Science and Human Origins conclusion: It IS possible we came from just two parents

CLAVDIVS- Design explains the origin of life. And you have no idea what you are even saying. It's as if you are just posting to post. You keep asking for an alternative yet your scenario is a non-starter. Joe

Joe @ 106 Thanks for bothering some more :-)

In YOUR scenario organs and nerves did NOT exist in the first population(s). So how the heck did ordinary means of reproduction create and knit them into organisms? You keep forgetting to tell us that. Also ordinary means of reproduction requires exiisting living organisms so it cannot explain them, duh.

Okay -- My scenario doesn't explain the origin of life and neither does yours, right? So we're both on the same footing there, right? We just have to both acknowledge we don't know where the original organism/s came from, just like everybody else on the planet, although I have already granted to you that however first life came about it involved intelligent design. What I'm saying is, subsequent to the origin of life, we've got a pattern of similarities and differences that is explained by common design + common descent. Design explains the telic nature of body plans and descent (biological reproduction) explains the mechanism for how organisms are constructed according to the designer's plan. Do you agree with this theory? If not, what is your alternative explanation for how organisms are constructed according to the designer's plan? If your answer is "I don't have an alternative explanation", that's fine, please just say so. Cheers CLAVDIVS

CLAVDIVS- In YOUR scenario organs and nerves did NOT exist in the first population(s). So how the heck did ordinary means of reproduction create and knit them into organisms? You keep forgetting to tell us that. Also ordinary means of reproduction requires exiisting living organisms so it cannot explain them, duh. And as I told you, science is what we use to help us figure out how the designer did it. As I said you are ignoring what I post and prattling on like a little child despite yourself. From comment 100: As I have been saying, CLAVDIVS, figuring out how to ancients constructed structures that are allegedly within our capability is proving to be difficult. Seeing that the design of living organisms is well beyond our capability it is going to be even more difficult. That said a targeted search could be used. Joe

Joe @ 104

Common Design is NOT Common Descent- you have design and common descent but Common Design is an alternative to UCD that explains the same evidence. But as I said you have ignored too much of what I have posted so I am not going to bother any more.

Seriously, Joe, I have spelled it out for you at a kindergarten level and you're still not getting it. Of course common design is not common descent - that's why my theory has two parts (i) common design and (ii) common descent. You say common design is an alternative to common descent. So your theory has a common designer who designs body plans etc. but who doesn't use the processes of common descent to actually assemble the physical bodies of organisms, right? That's what you're saying. So, my question is - for what must be the 5th time - on your theory, how does the common designer actually physically implement the body plans? It's one thing to design something in your mind, or on paper; it's another thing entirely to actually construct something out of physical materials. Your theory has got the design part (just like mine) but it's lacking the construction part. That's what I've been saying all along -- there's only one empirically confirmed process, based on uniform experience, that even comes close to the capability of constructing living organisms, and that's the process of common descent via ordinary reproduction. It doesn't necessarily have to be unguided and it doesn't necessarily have to be universal. Your inability to describe any alternative, even in broad outline, really makes it clear that your position doesn't measure up to the standards of objective, empirical reasoning. So thanks, and cheers. CLAVDIVS

CLAVDIVS- Common Design is NOT Common Descent- you have design and common descent but Common Design is an alternative to UCD that explains the same evidence. But as I said you have ignored too much of what I have posted so I am not going to bother any more. Joe

Joe @ 102

ID is OK with UCD but a Common Design explains the SAME evidence without UCD.

Great, we agree common descent does not contradict ID. You can have a theory of common design + common descent, without contradiction. But what I have been asking and asking but you have never answered is: What's your alternative theory to common design + common descent. You keep answering 'common design' which is already part of my theory, so all you are really saying is you agree with part of my theory, without ever putting forward any alternative theory of your own. If you're going to explain biological origins you'll need to explain at least two things: (i) the telic arrangement of body plans; and (ii) the mechanism by which organisms are physically assembled. In my theory, (i) common design explains the telic arrangement of body plans, and (ii) common descent is the mechanism by which organisms are physically assembled. What you have never yet done is give us your alternative for (ii) the mechanism by which organisms are physically assembled. We already agree on (i), so there's no need to keep repeating it. What we want to hear is Joe's explanation for (ii).

And how do you know universal common descent explains the pattern you imagine you see?

Well, Joe, in terms of hypothesis testing it actually makes a difference whether you have a viable alternative hypothesis or not, in terms of the statistical methods to be used. Which is why I've been asking for the alternative. In any case, the hierarchical pattern of similarities and differences between organisms is not imaginary but can in fact be rigorously established by statistical methods. It can also be strongly inferred from statistical, genetic and fossil evidence that the pattern observed is due to common ancestry. One key argument, for example, is that common descent is a branching process, and a hierarchy of groups-within-groups, which is the observed pattern amongst organisms, is the mathematically necessary result of a branching process. I know you don't appear to agree with this line of reasoning (which is a puzzle because you acknowledge common descent is compatible with ID, so, I ask, where's the beef?) -- but I put that down to your selective hyperskepticism, because the inference is based on standard statistical techniques that apply equally across engineering and medicine as well a biology. So my question still stands: If you don't accept common design + common descent, what is your alternative? Cheers CLAVDIVS

CLAVDIVS- I am the result of common descent from my ancestors, all iof which were HUMAN. Also it has been clear for ages that universal common descent did not, ever, contradict ID. ID is OK with UCD but a Common Design explains the SAME evidence without UCD. And how do you know universal common descent explains the pattern you imagine you see? But anyway you are ignoring my posts so good luck with ever producing any evidence to support your imagination. Joe

Joe @ 100

CLAVDIVS: What I’m saying is that the designer could have made use of the process of biological reproduction, by influencing or directing, for example, intergenerational variation over many generations in an incremental, branching manner. The reason I suggest this is because it matches the pattern of morphological and genetic evidence that we can observe. JOE: Yes, that is a possibilty. I have asked you how you test it to the exclusion of others that explain the same evidence and could produce the same pattern, and you have refused to answer.

Finally, something we can agree upon -- directed variation over many generations in an incremental, branching manner i.e. common descent, is a possibility. In other words, common descent does not necessarily contradict intelligent design. You ask: How do we test common descent "to the exclusion of other[ theories] that explain the evidence and produce the same pattern."? Any my question to you -- which I have been asking all along and which, by the way, I asked first -- is what other theories explain the evidence and produce the same pattern? Please don't just answer 'common design' because my proposed theory of guided common descent already includes common design operating alongside and through the process of common descent. Your answer would have to be something like: "Another theory that explains the evidence and patterns is common design operating alongside and through X" <-- "X" being the part that needs to be filled in by you. Knowing the alternative X, if there is one, makes a difference to the kind of empirical test required to answer your question. CLAVDIVS

CLAVDIVS:

Thinking about the cetaceans and ilk — like pakicetus, ambulocetus, kutchicetus, dolphins etc. — where did their physical bodies come from?

It is a loaded question as I do not accept pakicetus nor ambulocetus as being cetaceans.

The question is about the actual physical process by which the organisms’ physical bodies were constructed. Saying ‘design’ and ‘body plan’ doesn’t tell us anything about this process.

That is what science is for. If we knew all the answers we wouldn't need science, would we? As I have been saying, CLAVDIVS, figuring out how to ancients constructed structures that are allegedly within our capability is proving to be difficult. Seeing that the design of living organisms is well beyond our capability it is going to be even more difficult. That said a targeted search could be used.

