggesting that organisms don’t compete for limited resources?

Cooperation is the rule. Competetion dwarfs in comparison.

Since DNA supports the fossil record here, I would say he was probably right.

How can DNA support the fossil record when we don't even know if such transformation are even possible?

Since there are many natural explanations for the slightly accelerated pace of evolution in the early Cambrian, this is not quite the obstacle some would like it to be.

Not one scientifically testable explanation. Joseph

jerry, #22

As I said last week about Darwin "Darwin on evolution was essentially a failure. He was wrong about gradualism.

Darwin himself stated in Origins that different species evolve at different rates, so I don't see how this was a failure on his part.

He was wrong that natural selection was a major factor in evolution.

Can you identify another mechanism which has more influence on which organisms survive to reproduce?

He was wrong about the Malthusian struggle for resources.

Are you suggesting that organisms don't compete for limited resources?

He is probably wrong about common descent.

Since DNA supports the fossil record here, I would say he was probably right.

On another thread the discussion of the Cambrian is a major obstacle in the common descent scenario."

Since there are many natural explanations for the slightly accelerated pace of evolution in the early Cambrian, this is not quite the obstacle some would like it to be. camanintx

I am wrong, wrong, wrong, wrong, wrong but notice this "wrong thrower" throws no defense of Darwin. The reason is because no one can. All that is thrown by those who defend Darwin is rhetoric or irrelevancies or diversions. There must be overwhelming evidence somewhere and you would think someone would present it some day. Will Provine, a committed atheist and Darwinist, admitted it and said it was all based on faith. If I am wrong then when is someone going to throw out some information or results or studies or findings that support Darwin? When will anyone be able to defend Darwinian macro evolution? The answer it seems is never. But they are wrongfully abused by us. Poor dears. Those who are so easily wronged make our case so easy by their silence on what really counts, science. So keep up the good work. jerry

Cabal said that universal common descent is still going strong. How can that be when there isn't any genetic data which demonstrates the transformations required are even possible? Joseph

Daisy:

What Intelligent Design theory needs most right now is a solid methodology for using the design inference to make new discoveries.

That's already in place. SETI uses such methodology. How do you think design-centric venues operate?

The big question, of course, is whether the design inference can be useful in modern science.

Of course it can be useful. For example the design inference is the only position fropm which we can argue that there is software involved in the development and daily functions of all living organisms. This software is separate from the DNA hardware. Joseph

Gaz:

Anyone is entitled to infer intelligent design if they want to, the reason most scientists don’t is that when you dig into the evidence there really isn’t any solid evidence for it.

Is that why biologists have to keep reminding temselves tat what they are looking at is not designed? What was the methodology used to make the determination that chance and necessity can account for all we observe?

Additionally, inferring design is a dead end. What research can be done after that? You can’t (according to ID theology) infer who the designer is, or when they did the design, or pretty much anything at all.

1- ID is only abouyt the DESIGN 2- Yes the design inference opens up new questions- those new questions are separate from the design inference (just as the OoL is held separate from evolution) 3- No one is preventing anyone from trying to answer those new questions 4- Also reality tells us it matters a great deal to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely. But you are right. No one has to listen to the design inference. But it is worth noting those who don't can't substantiate the claims of their position. If they could ID would go away. Joseph

Jerry,

That is why it is so hard to defend him and his ideas on evolution. He got it all wrong and if the people of his day knew about the information content of the cell and the problems with the origin of new information they would have laughed him out of the building.

Quite simply, you are wrong. Let's look at the facts. Today we're aware of the information content of the cell and it's inner workings. Yet nobody, except for a few people who refuse to get their work peer reviewed, has "laughed Darwin out the building". If what you say were in fact true then when the "information" content of cells and their workings was discovered then "Darwinism" would have been dropped in favour of "something else". Yet that has not happened. Therefore you are wrong. Wrong about what would have happened in Darwin's day, wrong about what is happening today. Wrong. Blue Lotus

OT: What are the chances? :

AT LEAST three human genes evolved "from scratch" via mutations in non-coding (ed: Junk) stretches of DNA, a process thought to be virtually impossible until recently.. Most new genes arise when existing ones are duplicated and the copies slowly acquire different functions. The three new genes, called CLLU1, C22orf45 and DNAH10OS, suddenly sprang into existence as a result of mutations in DNA sequences that did not previously code for proteins.

