Theistic Evolution

[The Barbarian]

But if beneficial mutations are so rare how do they come in such a short time.

Lots of mutations. You and I have a dozen or so that didn't exist in either of our parents. And huge numbers of bacteria, with very short generation times, makes it easier to track.

Also as noted in Halls experiment the new function in lactose tolerance was associated with existing genetic info.

Yep. That's how evolution works. Everything new is merely a modification of something already there. That's what Darwin discovered.

That sort of makes more sense if it happened fast as the change does not have to mutate new genetic info which would require a trial and error process.

Every mutation is new information. Do you know how information is determined in populations? Could you tell me what you think happens?

If it was a case of Darwinian processes only then this should not happen fast.

I'd be interested in seeing your data for that. What do you have?

AS Darwin himself said it is a slow and gradual process.

It was indeed gradual. But it's the fastest known example of evolution of a new trait. Show us the numbers that say it can't happen in a few decades.

According to many that are exactly what is produced by Darwinian evolution. But that is not what I meant. I mean that what may be interpreted as a random mutation producing the changes may be some other mechanism.

It always comes down to evidence. What do you have?

If that’s the case then it seems strange that what began as a single-celled organism can evolve into something that certainly has increased genetic info that was not there, to begin with. You can only recombine and re-jig existing info so much.

Can you show us a population that is at its limit of variabilty and can change no more? If so, show us how you know.

Also, we have HGT especially with bacteria.

In this case, that didn't happen. Would you like to know how we know?

Yes, please.

Because the culture came from a single bacterium. Hence genetically identical at the start. You can assure this by serial dilution until the innoculation of a plate produces only a few discrete colonies. Each of them come from a single bacterium.

But didn’t humans already have that ability to utilize lactose as infants and then gradually lost that ability. So they can get it back again.

Right. The gene that normally expresses lactase is suppressed in humans. Some populations evolved a means of reversing that suppression. A lot of evolution is like that.

What I find hard to believe with these types of changes is that for random mutations to produce the right genetic changes to get that rare beneficial change in producing that spiral valve it has to also be able to produce non-functional mutational changes.

Almost certainly, it did. Can you guess why we don't see them around, today?

Yet any non-functional change to a sensitive feature like a valve for digestion could be lethal.

Nope. It's a way of increasing the surface area of the gut without lengthening it. So lots of possible mutations, none of which would be lethal. It's like the evolution of streamlining in rapidly-swimming organisms. Lots of convergence. Sharks have a similar structure.

It makes more sense that the Lizards development mechanism responded to the pressure the lizard was under and produce the right feature in one go without a trial and error of Darwinian processes.

Twenty years is a lot of lizard generations. So not one go.

I thought the evolution of new traits takes thousands if not millions of years.

It can happen in a single generation. Depends on the trait.

If it happens in a few decades, then why do scientists say that for example most of the main phylum came about over ½ a billion years ago

Phyla. The plural is "phyla."

and many have taken 10 million years to change from one to another to get today's creatures.

There have been hominins around for more than 10 million years. The world is a lot older than you seem to think.

If mutations are random and beneficial ones are very rare then they are not going to throw up anything of use for some time.

No, that's wrong. For example, Hall's bacteria quickly evolved a gene with somewhat better lac activity. But over time, it got better and better. A lot of evolution is like that. When we became bipedal, another set of arms would have been great. But there's apparently no way to evolve it by Darwinian means. It could be done your way, but apparently, that way doesn't actually exist.

Also, a trait is not going to happen in one go.

Like a second pair of arms. You see each stage would have to be at worst, neutral. And that's not possible for new arms to evolve.

Like the eye example that started as an eye patch. It took time for each stage to get to the complex eye.

Yep...

Not so fast -- researchers find that lasting evolutionary change takes about one million years

It determined that rapid changes in local populations often don't continue, stand the test of time or spread through a species.

Often they don't. But sometimes, they do. For example, blue eyes in humans.

New research shows that people with blue eyes have a single, common ancestor. Scientists have tracked down a genetic mutation which took place 6,000-10,000 years ago and is the cause of the eye color of all blue-eyed humans alive on the planet today.
Blue-eyed humans have a single, common ancestor

I emphasized the part you missed, in red.

Darwinian evolution works by modifying things that are already there.

Yes but that existing genetic info will only produce certainly limited results. For example, for an eye patch to evolve into a complex eye there needs to be more genetic info then what an eye patch contains.

Eye patches don't have "information." What happens is that if the sensitive patch is slightly depressed, it can give the organism information about the direction from which the light is coming. And that's quite useful. So a rather tiny mutation can quickly spread through a population, if it's as advantageous as that.

It has to come from outside from somewhere.

It's merely that a light-sensitive spot in a depression is favored by natural selection, since it increases the likelihood that the organism will live long enough to reproduce. It gives the organism more useful information, and that is favored by natural selection.

Natural selection is good at explaining the survival of the fittest but not the arrival of the fittest.

No, that's wrong. Natural selection determines what alleles will survive for the next round of reproduction, and thus determines what direction evolution will take. But only roughly. It will lead to streamlined tails that provide propulsion in large animals that move about in water, but precisely how that will happen is partially random mutation, and partly what is already there. This explains why whales have horizontal flukes and fish have vertical tail fins. Would you like to learn how this happened?

Barbarian asks:
Why would anyone suppose that other soil organisms would not produce resistance to penicillin? Penicillium was using it to kill off competitors. Of course, some of them would evolve resistance.

Then why do some use this as an example of evolution by saying that this is a new adaptation

Because we see it evolving in organisms that formerly did not have it. And there are different alleles in bacteria that confer resistance in different ways. Like the whale flukes and fish tails. Different paths to the same effect. Because it's random mutation and natural selection. If it was directed, we'd see one efficient way, and that's not what we observe.

because antibiotics have only been around since recent time for bacteria to evolve resistance to the antibiotics.

No. They've been in soil organisms for a long, long time. We just find them, and use them against new organisms that don't have any protection against them. Sometimes we chemically modify them to get around resistance.

Then why do these papers talk about antibiotic resistance happening thousands of years before Fleming discovered antibiotics.

Because they existed in microorganisms, as a means of defense against other microorganisms.

So if bacteria were able to resist antibiotics thousands of years ago chances are they have been able to do this all along.

If that was true, then penicillin would never have worked. As Flemming noted, natural selection tends to produce new modes of resistance.

But there should be way more dysfunctional outcomes than functional ones because harmful mutations are 1000's of times more likely.

So let's look at that. We have a maybe 2 dozen mutations each, that didn't exist in either parent. Let's say 10 to be conservative. Let's say a population of 10,000 individuals, and a generation time of 20 years. So in one generation, 100,000 mutations, or by your numbers, 100 useful ones.

In a thousand years, 5,000 useful mutations, and in a million years, five million of them. Seems like a lot. And those are conservative estimates.

From what I have read most living things are well defined and functional. Can you give some examples?

Humans have suboptimal lower backs, hips, knees, feet, and hands. And if you live long enough, you will almost certainly have trouble with one or more of them. It's because we are only partially adapted to bipedalism. Our bodies are not completely adapted to an upright posture. For much of my working life, I was an ergonomist and spent a lot of time working around the limitations of our bodies.

I thought I posted the link. Around at least 15 million years before scientists had attributed bipedal apes. The strange thing is that it is more about how this happened rather than when it happened. It seems that there was a change in the control gene that produces either a 4-legged body plan or a 2 legged one.

There was a whole suite of changes that happened pretty much in concert. Not because of some teleological principle, but because a single gene or a few of them retarded maturation.

We retain a lot of juvenile ape traits, among them relatively longer legs and a foramen magnum (where the spinal cord enters the skull) that is far forward under the skull, instead of back, as it is in adult apes.
Both of these are important adaptations to bipedalism.

So it may have been that a 2 legged infant aged was born and walking around with their siblings who were still unable to walk upright.

Today's apes can walk upright. It's just clumsy for them, as adults. While there were bipedal apes from a long time ago, none of them had the adaptations that make humans effectively bipedal, and able to move long distances quickly. Even the advanced Australopithecines retained traits that made them less effective than any species of Homo.

Yes but it is the ability of a random process to produce that second beneficial mutation. It is when one random mutation has to rely on a second or third on etc to make the beneficial change which is often the case.

Can't think of one. At worst, the mutation could be generally neutral. Bipedalism for example, shows a slow path toward our (still imperfect) condition. And it moved not in one direction, but several. Oreopithecus, for example, has ape-like feet, along with an upright stance, which would have required a very different sort of bipedal locomotion.

This is consistent with random mutation and natural selection, but not directed evolution.

Research shows this is very hard and probably impossible to do

Hall's bacteria show otherwise. The fossil record of whales also shows otherwise. Your assumption is not consistent with the evidence.

The waiting time problem in a model hominin population

So for a string of five, this means it is necessary to wait until almost 1,024 mutations have occurred within the same short stretch of a given DNA molecule.

That's pretty close to what Hall observed to happen in his bacteria. And it fits the numbers for human mutation in a small population.

The infinite monkey theorem states that a monkey hitting keys at random on a typewriter keyboard for an infinite amount of time will almost surely type a given text, such as the complete works of William Shakespeare. Evolutionary biologist Richard Dawkins employs the typing monkey concept in his book The Blind Watchmaker to demonstrate the ability of natural selection to produce biological complexity out of random mutations.