What I’m saying is that the designer could have made use of the process of biological reproduction, by influencing or directing, for example, intergenerational variation over many generations in an incremental, branching manner. The reason I suggest this is because it matches the pattern of morphological and genetic evidence that we can observe.

Yes, that is a possibilty. I have asked you how you test it to the exclusion of others that explain the same evidence and could produce the same pattern, and you have refused to answer.

If you don’t agree with this suggestion, then what is your alternative for how the physical bodies of organisms like the cetaceans originated?

Alternative to what? You ignored just about everything I posted- Ordinary means of reproduction does not explain the differences observed. That means that there isn't any genetic nor morphological evidence that puts Pakicetus with cetaceans. as Ordinary means of reproduction does not explain the differences observed. So again I ask, alternative to what? Your imagination? Joe

Joe @ 98 Do you not understand the question, Joe? Or is it just that you don't want to answer it? Here it is again: Thinking about the cetaceans and ilk -- like pakicetus, ambulocetus, kutchicetus, dolphins etc. -- where did their physical bodies come from? The closest you came to answering this was to say "As far as anyone knows their body plans came from the designer(s)". But I've already stipulated that a designer was involved in the process. The question is about the actual physical process by which the organisms' physical bodies were constructed. Saying 'design' and 'body plan' doesn't tell us anything about this process. Did the designer assemble every single organism atom by atom, like lego? Or something else? What I'm saying is that the designer could have made use of the process of biological reproduction, by influencing or directing, for example, intergenerational variation over many generations in an incremental, branching manner. The reason I suggest this is because it matches the pattern of morphological and genetic evidence that we can observe. If you don't agree with this suggestion, then what is your alternative for how the physical bodies of organisms like the cetaceans originated? Cheers CLAVDIVS

CLAVDIVS:

Where did various organisms come from, if not by ordinary reproduction from ancestors?

Right humans gave rise to other humans, chimps gave rise to other chimps.

Take the cetacea and their ancestors, such as pakicetus, ambulocetus, kutchicetus, rodhocetus, basilosaurus, durodon, and the extant cetacea like dolphins.

Only wishful thinking places Pakicetus with cetaceans. The same goes for Ambulocetus.

Common descent claims that the pattern of similarities and differences between these organisms shows that they descended from a common ancestor with variations – which we have stipulated to be designed – stacking up and branching out over many generations.

Common descent can claim all it wants. It can live with just about any pattern and imagination will fill in the branches.

If you don’t think these organisms are descended from a common ancestor, by ordinary means of reproduction, then where did their bodies come from?

Ordinary means of reproduction does not explain the differences observed. And you said we weren't talking about origins. As far as anyone knows their body plans came from the designer(s)- no one knows what determines a body plan. So how can we test that changes to their genomes produced the alleged transformations required? What makes an eye a human eye as opposed to a chimp eye? Is a human eye a trait? Or is it just the happenstance outcome of some certain combination of biochemistry? How can we test your common descent scenario to the exclusion of the other alternatives- design, special creation and convergence? Joe

Joe @ 95

CLAVDIVS: Let’s just stipulate, for the sake of this discussion, that evolution operates under common design and/or convergence. How does that affect the conclusion of common ancestry? JOE: That conclusion could be wrong. Ya see common design and convergence explain the same evidence. CLAVDIVS: We observe similar, but not identical, species. They had to come from somewhere — they didn’t just spontaneously assemble out of raw atoms, right? JOE: No one knows how organisms originated. The Origin of Species did not cover the ORIGIN of species.

Joe, we're still dancing around the point of common descent. Let's get origin of life, common design and/or convergence off the table, and grant to you - just for purposes of this discussion - that the origin of life and its subsequent development required intelligent design. Now the question that remains is: Where did various organisms come from, if not by ordinary reproduction from ancestors? Take the cetacea and their ancestors, such as pakicetus, ambulocetus, kutchicetus, rodhocetus, basilosaurus, durodon, and the extant cetacea like dolphins. Common descent claims that the pattern of similarities and differences between these organisms shows that they descended from a common ancestor with variations - which we have stipulated to be designed - stacking up and branching out over many generations. If you don't think these organisms are descended from a common ancestor, by ordinary means of reproduction, then where did their bodies come from? We know they existed - we have the fossilised remains - so they must have come from somewhere. We know the atoms in their bodies did not spontaneously assemble by accident, because its too unlikely. So if you don't accept common descent with designed variation, then what is your alternative? How did the atoms and molecules that make up these dolphin-like organisms come to be assembled together, if not by ordinary biological reproduction? Cheers CLAVDIVS

The book cometh, finally... Joe

CLAVDIVS:

Let’s just stipulate, for the sake of this discussion, that evolution operates under common design and/or convergence. How does that affect the conclusion of common ancestry?

That conclusion could be wrong. Ya see common design and convergence explain the same evidence.

We observe similar, but not identical, species. They had to come from somewhere — they didn’t just spontaneously assemble out of raw atoms, right?

No one knows how organisms originated. The Origin of Species did not cover the ORIGIN of species.

Where did the organisms’ bodies and organs and nerves come from, if not from the ordinary process of reproduction?

Prokaryotes don't have them- organs nor nerves. And there still isn't any evidence that a prokaryote can evolve into something other than a prokaryote so that would be a huge problem for your scenario. It would make it a non-starter, uniformitarianism and all.

This doesn’t make logical sense to me. The whole point of uniformitarianism is extrapolation.

Your position doesn't have anything to extrapolate from. Joe

paulmc:

The nearly neutral theory is now 40 years old and models the limits of purifying selection in small populations.

So what? It sure as heck dioesn't support the evolution of humans from knuckle-walkers. Nothing you have posted supports that.

So you reject this study solely on the basis that it is laboratory-based,

I didn't reject anything. Obviously you have other issues. But anyway 600 generations plus- put that in perspective of chimps and humans. Do the math and you lose. Joe

Joe @ 88

CLAVDIVS: Exactly, and that is why we don’t need to personally observe macro-evolution, we can infer it from the evidence left behind. JOE: And I can use that same evidence to support and common design and/ or convergent evolution.

Please try to pay attention, Joe. We're discussing common descent. Let's just stipulate, for the sake of this discussion, that evolution operates under common design and/or convergence. How does that affect the conclusion of common ancestry? We observe similar, but not identical, species. They had to come from somewhere -- they didn't just spontaneously assemble out of raw atoms, right? So what's the only empirically confirmed process we know of that can create organisms? It's biological reproduction, right? Perhaps you're correct that it's guided or front-loaded or whatever. But, even so, it's clear from the pattern of similarities and differences between organisms, and from our uniform empirical experience, that most were descended from common ancestors via ordinary reproduction. What's the alternative? Where did the organisms' bodies and organs and nerves come from, if not from the ordinary process of reproduction?

JOE: And given uniformitarianism, the processes of today cannot be extrapolated to produce the changes required.

This doesn't make logical sense to me. The whole point of uniformitarianism is extrapolation. Cheers CLAVDIVS

Yet some persist- not so purifying after all.

Is that meant to be some sort of a revelation? This is a well-studied area and we understand the probability of fixation and extinction of different mutations, given their fitness coefficients, rather well. The nearly neutral theory is now 40 years old and models the limits of purifying selection in small populations. So what, if anything, is your point?

Sorry, meant to say 1000, but his populations fix due to artificial selection, ie design.

Right. So you reject this study solely on the basis that it is laboratory-based, while uncritically accepting the laboratory-based example of Burke et al. (2010) that you give in your next sentence. If everything else was the same except that Burke happened to identify a hard selective sweep in their Drosophila populations, you would be rejecting that paper too, even though nothing in their methods would have changed.