Three human genes evolved from junk steveO

As I’ve said before...the most critical thing for the ID movement to be doing right now is developing its own intricacies and methodologies, designing and supporting a much more intense program for conducting new empirical research — funding this through our own donations and volunteers if necessary. Ten years from now, if we’re still talking about whether or not evolutionism is true, the movement will have been an utter failure. Instead, the topic by then needs to be why scientists working under the paradigm of Intelligent Design theory are producing new and valuable discoveries, while scientists working under the paradigm of Evolution theory are stagnating under the weight of their own assumptions.

This is absolutely brilliant, and I think that if this were to happen it would be a wonderful thing. It would be one of the greatest paradigm shifts since Einsteins Theory of Relativity, and I couldn't imagine not wanting to be a part of it in some way. Having said that, I (and many others I'm sure) believe that such a thing will never come to pass. From what I know of the theory there doesn't seem to be any way to turn it into anything that's actually useful in the way described above. The ultimate conclusion of the theory seems to be that Some Guy Did It. By what means? Don't know, can't know. For what purpose? Don't know, can't know. What does it tell us about what we're likely to see in biology as a result? Only that we're likely to see whatever that guy happened to have done. So what exactly has he done? We'll have to determine that by seeing whatever we happen to see. I truly and honestly hope that I'm wrong, because I want to be one of the people that was alive and participating (even if only as a naysayer) when the scientific revolution came. I just don't hold out much hope that it will actually come to pass. VentureFree

This is an interesting analysis by Cornelius that I had not seen before. That the code was optimal from the get go, when all those supposedly primitive cells used the 19 left handed amino acids plus one to make all the incredible machinery that is in the present day cell. What are the odds that this would be all it would take so early in the game? All those incredibly future machines in the cell from those original 20 lego forms. That would be like saying that all we needed to build the space shuttle and orbiting station would be the same parts from Clinton's steam engine just arranged in a different way. Good insight Cornelius or whoever came up with it. jerry

"Darwin’s theories are no more dead than Newton’s are." As I said last week about Darwin "Darwin on evolution was essentially a failure. He was wrong about gradualism. He was wrong that natural selection was a major factor in evolution. He was wrong about the Malthusian struggle for resources. He is probably wrong about common descent. On another thread the discussion of the Cambrian is a major obstacle in the common descent scenario. Darwin was a decent scientist in his work on barnacles and worms and did a decent job of classifying species during the Beagle trip and apparently was insightful with his analysis of geology in South America but in evolutionary biology he was a bust. That is why it is so hard to defend him and his ideas on evolution. He got it all wrong and if the people of his day knew about the information content of the cell and the problems with the origin of new information they would have laughed him out of the building. He would have probably never have left Down House except to present his work on barnacles and worms." jerry

DATCG, #11

Big Bang Explosion of Information by Eugene Koonin He has admitted the data does not match the Darwin TOL.

And yet he agrees that there is still a TOL.

Here, I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees.

Sounds more like he's comparing the TOL to a Banyan tree when Darwin compared it to an Oak. Darwin's theories are no more dead than Newton's are. camanintx

CY and DATCG,

I’ve always wondered about HGT myself. I’m not a scientist, but it doesn’t really seem as if it fits with a Darwinian perspective – unless of course it’s some sort of magic process that we don’t yet have an explanation for (but will) -then yes, it fits.

Can you describe exactly how HGT is a problem for evolution, or how it helps ID? I don't see how. Of course Charles Darwin didn't know about HGT, but he died 127 years ago. According to wikipedia, the first instance of HGT was observed "just" 50 years ago. yakky d

This is the problem of writing without much attention. Corrections to my comment at 18: - Take away the "1)". - Evidences do not "opens". They open :-) Edson