I haven't read that book; would you mind quoting Dawkins and give the page where he said that this was a good model for evolution? I don't agree with him on much, but I don't think he's stupid.

I have heard of Aquinas and sort of understand his contingency concept but can you explain this in layman's terms for me as I find it hard to fully understand.

A contingent event is one that is possible, but one which we cannot predict it. Aquinas writes that the essential nature of divine providence is that something will happen. So, he writes, such things can be such that they arise from necessity or from contingency. God does not have our limitations so that which is conceived by Him to happen by necessity happens by necessity, and that which is conceived by him to happen by contingency, happens by contingency.

I am meaning the actual process of evolving life from that first organism to complex ones like us. They say this evolution has no purpose, direction and end goal.

In the sense that gravity has no purpose, direction, and end goal. Nevertheless, it's essential for us to be here. If God made the universe so as to ultimately bring us about, that's good enough. He doesn't have to pull everything around to fit His intentions; He can just create it to do so.

It is just blind, pitiless and without any God or intelligence behind it.

That is a religious belief; science can't make such determinations.

 

[stevevw]

Hi Crossnote! What about the law of entropy (2nd law of thermodynamics). Do you believe that was imbedded into creation [by implication, I am referring to creation that occurred and was completed before sin]? My personal view is that while God did in fact create 'laws', the way the present creation exists is the result of the curse of sin and not the same state at which it would be if there had never been any sin... the way it will be again when we are with God in the eternal heaven (the new heaven and new earth).

This is an important point when you think about it and I wonder how it fits in with evolution theory. There had to have been a previous state where humans were without sin as the need for salvation came because sin entered our world. If we are the products of a common ancestor that has spawned the same basic genetic info and made of flesh and blood and all life and the planet has been subject to decay and corruption since the beginning of evolution then where does this uncorrupted state fit in. Did God just create us through evolution to be subject to decay and sin from the beginning or was there a time when we were pure.

 

[The Barbarian]

What about the law of entropy (2nd law of thermodynamics). Do you believe that was imbedded into creation [by implication, I am referring to creation that occurred and was completed before sin]?

Since Adam and Eve had to eat, even before the fall, entropy was part of the world then. We see, in the fossil record that it was there long before there were humans.

My personal view is that while God did in fact create 'laws', the way the present creation exists is the result of the curse of sin and not the same state at which it would be if there had never been any sin...

That's contrary to God's word in Genesis. After the fall, God expresses concern that Adam might become immortal, which tells us that He wasn't immortal before the fall, which like eating, would mean the 2nd law was operating even then.

This is an important point when you think about it and I wonder how it fits in with evolution theory.

Since the evidence shows thermodynamics before Adam worked just as it does now, that's really not an issue.

There had to have been a previous state where humans were without sin as the need for salvation came because sin entered our world.

Other animals are without sin, since they lack a sense of good and evil. Babies are innocent until they understand this. At whatever point humans developed to the point that they were capable of this, then we could sin.

Of course, there's the possibility that the Garden in which they lived was a special place, miraculously exempt from the usual rules. There's nothing to rule that out, although it could be figurative for our previous innocence.

 

[FatalFantasy]

Can someone please explain to me what Theistic Evolution is. Are there different versions of this. If Theistic Evolution is just the world view version of evolution with God thrown in as the initiator of life then what is the difference between Theistic Evolution and the world view version. Isn't this just reducing Gods role down to abiogenesis which is not really a part of evolution anyway as evolution begins at the point the first single living cell is in existence already? If Theistic evolution starts after God created the first single-celled life then there is no need to include God at all as this is irrelevant to evolution.

That falls under the ID/Gap theory branch of study, where the particular Christian contorts the Genesis account out of desperation to retain their view that Genesis is a literal account of evolution.

But it's not.

 

[stevevw]

If He left proof, then any person of reasonable intelligence would clearly see it. And that's not the case. I think He wants us to have the freedom to accept or to reject Him.

I think it is the freedom to choose that some can still know that there is something behind what they see, but they choose to deny this. Materialistic thinking can then step in and help rationalize away any thought that there may be a God. Worldly ideas have become a strong factor in many moving away from the church and losing faith by replacing this with the power of humanities, and science answering all our worries and problems.

The "invisible things, clearly seen"
Romans 1:20 For the invisible things of him from the creation of the world are clearly seen, being understood by the things that are made, even his eternal power and Godhead; so that they are without excuse:

Are closely connected to one's acceptance of God. You can see these things if you have a mind prepared to do so.

When it mentioned people are without excuse for not seeing Gods invisible power and Godhead, I think this is referring to everyone including those who do not accept God because those who accept God will not be denying God that they are without excuse for not acknowledging God. Only those who do not accept God will be without excuse because they know deep down that there is more to what they see but deny this by looking for materialistic explanations. Eventually, they are given over to their disbelief.

That never made any sense to me. The reason Paley used a human artifact to make his point, is clear; if he had used a natural object, no one would have seen his point.

I am not sure of that as there are examples of using intelligent design in nature.

Fred Hoyle mentioned that it seems like someone had monkeyed with physics about the Big bang resulting in a fine-tuned universe for life. There have been many other examples used about nature and our DNA being referred to as a code or the universe being made up of mathematics like someone had put all these calculations into it. IE

“DNA is like a computer program but far, far more advanced than any software ever created.”
― Bill Gates,


“This most beautiful system of the sun, planets and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being.” ― Isaac Newton


“Scientists are slowly waking up to an inconvenient truth - the universe looks suspiciously like a fix. - Paul Davies

Even non-believing scientists describe the universe and nature as being the result of calculations that imply intelligence is involved so that the deeper, we look the more intelligence we see. If this is applied to anything else like digging up some ancient artefact and knowing it is the result of some intelligence we would not hesitate in relating the two.

What's the Universe Made Of? Math, Says Scientist
What's the Universe Made Of? Math, Says Scientist

It's impossible for science. Since science is limited to methodological naturalism, it can neither affirm nor deny the supernatural.

It all depends on what is termed supernatural. If science puts an explanation of some weird occurrence that has all the hallmarks of being supernatural as in not conforming to natural events then they are the ones in control of determining what is science and what is supernatural. As far as I can see the closer we are to getting to the point where something comes from nothing things are breaking down in classical cause and effect. So, this is moving into what could be attributed to the supernatural in some ways.

For example, scientists are describing strange observations where quantum particles can be in more than one place at a time, where cats can be dead and alive at the same time, where particles can affect each other at distances across the universe and go through walls. Just because they have attempted to describe these things and put new names on them does not mean that a materialistic explanation has been found that makes it a natural occurrence. All they may be doing is describing what they are seeing and what they are seeing may be supernatural.

Afterall describing how massive big bits of matter can float in mid-air in space is not explaining how it can happen. What is gravity anyway. It could be something God uses to keep the universe in order. It is even more strange in that the explanations we have given for this do not work out anyway because there is not enough matter to fit in with relativity and gravity theory. So, scientists have to come up with even more strange ideas like dark matter and dark energy. Just because they make up another idea does not mean it then brings everything into a natural materialistic explanation. They may just be explaining some phenomena that God has installed into existence beyond our understanding.

That would make no sense at all, since science has no way of determining such things. You might as well say that even if something was pointing to God, many plumbers will find anything even a far-fectched idea and label it to plumbing to plumbing to avoid acknowledging there is a God.

Using the idea that when someone digs up some ancient plumbing works that we immediately know it points to someone intelligent having made it is the same as looking through the microscope and discovering molecular machines that build DNA or bacteria look like they are the product of intelligence.

In these cases, someone that denies God with his creation of DNA and the finely tuned universe, for example, would be then saying that the plumbing they found was not really a result of some intelligence but a natural process that somehow produces plumbing shapes that give the appearance of being designed. Similar to what Dawkins says with evolution

Biology is the study of complicated things that give the appearance of having been designed for a purpose. Richard Dawkins, The Blind Watchmaker (1996) p.1

We see design all around us in things like Fibonacci patterns, mathematical equations throughout the universe and nature, the fine-tuned universe for life, our DNA etc. All are described with all the hallmarks of being designed except some scientists will then say it only looks that way and then credit the created as the creator. This is the only thing we choose to do this too and in all other areas, we immediately acknowledge the intelligence behind what is designed. I like what John Lennox says about the signs of God’s creation such as in the universe.

The self-described main objective of the ID movement is to make it impossible to do science without acknowledging God. And that is impossible. This is why IDer Michael Behe admitted under oath that ID is science in the same sense that astrology is science.

I am not sure that is Behe take on ID. Yes, ID in Behe's version is science but that science is looking for evidence of design based on science. In fact, they make scientific predictions that can be testable. But there are several versions of ID so I don’t think we can stereotype it into one box.

For example, John Lennox is not a supporter of Behe's ID version in but has more of traditional faith and talks about the logic of Gods creation being seen in things like how the universe is full of mathematical equations. Some supporters of ID do not even include God in their explanations but just base things on there is some intelligence in nature whether that stems from God or another alien race that seeded our planet.

Formally, it's "methodological naturalism", as opposed to ontological naturalism. Science can neither affirm nor deny the supernatural.