Burke, M. K. et al. 2010. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature. 467 (7315): 587-590

Burke et al. didn't observe fixation of any newly arising mutations in 600 generations, which implies that strongly selected variants were rare so no immediately arising mutations caused a hard selective sweep. This absolutely doesn't mean fixation doesn't happen - as they state, 600 generations may have been insufficient for fixation, and they did detect evidence consistent with incomplete sweeps. paulmc

paulmc:

Yes, it was made up to describe the phenomenon of the bias against reproductive success of deleterious alleles.

Yet some persist- not so purifying after all.

Because I know you only accept direct observations rather than inferences when it comes evolution, let’s take an obvious example. Do you think that Lenski’s E. coli populations are larger than 100 or not?

Sorry, meant to say 1000, but his populations fix due to artificial selection, ie design.

Could you elaborate on who ‘they’ were? Also, how many generations? What population size? What fitness effects of the mutations?

5.Burke, M. K. et al. 2010. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature. 467 (7315): 587-590 Joe

Joe:

“Purifying slection” is a made-up term.

Yes, it was made up to describe the phenomenon of the bias against reproductive success of deleterious alleles.

They [mutations] can [fix] in a design and/ or severe bottle-neck scenario. But once population size > 100, all bets are off.

Because I know you only accept direct observations rather than inferences when it comes evolution, let's take an obvious example. Do you think that Lenski's E. coli populations are larger than 100 or not?

As I said there are experiments with fruit-flies under controlled lab conditions and they couldn’t get fixation.

Could you elaborate on who 'they' were? Also, how many generations? What population size? What fitness effects of the mutations? paulmc

CLAVDIVS:

It’s obvious you have no explanation for the pattern of similarities and differences amongst organisms, and your entire argument against common descent consists of substanceless, hyperskeptical, reflexive nay-saying.

Common design and/ or convergence explains the similarities and differences amongst organisms. For example building codes make sure that houses are similar on some level- the basic structure, stud spacing, joist spacing, rafter spacing- and personal touches of the developer makes the difference- different demands. Then there are computers and there peripheral devices- have to have common communication ports. And if the devices have a micro then there would be some common design there too. The differences would be due to the different functions.

So how does evolution theory explain how organs are produced and knit together into a living organism? Well, of course, by means of biological reproduction which is a well understood and empirically confirmed process that can make new organisms.

Umm biological reproduction requires existing organisms complete with organs that are already knitted together. IOW CLAV, that was more than a tad dishonest as you do not get to use what requires an explanation in the first place. Joe

CLAVDIVS:

Exactly, and that is why we don’t need to personally observe macro-evolution, we can infer it from the evidence left behind.

And I can use that same evidence to support and common design and/ or convergent evolution. And given uniformitarianism, the processes of today cannot be extrapolated to produce the changes required. Joe

OK PaulMC- what is the testable hypothesis for humans evolving from knuckle-walkers via accumulations of random mutations?

You earlier stated that you don’t even accept that there is evidence for purifying selection acting on deleterious mutations,

"Purifying slection" is a made-up term.

or that mutations can fix in a population.

They can in a design and/ or severe bottle-neck scenario. But once population size > 100, all bets are off. As I said there are experiments with fruit-flies under controlled lab conditions and they couldn't get fixation. So add in a changing environment and you should see the problem. Cooperation really fights against fixation also as mildly deletrious traits that would be eliminated can get passed on.

With this level of denial, there is no possibility that we can discuss hominin evolution meaningfully.

Given your inability to produce a testable hypothesis for your position, there isn't anything to discuss. I smell chicken... Joe

Joe @ 83

PAULMC: Actually, much of science is about inferences made from evidence other than direct observations. JOE: Exactly and that is why we don’t need to see the designer, we can infer one existed due to the evidence left behind.

Exactly, and that is why we don't need to personally observe macro-evolution, we can infer it from the evidence left behind. Plus there's a complete absence of any other empirically confirmed explanation based on uniform experience. Cheers CLAVDIVS

Joe @ 80

CLAVDIVS: What is the empirically confirmed process by which ‘design’ produces organs and nerves and knits them into a living thing? JOE: What is the empirically confirmed process by which ‘common descent’ produces organs and nerves and knits them into a living thing? Why don’t you answer that?

And you've ducked the question again. It's obvious you have no explanation for the pattern of similarities and differences amongst organisms, and your entire argument against common descent consists of substanceless, hyperskeptical, reflexive nay-saying. So how does evolution theory explain how organs are produced and knit together into a living organism? Well, of course, by means of biological reproduction which is a well understood and empirically confirmed process that can make new organisms. So what process, other than biological reproduction, does your 'design' hypothesis propose? Cheers CLAVDIVS

OK PaulMC- what is the testable hypothesis for humans evolving from knuckle-walkers via accumulations of random mutations?

You earlier stated that you don't even accept that there is evidence for purifying selection acting on deleterious mutations, or that mutations can fix in a population. With this level of denial, there is no possibility that we can discuss hominin evolution meaningfully. paulmc

paulmc:

Actually, much of science is about inferences made from evidence other than direct observations.

Exactly and that is why we don't need to see the designer, we can infer one existed due to the evidence left behind. Also the fossil record assumes common descent. Hey, using the "dog" example, looking at the cranial difference between chihuahua and St Bernard, we could draw all sorts of evolutionary stories to explain it, if we didn't actually observe reality. OK PaulMC- what is the testable hypothesis for humans evolving from knuckle-walkers via accumulations of random mutations? Joe

And how do you know that Schulz et al., are not just speculating given the evolutionary scenario?

In the famous words of several people in this thread - have you read it?

Ya see they cannot provide a history because they were not around so they can only speculate given a certain scenario.

So, the standard of your critique has dropped to a Ken-Ham-styled "Were you there?" Actually, much of science is about inferences made from evidence other than direct observations. When I walk into a forest, I do not simply assume that those trees have grown from seeds of other trees (or coppiced or reiterated from them) I infer they have from observations of seeds, seedlings, saplings and juveniles. Schultz et al. use the fossil record of brain size and vocal anatomy evolution, paired with archaeological evidence of language evolution. They are not simply speculating, as you accuse. Their timeline would need to be off by many millions of years to accommodate the claims by Luskin and Gauger. paulmc

OK PaulMC- what is the testable hypothesis for humans evolving from knuckle-walkers via accumulations of random mutations?

It’s called the theory of the origin of species by means of natural selection.

Call it whatever you want, that is not a testable hypothesis. Joe

CLAVDIVS:

Well, then, you’ve conceded my point: that dogs are highly phenotypically plastic, and this is observational evidence that small intergenerational changes stack up over time into much larger changes.

They are all still dogs.

What is the empirically confirmed process by which ‘design’ produces organs and nerves and knits them into a living thing?

What is the empirically confirmed process by which 'common descent' produces organs and nerves and knits them into a living thing? Why don't you answer that? Joe

Joe @ 77

OK PaulMC- what is the testable hypothesis for humans evolving from knuckle-walkers via accumulations of random mutations?

It's called the theory of the origin of species by means of natural selection. It's already been properly tested, Joe. So it's not an hypothesis any more; it's a theory. What test of this theory do you propose that we haven't done yet? Cheers CLAVDIVS

Joe @ 69

C: We know, as an empirical fact, that small intergenerational changes stack up over many generations when under selective pressure, producing e.g. both chihuahuas and St Bernards from wolves within human history. J: Except we do not know if dogs evolved from wolves. We just assume that is what happened. No one has taken wolves and via artificial selection made a dog. And also for all their phenotypic plasticity the dogs are still dogs.