Hi, Gaz(6). As DATCG said in 13, ID is not theology. Many proponents of ID surely reinforced their religious beliefs because the specific evidences in science which we are knowing better opens the scenario for wondering who the designer was and what were (and maybe what are) his purposes. Some people still face it as being the contrary, as something like "Our beliefs cannot be wrong. Let's just make the evidence be what we want". 1) This statement could well characterize atheistic darwinism and six-day-creationism. ID defenders are showing to have their feet well on earth, some of them making concessions for common descent, for example. The main point is that evidences is really leading us to infer design. It's not like imagining dog forms in the clouds. I don't see much sense in the feeling that scientists need to keep ID alive, as if it needed their thoughts to exists and as if it was threatened by new discoveries and fighting against them, for they could beat it and prove it wrong. For these reasons, it's not logical to think ID as a dead-end. It have made correct predictions, many of which weakened the case for pure materialism, and will surely continue to firm itself by new predictions it will make right. And, again, it's not a matter of choosing what to believe in, but rather, finding the truth. Edson

Dr. Hunter: These fact-free assertions are what evolution is all about. In evolutionary thought, science has become a mechanism for story-telling." Eventually they will be able to refine the fable so that it joins harmoniously with the multitude of other fables that make up the Darwinian paradigm...er myth, catching unawares the unquestioning hoards. It's kind of like a Star Trek mythology, where they try to make it fit as authentically as possible with the rest of the myth, so that the causal viewer will only notice what fits. Problem is, just as there are holes in the Star Trek myth, there are holes in the Darwinian myth that people notice if they are keen enough. Joseph, "As far as I can tell the only thing tat needs to develop is to allow the design inference." I fully agree. But reality is not allowed in the Star Trek myth. It's not authentic enough. A design inference is too conventional. They don't want convention, but spooky. Evolution is spooky. "Allen MacNeil from Cornell University, an avowed unguided evolutionist that has posted here many times admitted Darwin is dead and Modern Synthesis is superceeded." With all the exchanges I (the least among many others) have had with Allen here, I was not aware that he made this admission. When and where? DATCG,"Well, that is wonderful. You found HGT. You realize HGT undercuts everything Darwinist have believed in, worhipped for the last 150yrs, but now you have to deal with it. So you roll out a 'scenario' whereby a non-Darwinian processes enabled complexity prior to the assumed 'Darwinian Transition' phase." I've always wondered about HGT myself. I'm not a scientist, but it doesn't really seem as if it fits with a Darwinian perspective - unless of course it's some sort of magic process that we don't yet have an explanation for (but will) -then yes, it fits. CannuckianYankee

They do not address Darwinism...

"A Darwinian transition corresponds to a state of affairs when sufficient complexity has arisen that the state is incapable of tolerating ambiguity, and so there is a distinct change in the nature of the evolutionary dynamics—to vertical descent." This is not a fact. It is merely their token comment on Darwinism. "We envision that such Darwinian transitions occurred in each of the three major lineages. The present work does not address the Darwinian transition itself, but explains how the communal state could have arisen in the first place: in our scenario, it is the inevitable by-product of the establishment of an innovation-sharing protocol—the genetic code—leading to the explosive growth of complexity."

Well, that is wonderful. You found HGT. You realize HGT undercuts everything Darwinist have believed in, worhipped for the last 150yrs, but now you have to deal with it. So you roll out a "scenario" whereby a non-Darwinian processes enabled complexity prior to the assumed "Darwinian Transition" phase. Kudos for recognizing non-Darwinian processes exist. Thats a first step. There will be more in the future as Darwinist wake up from their denial of Design. DATCG

On a more serious note. Congrats to these scientist for recognizing the failures of Darwinism in light of HGT. But as Koonin, Baptiste, et al, and many biologist understand today, they are cornered. They have no where to go and realize as much. But this is a big admission. Lets read on...

Our framework fits naturally the recently proposed picture that early evolution was dominated by horizontal gene transfer, as evidenced by detailed phylogenetic[15], biochemical[16] and structural[17] analyses of the aminoacyl-tRNA synthetases." Gosh, has HGT stopped today? They're saying it was much more robust in the past due to their phylogenetic studies? Hmmmm... frankly I do not give to much weight to phylogenetic interpretations these days. "The broader implication of this scenario is that innovation sharing led to the emergence of modern cell designs [18] from a communal state - not a unique, shared ancestor." Or, Design allowed for shared material that supported rapid adaptation, not "gradual" processes over long periods of time. "Such a communal state existed prior to the point of emergence of vertical evolution, which has been termed the Darwinian transition[18]." Chuckles... obligatory Darwin statement. This is to funny. OK, we give up on Darwin prior to this specific point due to the obvious non-Darwinian nature of nature. But hey, then this magical mystery transition takes place... and poof! Darwin! yada, yada. "The defining property of the communal state was that it was capable of tolerating and utilizing ambiguity, as reflected in the pervasive role of horizontal gene transfer."