I think it is more the scientists who inject the atheism and materialism into it. Unfortunately, this can be a subtle way of turning science into a tool for atheism. In some ways, some elevate science into a God-like status such as it is the answer to all our problems, it can do anything, and humankind will be able to achieve anything with science.

I don't see that. The chair of my department was a confirmed theist, and he seemed to be doing well. Francis Collins is an outspoken Christian and was placed in charge of the Human Genome project. One can't really do modern biology without realizing the contributions of scientists who were and are theists.

I am talking more about the way religion is becoming less popular especially among young people and being ridiculed with the way the rights campaigners are making out religious views are bigoted. We see a lot of universities promoting more secular humanist view and students are pushing certain positions while excluding certain views including religious dogma etc.

Since it's directly observed, that's not an issue any more.

Not exactly and this is my point. Traditionalist thinks there is no issue because they focus exclusively on Darwinian evolution and exclude a host of other factors which for many other scientists are now saying are causes of evolution. So, it is about to what extent does the Modern synthesis processes play in the overall way life can change and/or is the processes mentioned in the Extended Evolutionary Synthesis more responsible.

The evidence for these influences from the EES is becoming more prominent as time goes by because we are able to understand better how life works through a number of fields like genomics, embryology, development, psychology, sociology and ecology and not just the narrow view Darwinian evolution takes with genes and adaptive evolution.


Charles Darwin conceived of evolution by natural selection without knowing that genes exist. Now mainstream evolutionary theory has come to focus almost exclusively on genetic inheritance and processes that change gene frequencies.


Yet new data pouring out of adjacent fields are starting to undermine this narrow stance. An alternative vision of evolution is beginning to crystallize, in which the processes by which organisms grow and develop are recognized as causes of evolution.

The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science1, 2. We contend that evolutionary biology needs revision if it is to benefit fully from these other disciplines. The data supporting our position gets stronger every day.
Does evolutionary theory need a rethink?

It's been modified a number of times as details become clear. That's true of all theories that hold up over time.

Yes and I think there is another big change coming. Not just a modification but a reconceptualization. Some say even a paradigm shift.

The EES is thus characterized by the central role of the organism in the evolutionary process, and by the view that the direction of evolution does not depend on selection alone and need not start with mutation.


Hence, the EES entails not only new research directions but also new ways to think about, and interpret, new and familiar problems in evolutionary biology.


Nevertheless, our analysis suggests that the EES is more than simply an extension of ‘business as usual’ science: it requires conceptual change [15]. The additional evolutionary processes that the EES highlights are more than just non-essential ‘add-ons’ [10] and may be as important in shaping evolution as those recognized within the field over the past century.

It comes down to evidence. And our observations are that Darwin's five points remain solidly documented.

There is also plenty of evidence for what has been put forwards from areas like the EES. As they say Darwins theory is too narrow. A new concept is formulating and the evidence for this is getting stronger everyday.

Things are changing pretty quickly now with new research which is questioning Darwinian evolution and proving it inadequate. We are beginning to formulate a new and more complete understanding of how life changes as referred to with the above article.

Often, evolution reduces complexity. Our skeletons are in many ways less complex than those of reptiles. In systems, complexity is associated with jury-rigged solutions, and as systems become more robust, they frequently become more elegant and simple. We see this in evolution quite frequently. Complexity is not fitness. Not always.

But you have to admit that from the simple single-celled life to what we have today with humans is an increase in complexity. It is that increase in complexity that is being questioned as to whether Darwinian processes are responsible or even capable of producing. As the more complex the genetic structures get the more important it is to maintain and preserve the current status. Any small change can undermine and destabilize the entire system.

Increases in complexity are not the result of adaptive evolution (natural selection) but other non-adaptive processes.

Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation.
Darwinian evolution in the light of genomics

The frailty of adaptive hypotheses for the origins of organismal complexity.
Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes

The goal here is to dispel a number of myths regarding the evolution of organismal complexity (Table 1). Given that life originated from inorganic matter, it is clear that there has been an increase in phenotypic complexity over the past 3.5 billion years, although long-term stasis has been the predominant pattern in most lineages. What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms.


It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement


The literature is permeated with dogmatic statements that natural selection is the only guiding force of evolution, with mutation creating variation but never controlling the ultimate direction of evolutionary change (for a review, see ref. 17).
The frailty of adaptive hypotheses for the origins of organismal complexity. - PubMed - NCBI

 

[stevevw]

Barbarian observes:
Darwin's observation about organisms altering their environment applies here. And from a systems perspective, random processes, combine with non-random processes, are non-random.

How could that be. If a creature controls its environment and determines how and when it changes then surely this is non-random. The creature is making the choices and creating the conditions in how it will change and survive and therefore eliminating any random influences. It is the same for when a human control their environment and dictates whether it will survive despite nature.

Yep. Darwinian, again. Darwin's discovery was that it isn't random.

But since then we have a much better understanding to what extent this happens to all living things. For Darwin and many supporters of the traditional view of evolution, niche construction was just a minor influence and could not control evolution or was not a cause of evolution. Today it is one of several causes of evolution in that it creates and/or influences variations other than random mutations and directs evolution other than natural selection.

Often it works the other way. Early organisms were anaerobic (no elemental oxygen present in the early Earth) oxygen was a waste product. The banded iron formations show these prokaryotes poisoning their environment with waste oxygen, dying off, and then recolonizing the area after the oxygen is diffused away or combined with other material.

But prokaryotes are a different proposition and can adapt to poisonous environments and have a high capacity for HGT. It is the day to day evolution of life where many can change and create beneficial environments so they can prosper and reproduce without the help of selection.

Over time, organisms tend to become more efficient at maintaining a good environment. Natural selection, again.

If an organism is the one who is maintaining and creating a better environment that they are the ones doing the selecting and controlling the direction of evolution. Niche construction will certainly control and direct natural selection if not bypass it altogether. By creating beneficial conditions, the creature is making themselves more selectable but they are also dictating which direction that selection goes in.

Usually selection will choose any condition that allows a creature to survive even if there are other effects which may cost the organism fitness overall. But living things that create their own conditions will usually choose positive ones that not only benefit themselves but for future generations and therefore are controlling the direction of evolution rather than natural selection. You could say it is a form or artificial selection.

The evolutionary significance of niche construction stems from: (i) organisms modify environmental states in non-random ways, thereby imposing a systematic bias on the selection pressures they generate; (ii) ecological inheritance affects the evolutionary dynamics of descendants and contributes to the cross-generational stability of environmental conditions; (iii) acquired characters become evolutionarily significant by modifying selective environments; and (iv) the complementarity of organisms and their environments can be enhanced through niche construction (modifying environments to suit organisms), not just through natural selection [73]. These findings have led to the claim that niche construction should be recognized as an evolutionary process through its guiding influence on selection [73], a position that is contested by some evolutionary biologists [88].
http://rspb.royalsocietypublishing.org/content/282/1813/20151019

Humans are intelligent enough for cultural evolution. Other primates show this in a very rudimentary state, but we've become really good at it. Archaeology of early humans show them to have been much less capable of this trait, but over time, more capable humans replaced them. This is what natural selection is observed to do.

As Darwin observed e.g. in his earthworm study, organisms alter the environment, often in ways that are beneficial to maintaining it in a usable way for them.

It is not just a case of intelligence. It can also be about maternal instincts, cultural and social influences, physiological influences and the natural affinity living things have with their environments. That is why I think the Standard theory is restrictive in its thinking. It tends to bring everything back to an adaptive view of things where creatures have to be changed to fit into an environment rather than a constructive view where living things have a say and can control the direction of evolution.

This is seen in how creatures build nests, burrows, change flows of rivers to create new environments, changing the chemistry of soil and quality of air, influence the way plants circulate water and nutrients. Through their behaviour, culture and socialisation which will bring positive rewards that put living things in a better position to thrive and survive. These influences not only change the environments for the creatures themselves but also change it for surrounding creatures which can benefit them as well and direct evolution of entire ecosystems.

I have to say, this is a better quality of exchange than one normally sees on such forums. Enjoying it.

So am I and thank you for an interesting, educational and courteous debate.

 

[The Barbarian]

Barbarian observes:
Darwin's observation about organisms altering their environment applies here. And from a systems perspective, random processes, combine with non-random processes, are non-random.

How could that be.

Let's take a random process. Roll a 6-sided die, and record the numbers. If you do it fairly, you'll get a random distribution.

Then do it again, but let's add natural selection. The numbers now have to "survive" the environment. Suppose even numbers are more fit than odd ones. Roll the die again. If the first number was odd, and the second roll is greater than 2, don't write the first number down. If the first number was even and the second number is greater than 4, don't write the first number down.

Will the result be random or non-random?

If a creature controls its environment and determines how and when it changes

That never happens. Many creatures can affect their environments. None controls them. For example, trees do this. They drop leaves on the forest floor. The leaves decay and the acids dissolve nuturients and carry them lower into the soil where smaller plants can't get to them easily. These acids were always there, but are increased in many forest species. Darwinian evolution. But there are lots of random issues like the type of soil, diseases and parasites, sunlight, rainfall, and such, that are not under the control of trees.

But as the dice show you, random variation plus non random factors give you a non-random result.

But since then we have a much better understanding to what extent this happens to all living things. For Darwin and many supporters of the traditional view of evolution, niche construction was just a minor influence and could not control evolution or was not a cause of evolution.