Well, then, you've conceded my point: that dogs are highly phenotypically plastic, and this is observational evidence that small intergenerational changes stack up over time into much larger changes. I also notice you are ducking and weaving to avoid answering my question about common descent: Can you name any empirically confirmed process that produces two organisms with the same anatomy – other than ordinary reproduction i.e. descent one from the other? i.e. What is the empirically confirmed process by which ‘design’ produces organs and nerves and knits them into a living thing? Cheers CLAVDIVS

OK PaulMC- what is the testable hypothesis for humans evolving from knuckle-walkers via accumulations of random mutations? And how do you know that Schulz et al., are not just speculating given the evolutionary scenario? Ya see they cannot provide a history because they were not around so they can only speculate given a certain scenario. But then again you seem to just agree with anything that you like... Joe

Highly relevant to the premise of Science and Human Origins, there is a new themed issue of Philosophical Transactions of the Royal Society devoted to the evolution of human cognition. Of particular relevance, Schultz et al. provide a history of the progressive increase in hominin cranial capacity over 3 million years that culminates in the emergence of modern human language only 100,000 years ago. This is massively at odds with Casey Luskin's (Chapter 3) picture of human evolution (that Homo erectus and sapiens hardly differ) and demonstrates that Ann Gauger's (Chapter 5) potential but unevidenced Adam and Eve bottleneck based on HLA-DR (at 4 Mya) cannot have occurred in hominins with a contemporary human language capacity, pre-dating its emergence by minimum of 3.9 million years. paulmc

Chapter 5 of Science and Human Origins, reviewed here. Feel free to pop over and comment. Fear not, I won't tolerate any abusive comments on my blog. paulmc

"Why, one would almost get the impression that it doesn’t matter what the book actually says – he intends to trash it however he can. ;)" But what if God is bad, as Nick fears, Nullasalus? Punishing Adam and Eve wouldn't have been fair. They'd just be a 'chip off the old block'. Axel

Your untestable spewage still do not amount to an argument, for example, that purifying selection exists nor taht the onion test means anything. And mutational fixation appears to be imaginary also- no one can test it. Heck we have experiments with fruit flies that demonstrate mutation fixation does not occur as advertised. Also for gene duplication, well again we have possible future needs to consider. Junk DNA is based on our ignorance alone. Joe

Your double scare quotes still do not amount to an argument against, for example, the mutational load argument (that no more than ~10% of a typical mammalian genome can be under purifying selection because of the deleterious mutation rate). Or the onion test. Or that for mutations where NeS is less than 1, fixation should equal the mutation rate, which effectively ensures the fixing of some duplications of genes and transposable elements in humans. Under that last point, some amount of pseudogene accumulation and Alu repeats are actually unavoidable in small populations. paulmc

paulmc:

That is literally the worst refutation of the junk DNA argument ever conceived.

Seeing that the "junk DNA 'argument'" is quite possibly the worst ever conceived... Joe

Joe

If you want weak arguments try the one that says the majority of our genome is junk. And for more weak arguments people just have to read your review of the book…

Do you ever have anything of substance to add to a discussion? That is literally the worst refutation of the junk DNA argument ever conceived. paulmc

CLAVDIVS:

We know, as an empirical fact, that small intergenerational changes stack up over many generations when under selective pressure, producing e.g. both chihuahuas and St Bernards from wolves within human history.

Except we do not know if dogs evolved from wolves. We just assume that is what happened. No one has taken wolves and via artificial selection made a dog. And also for all their phenotypic plasticity the dogs are still dogs.

The basic problem with this, is that postulating a being capable of producing anything without constraint is not a testable hypothesis.

Nice strawman. No one said the designer didn't have constraints.

Contrast this with evolution theory’s reliance on the observed process of reproduction which, as we are discussing, is highly constrained and thus testable.

Yeah chimps reproduce chimps and that does not help you. So what is the testable hypothesis that knuckle-walkers evolved into upright bipeds? But anyway it is obvious that all you have is to throw father time around as if that is a testable hypothesis... Joe

paulmc- If you want weak arguments try the one that says the majority of our genome is junk. And for more weak arguments people just have to read your review of the book... Joe

I have now reviewed up to and including Chapter 4 of Science and Human Origins, leaving only a formal review of the fifth chapter, which I have already made some comments on in this thread. Chapter 4 deals with junk DNA, and recycles some weak arguments that have been dealt with numerous times before. Enjoy. paulmc

Jon Garvey @ 63

I actually have no beef agsinst common descent, but was looking merely at the strength of your argument as it stands. My use of “identical”, as you ought to have realised, was comparative. I’ve delivered enough babies, operated on enough humans and dissected enough rabbits in the last 40 years to be well aware of generational variation and its usual extent. That extent, though, is a good deal less than the difference between any human and any chimp, wouldn’t you agree? And maybe about the same as that between any two complex hand-made artifacts.

Jon, I agree, of course, that the variation between any two generations is relatively small and this is what you have personally observed. But given that we know life has existed on earth for hundreds of millions of years and the number of extant and extinct species is in the millions, I do not believe examining a couple of species over less than a lifetime is a statistically relevant sample size for assessing the limits (if any) of cumulative intergenerational change over thousands or millions of generations. We know, as an empirical fact, that small intergenerational changes stack up over many generations when under selective pressure, producing e.g. both chihuahuas and St Bernards from wolves within human history. Now, this was the result of intelligent selection and I'm willing to stipulate - just for the sake of this discussion - that life on earth was intelligently designed to evolve. But this stipulation does not change the fact of common descent via normal reproduction and the stacking up of small intergenerational variations. The empirical fossil and genetic records tell us that, whatever method the designer used to guide the process, it certainly involved organisms reproducing in the normal way with variations ramifying out in a branching pattern.

But then if common design weren’t also plausible, it wouldn’t have been the prevailing paradigm over so many more millennia. People concluded that any being capable of making a self-reproducing animal would have no problem produce a variety of them.

The basic problem with this, is that postulating a being capable of producing anything without constraint is not a testable hypothesis. Contrast this with evolution theory's reliance on the observed process of reproduction which, as we are discussing, is highly constrained and thus testable.

So plausibility, though a good basis for forming a hypothesis, doesn’t decide the issue – after all, since we’re being picky, chimps and humans do not have the same anatomy as you unguardedly said – they have somewhat similar anatomy, but differing more than normal reproduction ever produces.

Actually, I said that humans do not have any organs not shared with chimps, and that chimp babies are anatomically more similar to humans than to any other organism, besides, of course, chimps. I believe both of these statements are correct, even to the level of the enervation of the muscles, the regions of the brain, the developmental trajectory of the organs etc.

After all, as you rightly say, the appearance of design is so universal that Dawkins includes it in his popular definition of life – making the implausibility of non-teleological evolution a counterbalance to the plausibility of descent with (large) variation.

My argument is, if we stipulate that evolution is teleological, this stipulation does not contradict common descent. Cheers CLAVDIVS

CLAVDIVS:

Biological reproduction does not invariably produce anatomically identical organisms. Instead, there is significant intergenerational variation.

ALL observations demonstrate biological reproduction produces anatomically similar organisms- that is similar to the parents. Humans always give rise to humans.

On the other hand, the ability of living things to self-replicate with variation is empirically demonstrable and in fact well understood.

Chimps always give rise to chimps, prokaryotes always give rise to prokaryotes- sure there is some modification but nothing that supports your claims. Joe

CLAVDIVS:

Of course I can’t refute your opnion Joe, because it’s an opinion not based on any evidence or reasoning – like whether you prefer chocolate or vanilla ice cream.