We get it. Stuck with HGT, Darwin is dead. DATCG

Cabal, You say the paper is meaningless to Darwinism. The papers fourth reason... "Finally, the evolutionary dynamic that gave rise to translation is undoubtedly non-Darwinian, to most an unthinkable notion that we now need to entertain seriously. Gee, seems they're talking about Cabal's "unthinkable notion." Yes, they need to review the "undoubtedly non-Darwinian" processes within translation, transcription, editing, error-correction, alarms, alerts, etc., within the cell. Along with dynamic communications across all levels of cells and tissue types, nerves, brain cells, etc. "These four considerations structure the approach we take in this paper." Gee, one of the four considerations is non-Darwinian. Go figure, more...

"If Darwin had been a microbiologist, he surely would not have pictured a “struggle” for existence as “red in tooth and claw”." chuckles, surely not, but he'd still predict bear to whale. "Our view of competition in a communal world as a dynamical process is very different from the widely-understood notion of Darwinian evolution. Wait, wait, wait! Huh? Different from "widely-understood notion of Darwinian evolution?" Well gee, seeing how Darwinian definitions changes over time, thats a logical outcome. So, they differ from the current notion of Darwinian evolution. "“Survival of the fittest” literally implies that there can only be one winner from the forces of selection, whereas in a communal world, the entire distributed community benefits and its structure becomes modified by the forces of a selection that is an inherently biocomplex phenomenon involving the dynamics between the community elements and the interaction with the environment." Gee, anyone feel a Margolis community organizer event on the horizon? "The most general sense in which we mean competition in this article is the complex dynamical rearrangement of the community structure." Bingo! Now, who is the community organizer?

LOL... this is fun reading. Essentially, Darwinian notions do not work at this level or in time before the grand magical mystery tour of "Emergence" miracles. DATCG

Gaz, "Additionally, inferring design is a dead end." No, that is a lie, a mantra that you have heard repeated ad naseum by Darwinist and atheist. No truth at all to this statement. If it were true, all great scientific Christians in the past would have stopped doing science. But they did not, did they? Isaac Newton? Pasteur? Thomas Bayes? And the list goes on and on from long ago to the many scientist today that contribute to great discoveries and inventions like Geneticist John Sanford at Cornell University. Please do not buy into a bunch of lies distributed by propagandist. "What research can be done after that? You can’t (according to ID theology)..." Oh really, now you are showing your colors Gaz. ID is not theology. It is a science of Design Detection. Now you are making your own theological arguments here which is a waste of time. If you want to argue theology of who the Designer is, maybe drift over to a theology web site. "... infer who the designer is, or when they did the design, or pretty much anything at all. It’s a dead end." Actually, it appears you are unfamiliar with ID. It does not attempt to identify who the Designer is and as to "when" that is not ID either. You are confusing different fields of science. "That still doesn’t stop anyone from inferring it if they want to. However, it doesn’t mean that anyone else has to listen to them." Why should anyone listen to your misreprensentations and misinformation about ID? This is truly sad. DATCG

Cabal, Do you read at all? Insults are grand aren't they? DATCG

Big Bang Explosion of Information by Eugene Koonin He has admitted the data does not match the Darwin TOL. This is just one example. There are more that have been posted and "read" here in the past. DATCG

Looking at the comments so far, I wonder: Do people read the paper CH built his case on:

Our framework fits naturally the recently proposed picture that early evolution was dominated by horizontal gene transfer, as evidenced by detailed phylogenetic[15], biochemical[16] and structural[17] analyses of the aminoacyl-tRNA synthetases.