Darwin's last major work, on Earthworms, showed exactly what you're talking about. He called it "bioturbation." The idea that living things also greatly affect their environment was one of Darwin's great discoveries.

Darwin was a rather surprising human, interested in a variety of things, and very good at figuring out how things work. He's the one who discovered how Pacific atolls form. If not for his work in evolution, and his foundational work in cirripedes, he'd be known as an important geologist.

(Barbarian expresses his pleasure for a productive and interesting exchange)

So am I and thank you for an interesting, educational and courteous debate.

It does seem a little unusual, doesn't it?

 

[The Barbarian]

The literature is permeated with dogmatic statements that natural selection is the only guiding force of evolution,

Even Darwin didn't say that. I've spent a lot of time in the literature, and haven't seen that. Even Dawkins, the hyperselectionist, doesn't say that.

 

[The Barbarian]

But you have to admit that from the simple single-celled life to what we have today with humans is an increase in complexity. It is that increase in complexity that is being questioned as to whether Darwinian processes are responsible or even capable of producing.

As Hall's bacteria showed such an increase in complexity by natural selection, we already know it happens.

As the more complex the genetic structures get the more important it is to maintain and preserve the current status. Any small change can undermine and destabilize the entire system.

And yet each human has a dozen or more mutations that existed in neither parent. So that's not an issue, either.

Increases in complexity are not the result of adaptive evolution (natural selection)

It was, in Hall's bacteria.

 

[The Barbarian]

But prokaryotes are a different proposition and can adapt to poisonous environments and have a high capacity for HGT. It is the day to day evolution of life where many can change and create beneficial environments so they can prosper and reproduce without the help of selection.

I happen to have a degree in bacteriology. HGT is a very primitive form of sex in prokaryotes. And it often works even between species. The proliferation of the nylon mutation in bacteria was greatly accelerated by horizontal gene transfer. Scientists supposed that it would take a very long time for bacteria to utilize plastics (because there are no enzymes in nature that are somewhat adapted to plastics) but it took a few decades. And yes, it was by modifying an existing gene.

It's much more rare in animals, although retroviruses can do it to us.

 

[stevevw]

Barbarian observes:
Darwin's observation about organisms altering their environment applies here. And from a systems perspective, random processes, combine with non-random processes, are non-random.

Let's take a random process. Roll a 6-sided die, and record the numbers. If you do it fairly, you'll get a random distribution.

Then do it again, but let's add natural selection. The numbers now have to "survive" the environment. Suppose even numbers are more fit than odd ones. Roll the die again. If the first number was odd, and the second roll is greater than 2, don't write the first number down. If the first number was even and the second number is greater than 4, don't write the first number down.

Will the result be random or non-random?

This can only happen if you take a narrow view of the influences on how living things can change and only include random mutations and natural selection. Here there are only two forces considered when in fact evolution is influenced by several forces. This is the point I am making that some traditionalists are leaving out important additional forces that cause and control evolution. When these other influences/forces are included it puts natural selection in among a number or random and controlling forces that diminish or eliminate natural selections influence and therefore its control on the direction of evolution.

It is like saying what makes a drug take drugs is their weak character when we know there are other factors like physical addition, psychological addiction, past trauma and environmental factors that also contribute. It sorts of gives a false impression of what is going on. Michael Lynch summed this up.

For the average person, evolution is equivalent to natural selection, and because the concept of selection is easy to grasp, a reasonable understanding of comparative biology is often taken to be a license for evolutionary speculation. It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise (6) in the popular literature. For example, Dawkins' (7⇓–9) agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, a view that is in some ways profoundly misleading.
The frailty of adaptive hypotheses for the origins of organismal complexity. - PubMed - NCBI

Lynch mentions the four main forces that influence evolution which include natural selection, genetic drift. Mutation and recombination. He states that 3 of the 4 forces are random which would, therefore, weight the dice towards an overall random process. But these random forces can also give some direction to evolution by encouraging certain outcomes such as deleterious mutations. In fact, according to him the origins orgasmic complexity stems from non-adaptive forces and natural selection plays a minimal role and may even be insufficient.

This narrow view underestimates other factors that are involved and this is part of the problem with the standard theory. It takes a narrow adaptive view and sees everything that way at the exclusion of other influences even to the point of overpowering selection. To start with natural selection is only one force among several that are included in evolution. Lynch names four main forces being natural selection, genetic drift, recombination and mutation. He states that 3 of the 4 forces are random though they will have some direction on evolution but in different ways to select and therefore will more likely dominate natural selection ability to control evolution. Also, many of the features associated with increased complexity come from these non-adaptive forces making natural selection insufficient in being a force for the evolution of orgasmic complexity.

The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.


This Analysis shows that many of the qualitative features of known transcriptional networks can arise readily through the non-adaptive processes of genetic drift, mutation and recombination, raising questions about whether natural selection is necessary or even sufficient for the origin of many aspects of gene-network topologies.


Second, all four major forces play a substantial role in genomic evolution. It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement (12, 13). Because all three nonadaptive forces of evolution are stochastic in nature, this conclusion raises some significant technical challenges. It is tempting to think that stochastic processes have no implications for the direction of evolution. However, the effects of mutation and recombination are nonrandom, and by magnifying the role of chance, genetic drift indirectly imposes directionality on evolution by encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations. (my emphasis added). All 4 forces are needed to understand evolution. But there are many aspects that have negligible contribution from natural selection.
The frailty of adaptive hypotheses for the origins of organismal complexity

Koonin seems to agree
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 duplications, 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. The emerging landscape of genome evolution includes the classic, Darwinian natural selection as an important component but is by far more pluralistic and complex than entailed by Darwin's straightforward vision that was solidified in the Modern Synthesis (16,184). The majority of the sequences in all genomes evolve under the pressure of purifying selection or, in organisms with the largest genomes, neutrally, with only a small fraction of mutations actually being beneficial and fixed by natural selection as envisioned by Darwin. Furthermore, the relative contributions of different evolutionarily forces greatly vary between organismal lineages, primarily, owing to differences in population structure.

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. In this dynamic worldview, each genome is a palimpsest, a diverse collection of genes with different evolutionary fates and widely varying likelihoods of being lost, transferred, or duplicated. 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 (274).
Darwinian evolution in the light of genomics

I have mentioned the other influences several times now that are associated with the EES. These influences also diminish and bypass natural selection. When taken altogether it makes natural selection one of many influences and not quantitively dominant. This will then skew the dice rolls even more. It would then be like saying certain numbers on the dice are fixed and the dice will always end up on them and therefore will control and direct evolution.

There are other factors which also cast doubt on natural selections ability to be non-random in the overall scheme of things. What actually controls evolution is living things adapting to the environment. So, in some ways, it is the environment which is an external factor that has power over evolution. Because environments are so changeable what may be deemed good at one point can suddenly change and be detrimental. So, because environments are so changeable this adds a degree of unpredictability and randomness to natural selection. So when all these factors are taken into consideration evolution is a more complex mechanism influenced by several forces that can affect the direction of evolution.

That never happens. Many creatures can affect their environments. None controls them. For example, trees do this. They drop leaves on the forest floor. The leaves decay and the acids dissolve nutrients and carry them lower into the soil where smaller plants can't get to them easily. These acids were always there, but are increased in many forest species. Darwinian evolution. But there are lots of random issues like the type of soil, diseases and parasites, sunlight, rainfall, and such, that are not under the control of trees.

But many other creatures are able to control the environment in that they can create a more suitable environment for themselves that overcomes those obstacles that the environment may bring. For example, some organisms will change the composition of the soil and therefore are changing the environment to suit their needs. A Beaver can dam up a river to create a pool which then provides the food and nesting it needs. It more or less brings the food to itself and changes the environment to suit its needs. An insect can build a nest where it shuts the outside world/environment out. It has made its own environment to suit.

Humans are the best at this as they can just about change any environment. In fact, the environment is not really a barrier as far as adaption is concerned as they can change the conditions of almost any environment. Though they are the best at this there are many other examples of how living things create their own environment to suit. Darwinian evolution underestimates the power of niche construction as being a driver of evolutionary change even overcoming the forces of natural selection.

This is the difference is how those supporting the standard theory and those supporting the EES think. This is the contentious issue that is up for dispute, the place random mutations and selection play in how living things change. When you add the other forces such as developmental bias, plasticity, extra inheritance beyond genes you begin to get a powerful synthesis that challenges Darwinian evolution that cannot be underestimated.

Darwin was a rather surprising human, interested in a variety of things, and very good at figuring out how things work. He's the one who discovered how Pacific atolls form. If not for his work in evolution, and his foundational work in cirripedes, he'd be known as an important geologist.

Yes he was a great man who has become an icon of evolution. It is interesting that some of these great men who were well known for one thing also did other great things. They seem to have been innovative thinkers who were ahead of their times and were changing the way we think because they had great minds.

 

[The Barbarian]

Barbarian asks:
Let's take a random process. Roll a 6-sided die, and record the numbers. If you do it fairly, you'll get a random distribution.

Then do it again, but let's add natural selection. The numbers now have to "survive" the environment. Suppose even numbers are more fit than odd ones. Roll the die again. If the first number was odd, and the second roll is greater than 2, don't write the first number down. If the first number was even and the second number is greater than 4, don't write the first number down.