Opinions are refuted by evidence. And you don't have any that demonstrates a knuckle-walker can evolve into an upright biped.

What is the empirically confirmed process by which ‘design’ produces organs and nerves and knits them into a living thing?

What is the empirically confirmed process by which 'descent with modification' produces organs and nerves and knits them into a living thing?

Biological change over time is empirically confirmed.

Yup and both baraminology and ID are OK with biological change over time. And biological change over time has never been observed to create new body parts and new body plans.

The common ancestry of organisms is an hypothesis that can be statistically tested – not by counting mutations but by characteristing the pattern of mutations.

THAT is just your opinion- and evidence-free opinion. Joe

CLAVDIUS I actually have no beef agsinst common descent, but was looking merely at the strength of your argument as it stands. My use of "identical", as you ought to have realised, was comparative. I've delivered enough babies, operated on enough humans and dissected enough rabbits in the last 40 years to be well aware of generational variation and its usual extent. That extent, though, is a good deal less than the difference between any human and any chimp, wouldn't you agree? And maybe about the same as that between any two complex hand-made artifacts. I've also read enough to know how much variation has been observed in any one species over time, and the limits seen around those changes that temper the plausibility of an ape-human transition somewhat. Interestingly no such constraints limit common design. You can modify a design forever, but eventually run out of options with selective breeding. Nevertheless you're right that common descent is plausible. If it weren't then Darwin's theory would never have achieved its popularity so quickly. But then if common design weren't also plausible, it wouldn't have been the prevailing paradigm over so many more millennia. People concluded that any being capable of making a self-reproducing animal would have no problem produce a variety of them. So plausibility, though a good basis for forming a hypothesis, doesn't decide the issue - after all, since we're being picky, chimps and humans do not have the same anatomy as you unguardedly said - they have somewhat similar anatomy, but differing more than normal reproduction ever produces. After all, as you rightly say, the appearance of design is so universal that Dawkins includes it in his popular definition of life - making the implausibility of non-teleological evolution a counterbalance to the plausibility of descent with (large) variation. Since, therefore, plausibility is clearly in the eye of the beholder, the evidence will have to decide it instead. Jon Garvey

Joe @ 60

C: That’s just your opinion Joe, and its a pretty weak one. J: Excvept it isn’t just mine and I notice that you cannot refute it.

Of course I can't refute your opnion Joe, because it's an opinion not based on any evidence or reasoning - like whether you prefer chocolate or vanilla ice cream.

C: Can you name a single anatomical organ that humans do not share with chimpanzees? J: Both a common design and convergent evolution can explain that.

I'll take that as a 'No'.

C: Can you name any empirically confirmed process that produces two organisms with the same anatomy – other than ordinary reproduction i.e. descent one from the other? J: I just did.

No, you did not name any empirically confirmed process other than ordinary reproduction. What is the empirically confirmed process by which 'design' produces organs and nerves and knits them into a living thing?

C: Based on empirically sound, uniform experience, common descent of humans and chimpanzees is the only reasonable inference. J: Except there aren’t any experiences with such a thing. All YOU have is change and eons of time, not exactly science.

Biological change over time is empirically confirmed. Eons of time are empirically confirmed. That's science.

Is there any math behind your scenario? How many mutations does it take to evolve an upright biped from a knuckle-walker?

Oh my goodness, yes, loads and loads of maths - mostly statistics. The common ancestry of organisms is an hypothesis that can be statistically tested - not by counting mutations but by characteristing the pattern of mutations. Cheers CLAVDIVS

Jon Garvey @ 59

C: Can you name any empirically confirmed process that produces two organisms with the same anatomy – other than ordinary reproduction i.e. descent one from the other? J: Now there’s an interesting equivalence here – reproduction observably produces anatomically identical organisms, but not anatomically similar ones. For example, chimps never beget humans or vice versa.

This is incorrect. Biological reproduction does not invariably produce anatomically identical organisms. Instead, there is significant intergenerational variation. Chimp babies are anatomically more similar to humans than to any other organism, besides, of course, chimps. Nonetheless you have a good point that living things have the appearance of being designed and manufactured for a purpose. But we do not have any empirical example of the design skill and manufacturing ability required to produce living things via direct assembly like cars. On the other hand, the ability of living things to self-replicate with variation is empirically demonstrable and in fact well understood. Thus this is the more plausible mechanism for the origin of species. Cheers CLAVDIVS

CLAVDIVS:

That’s just your opinion Joe, and its a pretty weak one.

Excvept it isn't just mine and I notice that you cannot refute it.

Can you name a single anatomical organ that humans do not share with chimpanzees?

Both a common design and convergent evolution can explain that.

Can you name any empirically confirmed process that produces two organisms with the same anatomy – other than ordinary reproduction i.e. descent one from the other?

I just did. However no one knows if descent with modification can produce the transformations required.

Based on empirically sound, uniform experience, common descent of humans and chimpanzees is the only reasonable inference.

Except there aren't any experiences with such a thing. All YOU have is change and eons of time, not exactly science. Is there any math behind your scenario? How many mutations does it take to evolve an upright biped from a knuckle-walker? Joe

"Can you name any empirically confirmed process that produces two organisms with the same anatomy – other than ordinary reproduction i.e. descent one from the other?" Now there's an interesting equivalence here - reproduction observably produces anatomically identical organisms, but not anatomically similar ones. For example, chimps never beget humans or vice versa. On the other hand, manufacturing processes often produce similar as well as identical products (eg Toyota produces saloons and sports cars), but aren't observed to produce organisms. So both hypotheses need to be extended to about the same extent in order to explain the variations in life. Jon Garvey

wd400, you asked what ID is against. I answered. Why pretend otherwise now? I think you already know that ID makes a positive inference to design, abductively, based on our current experience with the features of designed things, most notably specified functional and irreducible complexity. So why play coy? Design is the observation that Darwinian evolution is supposed to account for, but cannot; and there are indicia of design - namely sequence specificity in proteins and the DNA that codes for them. That's plenty of positive for anyone whose worldview doesn't overrule design on a technicality. Chance Ratcliff

Joe and Chance Ratcliff, So it's a critique of evolutionary theory, not a theory in its own right? wd400

Joe @ 55

paulmc: On paper, a pluralistic version of ID might be vague enough to be able to absorb universal common descent, but it is clear that in practice this is unpalatable to the authors of the book that is the subject of this thread. Joe: That is because the “evidence” for it is a joke.

That's just your opinion Joe, and its a pretty weak one. Can you name a single anatomical organ that humans do not share with chimpanzees? Can you name any empirically confirmed process that produces two organisms with the same anatomy - other than ordinary reproduction i.e. descent one from the other? Based on empirically sound, uniform experience, common descent of humans and chimpanzees is the only reasonable inference. Cheers CLAVDIVS

paulmc:

On paper, a pluralistic version of ID might be vague enough to be able to absorb universal common descent, but it is clear that in practice this is unpalatable to the authors of the book that is the subject of this thread.

That is because the "evidence" for it is a joke. That is the whole point of the book. Only people who want to be related to chimps buy the evidence that we share a common ancestor with them. And yes if religions are true they should have some evidentiary evidence. Newton used science as a way to understand God's Creation. Justice Lewis Powell wrote the following in his concurrence to Edwards v. Aguillard, “(A) decision respecting the subject matter to be taught in public schools does not violate the Establishment Clause simply because the material to be taught ‘happens to coincide or harmonize with the tenets of some or all religions’.” If we don't share a common ancestor with chimps, then so be it. Then next we try to figure out how we did get here. Joe

wd400:

What exactly is ID against. What evidence couldn’t fit into a IDists view of the world?