Universal common descent still going strong, where's the beef? Cabal

Cabal, People reference scientific papers here almost daily. It would do you well to read up on TOL failures and the failure of Darwins original theory, thus Modern Synthesis. Now even MS has failed admittedly by evolutionist. This is why they are turning to Margolis. Allen MacNeil from Cornell University, an avowed unguided evolutionist that has posted here many times admitted Darwin is dead and Modern Synthesis is superceeded. But hey, u are the great "Cabal" Lol.... If even the strongest supporters are admitting failures in all of these areas, why should we listen to you? Darwinian evolution is a failed theory in multiple ways. 1) fossil records 2) gradualism 3) macro evolution 4) vestigial organs 5) Bears swimming to Whale theory At best random mutation and natural selection are weak forces and cannot account for macro-evolution theories. Your trivial snide remarks are all that is left of Darwinism. You are evidently to blind a follower to see this, or to deaf to hear. DATCG

Joseph,

Scientific paper on the origin of the genetic code via non-telic processes? Please provide the reference.

You know that the paper CH built his case on is an analysis of (as far as I understand) pathways of evolution in the transition from prebiotic life to the root proper of the Darwinian tree of evolution. I don't see what difference CH thinks the paper makes. Darwinian evolution is still going strong. In the meantime I am waiting for more peer-reviewed papers on teleology. Cabal

As far as I can tell the only thing tat needs to develop is to allow the design inference. We don’t need any new methodologies.

I absolutely disagree. What Intelligent Design theory needs most right now is a solid methodology for using the design inference to make new discoveries. The big question, of course, is whether the design inference can be useful in modern science. Darwinists obviously think it is not, perhaps out of some paranoid fear that Intelligent Design theory means replacing all of modern biology with the three words "God Did It" -- a ridiculously oversimplified delusion in my opinion. But let's not be distracted by concepts of what is "allowed" by the current scientific paradigm. The only potential obstacle I see standing in the way of ID's own program of empirical research -- an ongoing and unambiguous demonstration that the design inference is a useful tool in modern science -- is the issue of funding, which is why I mentioned volunteers and donations. Daisy

Joseph (5), You miss the point. Anyone is entitled to infer intelligent design if they want to, the reason most scientists don't is that when you dig into the evidence there really isn't any solid evidence for it. Additionally, inferring design is a dead end. What research can be done after that? You can't (according to ID theology) infer who the designer is, or when they did the design, or pretty much anything at all. It's a dead end. That still doesn't stop anyone from inferring it if they want to. However, it doesn't mean that anyone else has to listen to them. Gaz

"It would be too unlikely (even for evolutionists) for the identical unique code to have evolved independently in the different evolutionary branches..." Too unlikely? For evolutionists? You mean like, 'we came from nothing'! That kind of 'unlikely'? :) IRQ Conflict

Daisy, As far as I can tell the only thing tat needs to develop is to allow the design inference. We don't need any new methodologies. All we need is for scientists, conducting scientific research, to be allowed to reach a design inference if that is what the data leads to. Joseph

Yet another solid and convincing argument for why Evolutionism fails. Unfortunately, this is only the first step. Too many ID proponents have been lulled into thinking that if only their arguments and logic and reason against Darwinism are sound enough, evolutionists will eventually see the light. Instead, those evolutionists sit back and sneer, "Well, maybe our theory has problems, but yours is no better." As I've said before in a previous thread, the most critical thing for the ID movement to be doing right now is developing its own intricacies and methodologies, designing and supporting a much more intense program for conducting new empirical research -- funding this through our own donations and volunteers if necessary. Ten years from now, if we're still talking about whether or not evolutionism is true, the movement will have been an utter failure. Instead, the topic by then needs to be why scientists working under the paradigm of Intelligent Design theory are producing new and valuable discoveries, while scientists working under the paradigm of Evolution theory are stagnating under the weight of their own assumptions. Daisy

Scientific paper on the origin of the genetic code via non-telic processes? Please provide the reference. Joseph

To make the story complete, for those that don’t bother to read scientific papers,

We have argued that there are three distinct stages of evolution, which we might classify as: (I) Weak communal evolution, which gave way via development of an innovation-sharing protocol and the emergence of a universal genetic code to (II) Strong communal evolution, which developed exponential complexity of genes, finally leading via the Darwinian transition to (III) Individual evolution—vertical and so, Darwinian.

Cabal