Will the result be random or non-random?

This can only happen if you take a narrow view of the influences on how living things can change and only include random mutations and natural selection.

No, it doesn't matter what you believe. If you do a large enough sample, the same thing happens every time. Your question was "how can it be" that a random process and a non-random process together be a non-random process.

Here there are only two forces considered when in fact evolution is influenced by several forces.

Of course. Founder Effect, sexual reproduction, mating choice, epigenetics, change in environment, etc. all are part of this. Even randomness, in the case of neutral mutations. The point is, all of these have been demonstrated to be real processes. I was just showing you that a random process, plus a non-random process is a non-random process.

For the average person, evolution is equivalent to natural selection, and because the concept of selection is easy to grasp, a reasonable understanding of comparative biology is often taken to be a license for evolutionary speculation.

Gould, who described himself as an "orthodox Darwinian" pointed this out. He was dismissive of the hyperselectionist thinking that ascribed everything to natural selection. Often, it's not the case. Time and chance happen to them all.

It has long been known that natural selection is just one of several mechanisms of evolutionary change, but the myth that all of evolution can be explained by adaptation continues to be perpetuated by our continued homage to Darwin's treatise

Of Darwin's five points, which is now known to be invalid? None of them are, just as none of Newton's theory of gravitation are known to be invalid. We've added to each of their theories, but their discoveries remain correct.

Lynch mentions the four main forces that influence evolution which include natural selection, genetic drift. Mutation and recombination.

Three of these are Darwinian.

He states that 3 of the 4 forces are random which would, therefore, weight the dice towards an overall random process.

As you now see, that's a false assumption. Let's say that there are four salesmen. One of them always sells more than the others. Yet prospects are randomly assigned to them, and the prospects themselves are random with regard to their interest in a particular product. Yet the salesman continues to excel over the others. Because the allocation is random, the need for the product is random, and the skill of the salesman is not random.

But these random forces can also give some direction to evolution by encouraging certain outcomes such as deleterious mutations.

If they favor certain things, then by definition, not random. However, they are random. We know that favorable and unfavorable mutation appear randomly.

In fact, according to him the origins orgasmic complexity

Did you mean "organismic?" "Orgasmic" refers to something else entirely.


stems from non-adaptive forces and natural selection plays a minimal role and may even be insufficient.

These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.

So Darwin said. The existing organism and environment limits evolution. So you see jaws being jury-rigged in utero from branchial arches, rather than appearing de novo. That is the standard theory.

This Analysis shows that many of the qualitative features of known transcriptional networks can arise readily through the non-adaptive processes of genetic drift, mutation and recombination,

As Darwin said. New traits arrive randomly. Natural selection is only necessary to favor the useful ones and to remove the harmful ones. That's why his theory was about random change, acted upon by natural selection. All those processes are important in the modern synthesis.

It is tempting to think that stochastic processes have no implications for the direction of evolution.

Not since Darwin's theory. It's a critical part of Darwinian theory.

However, the effects of mutation and recombination are nonrandom

This has never been observed to be true, except in the trivial sense of each random mutation has a specific selective value. Likewise, the chromosomes from each parent are determined randomly, meaning recombination is also random.

and by magnifying the role of chance, genetic drift indirectly imposes directionality on evolution by encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations.

In fact, genetic drift by definition doesn't put any direction on evolution other than that occurring by chance. Genetic drift is the variation in the relative frequency of different alleles in a small population, due to the random disappearance of those alleles as individuals die or do not reproduce.

Koonin seems to agree

Even in Darwin's day, there were Darwinians who favored more rapid change. Huxley, for example; Darwin's Bulldog thought saltation was a common process in evolution.

There are other factors which also cast doubt on natural selections ability to be non-random in the overall scheme of things.

Since it's been directly observed to be non-random, that's not an issue.

What actually controls evolution is living things adapting to the environment.

Or, as Darwin discovered, living things changing their environment. Both are an issue in natural selection.

So, in some ways, it is the environment which is an external factor that has power over evolution. Because environments are so changeable what may be deemed good at one point can suddenly change and be detrimental.

This is why some organisms are sexually-reproducing, and some are not. Sexual reproduction is a bad thing from an evolutionary standpoint, because an organism only passes on half of its genes. On the other hand, it's a good thing, since sexually-reproducing populations can more quickly adapt to a changed environment.

So, because environments are so changeable this adds a degree of unpredictability and randomness to natural selection.

To evolution, not natural selection.

So when all these factors are taken into consideration evolution is a more complex mechanism influenced by several forces that can affect the direction of evolution.

So Darwin said.

But many other creatures are able to control the environment in that they can create a more suitable environment for themselves that overcomes those obstacles that the environment may bring.

So Darwin discovered. It was the subject of his last great paper.

For example, some organisms will change the composition of the soil and therefore are changing the environment to suit their needs.

That's what the paper was about.

This is the difference is how those supporting the standard theory and those supporting the EES think.

In this case, EES borrowed from Darwinian theory.

Yes he was a great man who has become an icon of evolution.

In the sense that Newton has become an icon of gravitation or Einstein an icon of relativity. They each did foundational work upon which the work of others depends.

It is interesting that some of these great men who were well known for one thing also did other great things.

Darwin, for example, discovered the process by which Pacific atolls are made, and was foundational in the study of cirripedes. If he hadn't figured out the mechanism of evolution, he'd be a notable geologist.

Even in his old age, his study of earthworms demonstrated that populations aren't passively being acted upon by the environment; they also change the environment.

 

[stevevw]

Barbarian asks:
Let's take a random process. Roll a 6-sided die, and record the numbers. If you do it fairly, you'll get a random distribution.

Then do it again, but let's add natural selection. The numbers now have to "survive" the environment. Suppose even numbers are more fit than odd ones. Roll the die again. If the first number was odd, and the second roll is greater than 2, don't write the first number down. If the first number was even and the second number is greater than 4, don't write the first number down.

Will the result be random or non-random?

No, it doesn't matter what you believe. If you do a large enough sample, the same thing happens every time. Your question was "how can it be" that a random process and a non-random process together be a non-random process.

I agree if you use a purely random and non-random process without any other interference then yes, the non-random process would eventually direct things.

But your example was not like this. You have assumed more randomness to natural selection than it may have. When you specified what those random or at least the non-random part was you are qualifying it and if we are to have a fair calculation, we then have to include the opposing forces that act against selection and deminish its ability to be totally random or at least dominate all situations that cause change.

For example, genetic drift can overpower natural selection in smaller populations. If we consider that the origins of complex life involved small populations then this would make natural selection insufficient to influence the outcomes of the dice as its influence would continually be lost.

Gould, who described himself as an "orthodox Darwinian" pointed this out. He was dismissive of the hyperselectionist thinking that ascribed everything to natural selection. Often, it's not the case. Time and chance happen to them all.

Actually the dice example does show how people can oversimplify selection and adaptive evolution. I have heard people credit natural selection from everything such as why we like chilies to why certain financial outcomes are more likely than others. Natural selection is a logical mathematical idea that is easy to make a case and apply to almost anything. It is not so much a matter of time and chance but the purposeful and specific attributing of this idea at the expense of other ideas that may be the real reason for why it happened. It is just that the idea of adaptation is easy to make a case even if it is not supported.

Lynch seemed to think it was a big problem to the point that he was saying that natural selection was being credited with the evolution of complex organisms when it was more the case of non-adaptive forces and he was trying to dispel this myth that natural selection was the cause because it had become such a dominant assumption among mainstream evolution.

The goal here is to dispel a number of myths regarding the evolution of organismal complexity (Table 1). Given that life originated from inorganic matter, it is clear that there has been an increase in phenotypic complexity over the past 3.5 billion years, although long-term stasis has been the predominant pattern in most lineages. What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms.
The frailty of adaptive hypotheses for the origins of organismal complexity

Of Darwin's five points, which is now known to be invalid? None of them are, just as none of Newton's theory of gravitation are known to be invalid. We've added to each of their theories, but their discoveries remain correct.

But things are changing pretty quickly now with new research. We are beginning to formulate a new and more complete understanding of how life changes as referred to with the above article.

As you now see, that's a false assumption. Let's say that there are four salesmen. One of them always sells more than the others. Yet prospects are randomly assigned to them, and the prospects themselves are random with regard to their interest in a particular product. Yet the salesman continues to excel over the others. Because the allocation is random, the need for the product is random, and the skill of the salesman is not random.

Once again I agree with the example but that is not how it works in reality. As mentioned above the ability of natural selection to influence conditions in these situations can be overpowered. So using the salesman example it would be like a percentage of the salesman would have got decided to do their own investigation and bought the product before the salesmen got to the door. Or the customer did not need to be convinced by the salesman's skill because they already seen the value of it from other sources.

Therefore it was not really the salesman skill that made the sale but the ability of the customer to process things themselves. In other words the customer did the selecting and not the salesman. All the salesman did was confirm the already existing process. So to credit the salesman with the sale in the sense that it was his skill and ability is really denying the other forces and being misleading as Lynch as stated.

If they favor certain things, then by definition, not random. However, they are random. We know that favorable and unfavorable mutation appear randomly.