See comments 51 and 52. Dr Behe put the edge of chance and necessity at two new protein-to-protein binding sites. Joe

Joe, On paper, a pluralistic version of ID might be vague enough to be able to absorb universal common descent, but it is clear that in practice this is unpalatable to the authors of the book that is the subject of this thread. No number of Demski/Meyer/Behe quotes change that. I'll remind you that I did already say that different theorists will have different views as in every field and that what I am talking about is the approach taken by Gauger, Axe and Luskin. Science and Human Origins is published by the Discovery Institute and sets about to disprove common descent especially for humans, and tries to create enough doubt to allow for a literal Adam and Eve. Isn't that curious, when ID is so very neutral about the whole common descent thing? Again, while some pluralistic version of ID might be able to accommodate a common ancestor for humans and chimps, and junk DNA and so on, these authors actively seek to reject these possiblities. They set about creating a case against common descent, and junk DNA, and a large effective population size in humans, with explicitly Christian justifications, while offering no positive evidence for any alternative position. ID can be defined in general terms as a secular enterprise, but it remains, in practice, a vehicle for religious ideas explored by religious people. paulmc

"ID infers design in living systems. This precludes an origin rooted in law and chance. It also challenges the novel generation functionally specific biological novelty in similar fashion." should read, "ID infers design in living systems. This precludes an origin rooted in law and chance. It also challenges the generation of functionally specific biological novelty in similar fashion." Chance Ratcliff

"Joe, What exactly is ID against. What evidence couldn’t fit into a IDists view of the world?"

Same as always: 1) Materialistic origin of life; 2) neo-Darwinian mechanism of RM+NS. ID infers design in living systems. This precludes an origin rooted in law and chance. It also challenges the novel generation functionally specific biological novelty in similar fashion. Chance Ratcliff

Joe, What exactly is ID against. What evidence couldn't fit into a IDists view of the world? wd400

PaulMC- Just because IDists cast doubt on universal common descent, and given the "evidence" everyone should, that does not mean ID is against it: Intelligent Design is NOT Creationism (MAY 2000)

Scott refers to me as an intelligent design "creationist," even though I clearly write in my book Darwin's Black Box (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think "evolution occurred, but was guided by God."- Dr Michael Behe

Dr Behe has repeatedly confirmed he is OK with common ancestry. And he has repeatedly made it clear that ID is an argument against materialistic evolution (see below), ie necessity and chance. Then we have: What is Intelligent Design and What is it Challenging?- a short video featuring Stephen C. Meyer on Intelligent Design. He also makes it clear that ID is not anti-evolution. Next Dembski and Wells weigh in:

The theory of intelligent design (ID) neither requires nor excludes speciation- even speciation by Darwinian mechanisms. ID is sometimes confused with a static view of species, as though species were designed to be immutable. This is a conceptual possibility within ID, but it is not the only possibility. ID precludes neither significant variation within species nor the evolution of new species from earlier forms. Rather, it maintains that there are strict limits to the amount and quality of variations that material mechanisms such as natural selection and random genetic change can alone produce. At the same time, it holds that intelligence is fully capable of supplementing such mechanisms, interacting and influencing the material world, and thereby guiding it into certain physical states to the exclusion of others. To effect such guidance, intelligence must bring novel information to expression inside living forms. Exactly how this happens remains for now an open question, to be answered on the basis of scientific evidence. The point to note, however, is that intelligence can itself be a source of biological novelties that lead to macroevolutionary changes. In this way intelligent design is compatible with speciation. page 109 of "The Design of Life"

and

And that brings us to a true either-or. If the choice between common design and common ancestry is a false either-or, the choice between intelligent design and materialistic evolution is a true either-or. Materialistic evolution does not only embrace common ancestry; it also rejects any real design in the evolutionary process. Intelligent design, by contrast, contends that biological design is real and empirically detectable regardless of whether it occurs within an evolutionary process or in discrete independent stages. The verdict is not yet in, and proponents of intelligent design themselves hold differing views on the extent of the evolutionary interconnectedness of organisms, with some even accepting universal common ancestry (ie Darwin’s great tree of life). Common ancestry in combination with common design can explain the similar features that arise in biology. The real question is whether common ancestry apart from common design- in other words, materialistic evolution- can do so. The evidence of biology increasingly demonstrates that it cannot.- Ibid page 142

And from one more pro-ID book:

Many assume that if common ancestry is true, then the only viable scientific position is Darwinian evolution- in which all organisms are descended from a common ancestor via random mutation and blind selection. Such an assumption is incorrect- Intelligent Design is not necessarily incompatible with common ancestry.- page 217 of “Intelligent Design 101”

Joe

Wrong, as usual... again you have no idea what ID claims and it shows.

This is a plainly ignorant thing to say when I am in the process of reviewing a book by the DI's leading workers. I cannot purport to know what everyone claims but I do indeed know what *those authors* claim. And that is what I am commenting on. I don't think you're in the position to claim to speak for an imagined, unified ID front. I'm sure that Behe, Gauger, Luskin, Axe, Demski, Hunter amongst others associated with the DI all have different ideas about what intelligent design entails, just as various evolutionary biologists do for evolution. I don't know if you have read S&HO yet or not, but a substantial part of the book is aimed directly at casting doubt on common descent for humans specifically in an explicitly Christian context. It is obvious that the authors don't accept common descent - Luskin refers to our "supposed" common ancestor with chimps. Gauger claims there is insufficient molecular or morphological evidence to conclude this common ancestor. This is the basis for what I have said. paulmc

paulmc- Evolution does not expect a nested hierarchy based on characteristics. In order to have a nested hierarchy based on characteristics those characteristics have to be A) immutable and B) additive. Evolution is not like that. Also with a gradual evolution we would expect to see a blending of characteristics which would be OK for a Venn diagram but not for a nested hierarchy. Then there is the fact that the theory of evolution says NOTHING about the origins of living organisms, which means it would be OK with many trees. BTW a common design would create a nested hierarchy. Heck clades are based on similar characteristics, ie a common design. Joe

A series of mutations happened over many generations that allowed this substantial metabolic change in the E. coli strain.

All that occurred was the citrate was allowed into the E. coli. Read the paper, Paul. Geez paul, ID is not anti-evolution. Buy a vowel.

No? ID is certainly against evolutionary novelty being generated by mutation, selection and drift, as both Gauger in Chapter 1 and Axe in Chapter 2 show. And against universal common descent. Pretty major components of evolution, to my mind.

Wrong, as usual. ID is not against universal common descent, ask Dr Behe. ID is against blind and undirected chemical processes producing more than two new protein-to-protein binding sites- again you have no idea what ID claims and it shows. And again with Lenski- his experiment supports baraminology, not universal common descent via accumulations of random mutations. And definitely no new machinery was constructed. But then again you don't appear to know much about what actually happened. No surprise there... Joe

why is it if very common structures are found between the deerlike creature and whales, that’s evidence of evolution, but, if it’s found between the eye of a human and the eye of an octopus, that’s evidence of convergence.