That is really a simplistic view of mutations and one that the adaptive view likes to promote because it helps support Darwinian evolution that uses random mutation to create variation and therefore signifies the power of natural selection. The reality is more and more research is showing that mutations are not so random. They can form around hot spots where other mutations have formed or be biased by other internal mechanisms. In this sense that are directed towards one outcome only and not random outcomes for any location in the genome.

Both arguments ignore significant complications that arise in finite populations, and it is now known that genome composition is governed by biases in mutation and gene conversion, some of which (e.g., mobile-element proliferation) operate via internal drive-like mechanisms (13).

Because the population-level rate of transition from one allelic type to another is equal to the product of the mutation rate and the fixation rate, the ratio of probabilities of being in states A versus a at selection-mutation-drift equilibrium is simply meS (Fig. 1). This simple expression leads to two general conclusions: (i) regardless of the strength of selection, if 1/Ng ≫ |s|, the population will be driven to a state expected under mutation pressure alone; and (ii) the equilibrium composition of a population depends not on the absolute power of mutation, but on the relative rates of forward and reverse mutations (the mutation bias).
The frailty of adaptive hypotheses for the origins of organismal complexity

The emergence of complex organisms must have either happened in small populations or the selective advantage was very strong. This points to non-adaptive forces rather than adaptive ones. A strong selective advantage points to the variation stemming from re-existing mechanisms that produce certain outcomes over others that are well suited to the organism rather that random mechanisms that will not be selectively strong and therefore need natural selection more to sift things out.

But this would also threaten the complex genetic structures that make up complex organisms so it makes more sense that there was a mechanism that helped organisms to change by producing the variation needed that would have been selectively strong and therefore minimizing the role of selection because the selecting was already done.

Did you mean "organismic?" "Orgasmic" refers to something else entirely.

oops lol, yeah I meant organismic complexity.

stems from non-adaptive forces and natural selection plays a minimal role and may even be insufficient.

The paper is also talking about the the mechanisms for producing cellular genetic features at the core of creating complex organisms.

What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms.
The frailty of adaptive hypotheses for the origins of organismal complexity

As Darwin said. New traits arrive randomly. Natural selection is only necessary to favor the useful ones and to remove the harmful ones. That's why his theory was about random change, acted upon by natural selection. All those processes are important in the modern synthesis. [/quote] But it has been shown new traits can arrive non-randomly as well. In fact, what may have been assumed as being the result of random processes may actually come from non-random processes.

Not since Darwin's theory. It's a critical part of Darwinian theory.

Lynch is talking about how mutation, recombination and genetic drift can encourage the fixation of deleterious mutations and discourage beneficial ones. Genetic drift can overpower natural selection and control the direction of evolution.

Second, all four major forces play a substantial role in genomic evolution. It is impossible to understand evolution purely in terms of natural selection, and many aspects of genomic, cellular, and developmental evolution can only be understood by invoking a negligible level of adaptive involvement (12, 13). Because all three nonadaptive forces of evolution are stochastic in nature, this conclusion raises some significant technical challenges. It is tempting to think that stochastic processes have no implications for the direction of evolution. However, the effects of mutation and recombination are nonrandom, and by magnifying the role of chance, genetic drift indirectly imposes directionality on evolution by encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations
The frailty of adaptive hypotheses for the origins of organismal complexity

This has never been observed to be true, except in the trivial sense of each random mutation has a specific selective value. Likewise, the chromosomes from each parent are determined randomly, meaning recombination is also random.

Then why would Lynch mention this as the forces that affects the direction of evolution. I think he knows what he is talking about as he is one of the top population geneticists around.

In fact, genetic drift by definition doesn't put any direction on evolution other than that occurring by chance. Genetic drift is the variation in the relative frequency of different alleles in a small population, due to the random disappearance of those alleles as individuals die or do not reproduce.

according to Lynch it does in an indirect way.

It is tempting to think that stochastic processes have no implications for the direction of evolution. However, the effects of mutation and recombination are nonrandom, and by magnifying the role of chance, genetic drift indirectly imposes directionality on evolution by encouraging the fixation of mildly deleterious mutations and discouraging the promotion of beneficial mutations

Because the population-level rate of transition from one allelic type to another is equal to the product of the mutation rate and the fixation rate, the ratio of probabilities of being in states A versus a at selection-mutation-drift equilibrium is simply meS (Fig. 1). This simple expression leads to two general conclusions: (i) regardless of the strength of selection, if 1/Ng ≫ |s|, the population will be driven to a state expected under mutation pressure alone; and (ii) the equilibrium composition of a population depends not on the absolute power of mutation, but on the relative rates of forward and reverse mutations (the mutation bias).
The frailty of adaptive hypotheses for the origins of organismal complexity

 

[stevevw]

Since it's been directly observed to be non-random, that's not an issue.

The problem is observing what is happening does not differentiate from all the other influences involved. For example, what was thought to be only caused by natural selection in Darwin’s Finches was also caused by developmental processes which altered beaks. Niche construction also had an influence and so did plasticity. Also, inheritance beyond genes can also influence the way the finches make themselves more evolvable. Epigenetic influences can cause genes to be expressed in certain ways because of the environmental pressures the birds were under.

For example, phenotypic plasticity and non-genetic inheritance contributed to the adaptation of the house finch to cold climates during its North American range expansion ([68]; see [27,28,49,101,105,107] for further examples).

For example, the EES predicts that stress-induced phenotypic variation can initiate adaptive divergence in morphology, physiology and behaviour because of the ability of developmental mechanisms to accommodate new environments (consistent with predictions 1–3 and 7 in table 3). This is supported by research on colonizing populations of house finches [68], water fleas [132] and sticklebacks [55,133] and, from a more macro-evolutionary perspective, by studies of the vertebrate limb [57].
http://rspb.royalsocietypublishing.org/content/282/1813/20151019

Researchers have reported cases of cichlid fish, palm trees and finches adapting to different ecological niches and splitting into different species despite living in the same place. In 2008, evolutionary biologist Michael Doebeli of the University of British Columbia (UBC) in Vancouver and colleagues reported that E. coli bacteria can also diversify while sharing a test tube.

The modern variations for Finch beaks relate to the mixing of Finches with those beaks from previous generations through hybridization. So, the genetic info for those beaks was introduced into the gene pool and this is a case of the birds tapping into pre-existing genetic info through developmental processes. These form changes were perhaps triggered by environmental pressure triggering the genes for those beaks shapes to happen through the developmental process.

Evolution of Darwin's finches and their beaks

Or, as Darwin discovered, living things changing their environment. Both are an issue in natural selection.

Except if living things can change their environments then they do not need to be naturally selected. They have selected the conditions themselves that are natural best for them to survive.

This is why some organisms are sexually-reproducing, and some are not. Sexual reproduction is a bad thing from an evolutionary standpoint, because an organism only passes on half of its genes. On the other hand, it's a good thing, since sexually-reproducing populations can more quickly adapt to a changed environment.

Dont forget it is also beneficial in that well a species lives to fight another day

To evolution, not natural selection.

It does in that natural selection is said to be the driving force of evolution and directs evolution.

So Darwin said.

If Darwin agrees with ideas like the EES which makes it more of a complex and widely influence process and makes natural selection less of a force then why do supporters of the Neo-Darwinism and Standard synthesis resist the ideas of the Extended evolutionary synthesis.

So Darwin discovered. It was the subject of his last great paper.

So maybe if he was around long enough he would have probably agreed with the EES. It is much more understood now and Darwin could not have seen what we have discovered today.

That's what the paper was about.

Yes but his theory minimized this influence as far as being an evolutionary force in of itself and a cause of evolution. This is shown by the modern supporters of his theory minimizing niche construction influence.

Contemporary evolutionary biology textbooks support this interpretation (see the electronic supplementary material, table S1). Only selection, drift, gene flow and mutation are consistently described as evolutionary processes and coverage of developmental bias, plasticity, inclusive inheritance and niche construction is at best modest (e.g. [95]) and, more commonly, absent [96,97]. What coverage does occur is typically given the traditional interpretation outlined above.


However, for a second group of evolutionary researchers, the interpretation given in the preceding section underestimates the evolutionary implications of these phenomena (table 2). From this standpoint, too much causal significance is afforded to genes and selection, and not enough to the developmental processes that create novel variants, contribute to heredity, generate adaptive fit, and thereby direct the course of evolution. Under this perspective, the sharp distinction between the proximate and the ultimate is undermined by the fact that proximate causes are themselves often also evolutionary causes [90]. Hence, the EES entails not only new research directions but also new ways to think about, and interpret, new and familiar problems in evolutionary biology.
http://rspb.royalsocietypublishing.org/content/282/1813/20151019

In this case, EES borrowed from Darwinian theory.

No they have interpreted the influence differently and rather than influences like niche construction, inheritance beyond genes and developmental processes being acknowledge yet minimized as evolutionary forces they are shown to be evolutionary causes and influences in directing evolution and often minimizing or excluding the central role of natural selection which has been over emphasized and given the credit when it was more likely other forces like those in the EES that were responsible or also responsible.

In the sense that Newton has become an icon of gravitation or Einstein an icon of relativity. They each did foundational work upon which the work of others depends.

I agree. The central idea of Darwin’s theory is not totally rejected but rather some aspects are reinterpreted.

 

[FEZZILLA]

Can someone please explain to me what Theistic Evolution is. Are there different versions of this. If Theistic Evolution is just the world view version of evolution with God thrown in as the initiator of life then what is the difference between Theistic Evolution and the world view version. Isn't this just reducing Gods role down to abiogenesis which is not really a part of evolution anyway as evolution begins at the point the first single living cell is in existence already? If Theistic evolution starts after God created the first single-celled life then there is no need to include God at all as this is irrelevant to evolution.

"In the beginning, God created the heavens and the earth" (Genesis 1:1).

 

[The Barbarian]

The problem is observing what is happening does not differentiate from all the other influences involved. For example, what was thought to be only caused by natural selection in Darwin’s Finches was also caused by developmental processes which altered beaks.

Which developmental processes, and what makes you think that they weren't affected by natural selection? Do you have a cite?

For example, phenotypic plasticity and non-genetic inheritance contributed to the adaptation of the house finch to cold climates during its North American range expansion ([68]; see [27,28,49,101,105,107] for further examples).

From your link:
For instance, some more implicit features of contemporary evolutionary thought, such as the assignment of causal and informational privileges to genes in development, or the treating of development and heredity as separate phenomena, remain prevalent in spite of new data that appear to challenge these assumptions

The modern variations for Finch beaks relate to the mixing of Finches with those beaks from previous generations through hybridization. So, the genetic info for those beaks was introduced into the gene pool and this is a case of the birds tapping into pre-existing genetic info through developmental processes. These form changes were perhaps triggered by environmental pressure triggering the genes for those beaks shapes to happen through the developmental process.

Evolutionary Development fits nicely into the Modern Synthesis; the evidence for the evolution of homobox genes shows that they evolved over time by natural selection. The idea of evolution itself changing over time is not new, either. Evolvability was discussed by Gould in a number of papers. He mentions it in Wonderful Life.

Except if living things can change their environments then they do not need to be naturally selected.

They are naturally selected. The Darwinian notion of "environment affects life, and life affects environment" is precisely what is happening.

They have selected the conditions themselves that are natural best for them to survive.

However, brown bears and polar bears were affected by their environments more than they affected the environments. Which is why they are two different species, and why there is legitimate concern that as the arctic warms up, hybridization may eventually eliminate polar bears as a species. That process is already underway, as hybrids are now turning up in the wild.

This is why some organisms are sexually-reproducing, and some are not. Sexual reproduction is a bad thing from an evolutionary standpoint, because an organism only passes on half of its genes. On the other hand, it's a good thing, since sexually-reproducing populations can more quickly adapt to a changed environment.

Yes. This is true. Environment no doubt was important in the evolution of sexual reproduction. But if selective factors are strong enough, that can be reversed. Whiptail lizards, for example, have no males.

It does in that natural selection is said to be the driving force of evolution and directs evolution.

Random mutation and nattural selection determine evolution often. But a long time ago, Motoo Kimura showed how neutral mutations affect evolutionary history as well. And as you and Darwin know, organisms also push back against the environment, and affect their own evolution.

If Darwin agrees with ideas like the EES which makes it more of a complex and widely influence process and makes natural selection less of a force then why do supporters of the Neo-Darwinism and Standard synthesis resist the ideas of the Extended evolutionary synthesis.

So Darwin discovered. It was the subject of his last great paper.

So maybe if he was around long enough he would have probably agreed with the EES. It is much more understood now and Darwin could not have seen what we have discovered today.

I'm sure the addition of genetics would have pleased him greatly. Genetics cleared up a difficult problem with his theory that he could not explain.

Gould wrote about this. He disagreed with strict selectionists like Dawkins. I would think that he was part of the EES movement, since Gould and Eldredge brought us punctuated equilibrium. He still considered himself an "orthodox Darwinian" however.

And his acknowledgement of contingency as a factor in evolution seems to fit nicely into the standard EES.

Yes but his theory minimized this influence as far as being an evolutionary force in of itself and a cause of evolution.

His theory also minimized rapid evolutionary change, and neglected genetic drift. And there were Darwinians like Huxley who disagreed with Darwin on this point. Darwinians have since incorporated those into the Modern Synthesis.

This is shown by the modern supporters of his theory minimizing niche construction influence.

The existence of genes was at one time controversial, as was the notion of rapid evolution. If research validates new theories, they will be incorporated into evolutionary theory as genetic drift and punctuated equilibrium have been.

Barbarian observes:
In this case, EES borrowed from Darwinian theory.

No they have interpreted the influence differently and rather than influences like niche construction, inheritance beyond genes and developmental processes being acknowledge yet minimized as evolutionary forces they are shown to be evolutionary causes and influences in directing evolution and often minimizing or excluding the central role of natural selection which has been over emphasized and given the credit when it was more likely other forces like those in the EES that were responsible or also responsible.

The first cited example of niche construction in this article:
Niche construction - Wikipedia

Is Darwin's work on earthworms.

Barbarian observes:
In the sense that Newton has become an icon of gravitation or Einstein an icon of relativity. They each did foundational work upon which the work of others depends.

I agree. The central idea of Darwin’s theory is not totally rejected but rather some aspects are reinterpreted.

Which of Darwin's five points are no longer accepted?

 

[The Barbarian]

stevevw said: ↑
Can someone please explain to me what Theistic Evolution is. Are there different versions of this. If Theistic Evolution is just the world view version of evolution with God thrown in as the initiator of life then what is the difference between Theistic Evolution and the world view version. Isn't this just reducing Gods role down to abiogenesis which is not really a part of evolution anyway as evolution begins at the point the first single living cell is in existence already? If Theistic evolution starts after God created the first single-celled life then there is no need to include God at all as this is irrelevant to evolution.

I don't use the term much, precisely because it's kind of vague. But I suppose it's acceptance of the fact of evolution, with the realization that God is ultimately the cause of evolution.

Deists part with theists in that deists think God made everything and then walked away to let it go. Theists believe that God remains intimately involved with His creation, and to various degrees ascribe the evolution of living things to His involvement.

 

[stevevw]

I don't use the term much, precisely because it's kind of vague. But I suppose it's acceptance of the fact of evolution, with the realization that God is ultimately the cause of evolution.

Deists part with theists in that deists think God made everything and then walked away to let it go. Theists believe that God remains intimately involved with His creation, and to various degrees ascribe the evolution of living things to His involvement.

I am glad you mention this as I felt the debate was going in the wrong direction. I wanted to talk about Theistic evolution more from a philosophical point of view rather than debating about whether evolution is correct or not. That can be done on the other site we were debating. We have to assume evolution is assumed to be true because of theistic supporters whether a person believes this or not and this should not be debated.

What I have found though is there are many versions of theistic evolution which can range from the Deists position to a Darwinian position so it is not so straight forward. according to Wikipedia
Theistic evolution is not in itself a scientific theory, but a range of views about how the science of general evolution relates to religious beliefs in contrast to special creation views.

The executive director of the National Center for Science Education in the United States of America, Eugenie Scott, has used the term to refer to the part of the overall spectrum of beliefs about creation and evolution holding the theological view that God creates through evolution. It covers a wide range of beliefs about the extent of any intervention by God, with some approaching deism in rejecting the concept of continued intervention.


Just as different types of evolutionary explanations have evolved, so there are different types of theistic evolution. Creationists Henry M. Morris and John D. Morris, point out that there are different terms which have been used to describe different positions: "Orthogenesis" (goal-directed evolution), "nomogenesis" (evolution according to fixed law), "emergent evolution", "creative evolution", and others".[5]
Theistic evolution - Wikipedia

So it seems it is about how religious belief fits in with evolution and not so much about evolution theory itself which says more about faith than science. I can also see how some can associate how scientific evidence showing how living things may have inbuilt mechanisms that can produce predetermined outcomes makes sense to theistic evolution. For me, this is the position I take as I find it hard to understand how God did not provide a way for life to live on planet earth that he intended from the beginning. As the bible says

Colossians 1,17
And He is before all things, and in Him all things hold together.

So my question is more about how do believers in God reconcile the traditional Darwinian view of evolution with their beliefs. The Catholic church is the biggest supporter of evolution as a religion and supports Theistic evolution but when pressed as to the detail about how this happened many do not know, they just support evolution. This to me seems to be based on almost as much faith as their belief in God when perhaps it should not be because they are more or less proclaiming that they are also taking a scientific position and therefore should understand the premise for their position.

But if they take the Darwinist view of evolution they have to also accept all the theory including its evidence about human behaviour and how belief itself is an evolutionary thought which is associated with the evolution of the brain and conceptual thinking. According to evolution religious thought and belief in the supernatural are not really based on the reality of their being a God. It is just an evolved way of thinking. That makes the idea of Theistic evolution as just an extension of the evolution of religion and a way of trying to make it fit in with the mainstream thinking.

The Origins of Religion: How Supernatural Beliefs Evolved
There are many theories as to how religious thought originated. But two of the most widely cited ideas have to do with how early humans interacted with their natural environment,

In short, HADD is the mechanism that lets humans perceive that many things have "agency," or the ability to act of their own accord. This understanding of how the world worked facilitated the rapid decision-making process that humans had to go through when they heard a rustling in the grass. (Lions act of their own accord. Better run.)