Well, you have to consider that in the context of systematics. The shared structures between terrestrial artiodactyls and whales are predicted to be conserved from their common ancestor, while the eyes in humans and octopuses are derived traits - i.e. not shared. It is only by forming a nested hierarchy of characters - either morphological or genetic - that we can make sense of these things and make decisions about basal character states and derived ones. If common design were the explanation, no nested hierarchy would be formed. There are strong similarities between the human and octopus camera eyes, and similar genes are expressed in the two species. The evolutionary history of these genes show that they were present in the basal bilaterian that gave rise to both lineages - so even though the eyes in humans and octopuses have separetely evolved, they have done so from a common set of genes. There is a fairly thorough treatment here. paulmc

Hi es58, I think that it's a good question, and the wider context is important for understanding how evolution is purported to work. The broader point I was hoping to make was that there is no preordination in evolution, which is a problem for the type of approach that Gauger and Axe have taken. That means that a question such as "at what point will the e-coli develop new tissues, organs, multi-cellularity?" is not actually answerable. Why would we expect E. coli develop multicellularity? If framed in terms of fitness, how could we say that a multi-cellular analogue of E. coli would be 'better' than the current one? Even this approach is wrong, however. Any purported benefits of multi-cellularity are not accessible to E. coli --- positive selection cannot 'see' further than the next local fitness peak. In other words, stepwise, positive selection is not how major transitions and long-term evolutionary change happen. It is in this way that Darwin was somewhat wrong, although he had no way to know that at the time he was writing. I realise that evolution is often portrayed in this way --- positive selection shapes all the important traits that define species. Undoubtedly, such +ve selection is important, but not in the all-powerful way that some people portray. When we take the example of the transition from terrestrial ancestor to fully marine contemporary whales and dolphins, the problem seems enormous. However, it is not completely uncommon amongst the vertebrates. Several separate groups of mammals within the Carnivora have also made this transition to differing extents also --- I am thinking of seals, otters, polar bears. Within the birds, penguins are largely marine, as well. But the cetaceans have made a fuller and more remarkable transition. How can this transition be explained? It is worth considering that we have a fairly substantial fossil record showing the progressive transition to the marine environment in this lineage. We can therefore make only marginally indirect observations of much of the structural changes that occurred, and this allows us to consider a mostly likely scenario for that transition. This helps to reduce the guesswork involved, and hopefully reduces the doubt that the transition really occurred. But the major hurdle that you quite fairly point out, is that there are more morphological changes in the cetaceans than there are in E. coli. Why should this be, when there are many more replications of E. coli? There are two major reasons. Firstly, cetaceans are complex, and multicellular. Much of their change is change to regulatory genes that affect the timing of events in their development, and the major features of their terrestrial ancestry are anatomically quite obvious. Secondly, cetaceans have much smaller populations and therefore experience substantially weaker purifying natural selection. This means that they are less restricted in many aspects of their evolution than are large bacterial populations. I realise the idea of weaker selection being a creative factor in evolution may seem bizarre, but the world is a bizarre place :)

the 2 environments of these non-changing vs highly changing creatures don’t seem so different to me so, it’s like, there’s an answer either way, but it’s whichever answer is convenient at the time

At the DNA level, E. coli is indeed changing. E. coli genomes are far more variable than are those of any multicellular species. But the strong selective contraints limit how much outward change we observe (and of course there are fewer things to regulate in E. coli than a baleen whale).

If you’re following this: Can you point me in a direction that could clarify where I’m off? Also, how much study do you think it would require for me to get to a point where I could understand the answer clearly?

Well, I think the only way that you are off target is that you have expectations about predicting large evolutionary trajectories. Such expectations are unrealistic. The Lenski cit+ lineage of E. coli demonstrates the importance of rare, contingent events in shaping evolutionary trajectories. I understand that this might seem like a frustrating limitation, or even a fudge. But, we can also learn much from stasis, and the more 'routine', day-to-day types of evolutionary change that occur. The fact that most lineages don't make frequent, large shifts tells us much about evolution and its constraints. Those contraints and limits on evolution are fundamental to understanding how it proceeds. It is rather a technical read, but I would strongly recommend Michael Lynch's 2007 book, 'The Origins of Genome Architecture'. Lynch emphasises the importance of non-adaptive processes in shaping multicellular life, which I think is one of the most underappreciated aspects of biology, not just for the public, but for biologists. I hope this goes some way towards answering your question. paulmc

@paulmc one further question: why is it if very common structures are found between the deerlike creature and whales, that's evidence of evolution, but, if it's found between the eye of a human and the eye of an octopus, that's evidence of convergence. Thank you. es58

@paulmc hello, you wrote: The metabolism of citrate required a non-adaptive step that occurred thousands of generations before citrate was metabolised. here's what I'm sure is a dumb, rambling comment/response/question: if it took this long to get this result, at what point will the e-coli develop new tissues, organs, multi-cellularity, etc I don't want to put any words in your mouth, but often feel that answers I've seen to questions like this are of the form: if it never happens/happened, it's because it was already fit the way it was, and didn't need to change in that way (like jelly fish, coelcanth etc, that don't change for eons) because the environmental pressures weren't so powerful but, if a small deerlike creature can move back to the water (without just drowning) and change all the way to a whale, thousands of changes, and no where near the number of generations or offspring that the e-coli has the advantage of experiencing, then that's because their environmental pressures were so great they needed to adapt and, the 2 environments of these non-changing vs highly changing creatures don't seem so different to me it just seems likes it's asking an awful lot of the listener to buy with very little concrete evidence so, it's like, there's an answer either way, but it's whichever answer is convenient at the time; If you're following this: Can you point me in a direction that could clarify where I'm off? Also, how much study do you think it would require for me to get to a point where I could understand the answer clearly? es58

All that occurred was now the citrate was allowed to pass through the cell’s membrane. All the machinery to metabolize the citrate was already in place.

A series of mutations happened over many generations that allowed this substantial metabolic change in the E. coli strain. You can try and downplay that as trivial, but not metabolising citrate is a defining aspect of E. coli. The point being that Gauger and Axe's limit on preordanined mutations does not actually shut real-world adaptation down. It only shows us that what never happened is unlikely to happen.

Geez paul, ID is not anti-evolution. Buy a vowel.

No? ID is certainly against evolutionary novelty being generated by mutation, selection and drift, as both Gauger in Chapter 1 and Axe in Chapter 2 show. And against universal common descent. Pretty major components of evolution, to my mind.

That is because genetic drift has never been observed to do anything, so relying on it = relying on sheer dumb luck

Firstly, I was talking about genetic drift in the context of fitness landscapes. If you don't understand the relevance you probably shouldn't be commenting. Secondly, genetic drift does do things. In fact, just moments ago you were talking about the Lenski long-term experiment. The metabolism of citrate required a non-adaptive step that occurred thousands of generations before citrate was metabolised. I would say that with their ability to grow on the citrate medium, that strain of E. coli benefited from the sheer dumb luck you are so derisive of. paulmc

paulmc:

Also, Richard Lenski's lab has evolved a strain of E. coli that metabolises citrate as its sole energy source.

All that occurred was now the citrate was allowed to pass through the cell's membrane. All the machinery to metabolize the citrate was already in place.

Bacteria that degrade nyon for their energy have evolved in the natural environment in the short time since humans invented nylon.

And that scenario fits in well with Dr Spetner's "built-in responses to environmental cues". Geez paul, ID is not anti-evolution. Buy a vowel.

Axe goes on to discuss fitness landscapes, but he does so without mentioning genetic drift. It's all local fitness peaks and positive selection causing dead ends.

That is because genetic drift has never been observed to do anything, so relying on it = relying on sheer dumb luck, which isn't science. And Paul, if you had some evidence that undirected and blind processes can do the job now would be a good time to present it. Otherwise you just look like a little whiner... Joe

BTW, I have started reviewing Gauger, Axe and Luskin's book chapter by chapter here. paulmc

mk@37 - "acording to the evolution, a complex system can evolve without intelegent. so a car can be evolve naturally according to evolution." Thanks for that. Perhaps this wisdom is best used in a different thread. I was kind of hoping for responses to my criticism of chapter 5 of Gauger's book. paulmc

hey paulmc acording to the evolution, a complex system can evolve without intelegent. so a car can be evolve naturally according to evolution. so if we find 2 similar cars made of dna, what you will say about the cars? alsso,the human have a unique genes. if this genes need somthing like 1000 base, its a very positive case that there is no step by step from ape to human. mk

paulmc:

I know of no evidence that horses are the result of an intelligent agent.