But in addition to helping humans make rational decisions, HADD may have planted the seeds for religious thought. In addition to attributing agency to lions, for example, humans started attributing agency to things that really didn't have agency at all.
The Origins of Religion: How Supernatural Beliefs Evolved

So according to the same evolutionary theory belief in God or gods is just a way of attributing agency to something that has no basis.

 

[The Barbarian]

I am glad you mention this as I felt the debate was going in the wrong direction. I wanted to talk about Theistic evolution more from a philosophical point of view rather than debating about whether evolution is correct or not. That can be done on the other site we were debating. We have to assume evolution is assumed to be true because of theistic supporters whether a person believes this or not and this should not be debated.

What I have found though is there are many versions of theistic evolution which can range from the Deists position to a Darwinian position so it is not so straight forward. according to Wikipedia
Theistic evolution is not in itself a scientific theory, but a range of views about how the science of general evolution relates to religious beliefs in contrast to special creation views.

So my question is more about how do believers in God reconcile the traditional Darwinian view of evolution with their beliefs. The Catholic church is the biggest supporter of evolution as a religion

No. For the Catholic Church, it's an open question, which each believer can decide for himself. One may be an YE creationist, and remain a perfectly orthodox Roman Catholic. The only caveat the church offers is that one may not hold that all of this was not the creation of God, however He might have done it.

Cardinal Ratzinger, later Pope Benedict XIV, was expressing his opinion as to evolution of all life being "virtually certain", but that is not doctrine. Even if he had expressed that after becoming pope, it would not have been doctrine. That has to be given ex cathedra, to be so.

and supports Theistic evolution but when pressed as to the detail about how this happened many do not know, they just support evolution.

No. The document notes the evidence:
According to the widely accepted scientific account, the universe erupted 15 billion years ago in an explosion called the “Big Bang” and has been expanding and cooling ever since. Later there gradually emerged the conditions necessary for the formation of atoms, still later the condensation of galaxies and stars, and about 10 billion years later the formation of planets. In our own solar system and on earth (formed about 4.5 billion years ago), the conditions have been favorable to the emergence of life. While there is little consensus among scientists about how the origin of this first microscopic life is to be explained, there is general agreement among them that the first organism dwelt on this planet about 3.5-4 billion years ago. Since it has been demonstrated that all living organisms on earth are genetically related, it is virtually certain that all living organisms have descended from this first organism. Converging evidence from many studies in the physical and biological sciences furnishes mounting support for some theory of evolution to account for the development and diversification of life on earth, while controversy continues over the pace and mechanisms of evolution. While the story of human origins is complex and subject to revision, physical anthropology and molecular biology combine to make a convincing case for the origin of the human species in Africa about 150,000 years ago in a humanoid population of common genetic lineage. However it is to be explained, the decisive factor in human origins was a continually increasing brain size, culminating in that of homo sapiens. With the development of the human brain, the nature and rate of evolution were permanently altered: with the introduction of the uniquely human factors of consciousness, intentionality, freedom and creativity, biological evolution was recast as social and cultural evolution.
INTERNATIONAL THEOLOGICAL COMMISSION
COMMUNION AND STEWARDSHIP:
Human Persons Created in the Image of God

This to me seems to be based on almost as much faith as their belief in God when perhaps it should not be because they are more or less proclaiming that they are also taking a scientific position and therefore should understand the premise for their position.

And as you see, that is what the commission cites. Keep in mind, this is a report based on the work of scientists, in describing how nature reflects creation by God.

But if they take the Darwinist view of evolution they have to also accept all the theory including its evidence about human behaviour and how belief itself is an evolutionary thought which is associated with the evolution of the brain and conceptual thinking.

As Pope John Paul II wrote, the mind is not merely an epiphenomenon of the brain. That might be one of the things it is, but it is not only that. Keep in mind, the understanding that there is a unity of body and soul in us which remains a mystery, one that science can't solve.

According to evolution religious thought and belief in the supernatural are not really based on the reality of their being a God.

In the same sense that geology and chemistry are not really based on the reality of God.

It is just an evolved way of thinking. That makes the idea of Theistic evolution as just an extension of the evolution of religion and a way of trying to make it fit in with the mainstream thinking.

As the Cardinal wrote, facts matter. As John Paul II wrote, "truth cannot contradict truth."

The Origins of Religion: How Supernatural Beliefs Evolved

There are many theories as to how religious thought originated. But two of the most widely cited ideas have to do with how early humans interacted with their natural environment,

Romans 1:20 For the invisible things of him, from the creation of the world, are clearly seen, being understood by the things that are made; his eternal power also, and divinity: so that they are inexcusable.

In short, HADD is the mechanism that lets humans perceive that many things have "agency," or the ability to act of their own accord. This understanding of how the world worked facilitated the rapid decision-making process that humans had to go through when they heard a rustling in the grass. (Lions act of their own accord. Better run.)

But in addition to helping humans make rational decisions, HADD may have planted the seeds for religious thought. In addition to attributing agency to lions, for example, humans started attributing agency to things that really didn't have agency at all.

In other words, our natural creation predisposed us to seek God. Lucky for us, um?

So according to the same evolutionary theory belief in God or gods is just a way of attributing agency to something that has no basis.

No. Evolutionary theory makes no such claims. Can't. Science can't even comment on the supernatural. And apes and zebras and so on, also attribute agency to things. Yet they seem to have no concept of God.

 

[stevevw]

No. For the Catholic Church, it's an open question, which each believer can decide for himself. One may be an YE creationist, and remain a perfectly orthodox Roman Catholic. The only caveat the church offers is that one may not hold that all of this was not the creation of God, however He might have done it.

Cardinal Ratzinger, later Pope Benedict XIV, was expressing his opinion as to evolution of all life being "virtually certain", but that is not doctrine. Even if he had expressed that after becoming pope, it would not have been doctrine. That has to be given ex cathedra, to be so.

That's interesting as when I debate people some use the Catholic Church as an example of support for evolution giving the impression that if you are Catholic then you support evolution. Whereas in reality there may be a mixture of beliefs including some who reject evolution or support God-guided evolution or a number of other mixtures of views.

No. The document notes the evidence:
According to the widely accepted scientific account, the universe erupted 15 billion years ago in an explosion called the “Big Bang” and has been expanding and cooling ever since. Later there gradually emerged the conditions necessary for the formation of atoms, still later the condensation of galaxies and stars, and about 10 billion years later the formation of planets. In our own solar system and on earth (formed about 4.5 billion years ago), the conditions have been favorable to the emergence of life. While there is little consensus among scientists about how the origin of this first microscopic life is to be explained, there is general agreement among them that the first organism dwelt on this planet about 3.5-4 billion years ago. Since it has been demonstrated that all living organisms on earth are genetically related, it is virtually certain that all living organisms have descended from this first organism. Converging evidence from many studies in the physical and biological sciences furnishes mounting support for some theory of evolution to account for the development and diversification of life on earth, while controversy continues over the pace and mechanisms of evolution. While the story of human origins is complex and subject to revision, physical anthropology and molecular biology combine to make a convincing case for the origin of the human species in Africa about 150,000 years ago in a humanoid population of common genetic lineage. However it is to be explained, the decisive factor in human origins was a continually increasing brain size, culminating in that of homo sapiens. With the development of the human brain, the nature and rate of evolution were permanently altered: with the introduction of the uniquely human factors of consciousness, intentionality, freedom and creativity, biological evolution was recast as social and cultural evolution.
INTERNATIONAL THEOLOGICAL COMMISSION
COMMUNION AND STEWARDSHIP:
Human Persons Created in the Image of God
And as you see, that is what the commission cites. Keep in mind, this is a report based on the work of scientists, in describing how nature reflects creation by God.

It is interesting that they do not go into the emergence of Adam and Eve and how this fits in with how sin and death entered into humanity. I appreciate that this is the Church's position but I was referring to individual lay people. The above statement gives a broad explanation but lacks detail and I would say most would not understand evolution enough that they feel confident that it is correct so therefore will be trusting what others say like the church for their position.

As Pope John Paul II wrote, the mind is not merely an epiphenomenon of the brain. That might be one of the things it is, but it is not only that. Keep in mind, the understanding that there is a unity of body and soul in us which remains a mystery, one that science can't solve.

Yes and this is what some say about consciousness that it is something beyond the physical brain just as some say the soul is something beyond the physical body.

In the same sense that geology and chemistry are not really based on the reality of God.

So I guess there is a limit to where science can occupy in religious thought and belief. Though some want to try and find ways in how divine concepts can be related to natural phenomenon through science. I find this interesting but at the end of the day, there are limits to what science can know about religious thought and belief. Science asks how and religion asks why.

Romans 1:20 For the invisible things of him, from the creation of the world, are clearly seen, being understood by the things that are made; his eternal power also, and divinity: so that they are inexcusable.

In other words, our natural creation predisposed us to seek God. Lucky for us, um?

I've always thought this was about how we can see Gods creative ability in his creation. Though we tend to think of it as nature and many attributes everything to mother nature we can see that there is some agent behind things that have ability beyond what we can comprehend.

No. Evolutionary theory makes no such claims. Can't. Science can't even comment on the supernatural. And apes and zebras and so on, also attribute agency to things. Yet they seem to have no concept of God.

Yes that is what I mean, according to evolution just like the animals we attribute agency to things and this accounts for why we have religious belief and not the fact that there is any God to believe in. They attempt to give a naturalistic explanation as to why people believe in God.