Unfortunately no one can demonstrate any organim is the result of accumulations of random mutations. IOW your position doesn't have any evidence, paulmc, and it shows. Joe

mk @ 34 - I'm not sure I follow your reasoning there. You have quoted me referring to positive evidence for a severe human population bottleneck, only to refer instead to analogous evidence for an intelligent designer. I'm also not sure what a car 'made of DNA' would look like. Perhaps the closest biological analogue to what you mean would be an animal used for transport with macromolecules derived from the expression of DNA. A horse perhaps? I know of no evidence that horses are the result of an intelligent agent. paulmc

paulmc say: "Especially when that single line of argument does nothing more than leave a little room for doubt about one previous conclusion, without offering a shred of positive evidence to support the Adam and Eve story" actually there is a positive evidence: if we find 2 similar cars that made of dna we know that the cars was made by intelegent agent. so why not in the case of 2 similar organisem? mk

If God made man out of the best type of body in his creation then we would look like apes and have like DNA. Its always been just a line of reasoning that like form and DNA was evidence for like relationship from a earlier thing. It was never based on scientific evidence. Robert Byers

This is all rather underwhelming. Gauger's claim in the book boils down to this: because there are only 3-5 surviving, ancient haplotypes of HLA-DRB that are in linkage with neighbouring MHC loci and that also predate human and chimpanzee speciation, we could have descended from a two person, Adam & Eve scenario. This is an argument that sets about only to create sufficient doubt, rather than any positive evidence for such a bottleneck. Nor can it offer more than speculation about the patterns of diversity of HLA-DRB1 exon 2. Nonetheless, taken generously, there is some doubt that the MHC alone definitively rule outs an Adam and Eve scenario. But that's all. Gauger claims that the existence of ancient haplotypes in HLA-DR is the one of strongest arguments against Adam and Eve, tacitly acknowledging the existence of other arguments. However, her engagement with those other arguments ends there. If you are expecting a discussion, or even acknowledgement, of the other arguments against a 2-person bottleneck before Gauger's conclusion that Adam and Eve are possible, prepare for disappointment. Despite this, her conclusion is worded as being definitive, and should require multiple lines of evidence to be justified. She claims: "The argument from population genetics has been that there is too much genetic diversity to pass through a bottleneck of two individuals, as would be the case for Adam and Eve. But that turns out not to be true.". As one example, Li and Durbin's (2011) whole genome analyses that demonstrate the differing effective population sizes of human lineages over time (which never get close to two)--surely greatly more informative than an analysis of the MHC-- is not mentioned. No two-person bottleneck could possibly be inferred from their work, but the problem is sidestepped, along with everything else. Now, obviously, not everything can be covered in a book and Gauger does state that she focuses on the one argument, but considering the brevity of this book and the strength of the conclusion, there must have been space for more diverse coverage here. Especially when that single line of argument does nothing more than leave a little room for doubt about one previous conclusion, without offering a shred of positive evidence to support the Adam and Eve story, and while leaving the other major problems unaddressed. paulmc

Was the snake question also pertinent? Chance Ratcliff

lastyearon had a pertinent question and I don't think the "News" response was appropriate. Let's just ban everyone who disagrees with us, can we do that? If Eve was made from the rib of Adam, why did Eve not share the exact same DNA as Adam? What is the evidence that humans came from two parents who shared the exact same DNA? Why does someone have to read the book in order to pose that question? Mung

To paraphrase Nick Matzke, If you haven't read the book (or are one if it's authors), your discussion of it is worthless. Mung

At least Nick might take News up on the offer that Discovery Institute Press could send him a free copy. Oh...he has said he has ordered the book already. Whether or not his presuppositions, ideology, background beliefs allow him to assess the book 'neutrally' is a question seemingly worth asking outside of the 'objectivistic' realm of natural sciences. Iow, what Nick 'knows' (or claims to know) in biology or genetics actually says little about how his worldview influences his answers on questions of 'human origins.' Gregory

Does anyone else find it absolutely adorable that Nick hasn't read the book, that nothing substantial has really been posted here, but damnit, he doesn't want that to get in the way of him attacking it? Why, one would almost get the impression that it doesn't matter what the book actually says - he intends to trash it however he can. ;) nullasalus

NickMatzke_UD, We look forward to what you have to say when you have read the book! We post excerpts to create interest in reading it. O'Leary

hey ann,the apes have have 100 copies of erv called pterv1, and we not find it in the human genome: http://www.sciencedaily.com/releases/2005/03/050328174826.htm for fixation of one of them we will need somthing like milion years. so we need 100 milion years for this change. also,what if we will find a watch that made of dna and can be replicate? mk

Nick- YOUR position cannot explain introns nor alternative gene splicing. Also how can one tell if there is selection at any given locus? Joe

But so far I have found no model that can preserve multiple polymorphisms across multiple speciation events that date back more than 30 million years.

Ooh, not a good sign for your argument. This part is easy, if there is selection for diversity at a locus, coalescence will be extremely rare.

Especially when those trans-species polymorphisms are embedded in species-specific introns in a region of suppressed recombination.

Well, we'd have to see the evidence for "suppressed recombination", and you'd have to show recombination is *extremely* repressed, to the point that it almost never happens.

species-specific introns

Depends which introns, how long they are (some are huge) what their LD is with the exons of interest, and whether or not you've correctly understood what other authors mean by "species-specific". I've got the book on order, but until it shows up all I can do is remark on what UD posts. If they leave out crucial issues an argument would have to address in order to be credible, well then, at the very least the UD posters don't understand your argument. NickMatzke_UD

Talk to me when you have read the chapter, Nick. I sincerely want to know if there is a way to demonstrate a purely natural explanation for the pattern of HLA polymorphisms. But so far I have found no model that can preserve multiple polymorphisms across multiple speciation events that date back more than 30 million years. Especially when those trans-species polymorphisms are embedded in species-specific introns in a region of suppressed recombination.

Well, there's not much point in UD leaving out crucial parts of the discussion, then, is there? NickMatzke_UD

Hey if we look at what the ToE sez then we can trace our lineage back to one parent- the first to get the chromosomal fusion and then perhaps some inbreeding occurred to get that fusion to spread and then become fixed. Heck that must have been some bottle-neck for that to occur. Joe

Hi Ann, Thanks for your reply. I had thought we met at the Discovery Institute’s summer program in 2008 in Seattle. There was a woman with her leg up during the lectures and seminars who I spoke with. Am I confusing you with someone else associated with Discovery Institute who works at Biologic Institute with Douglas Axe (who I also met there)? I appreciate your acknowledgment of the “real possibility of two original parents” and that “not all of the facts are available.” Like you, I accept an ‘old earth’ (as if that's any more really in doubt!) and “don’t know when or where to place those first two parents.” But I have a guess, as you probably do also. We are also agreed that “choosing when we [i.e. persons, people, humans] first appeared on the planet all depends on what criteria you choose to define ‘human’.” As for me, I don’t trust zoologists or ethologists as much as I look to inspired anthropologists on the topic. You, Axe and Luskin are not anthropologists. DI-affiliated D. Klinghoffer has brushed off the ‘social-science field of anthropology.' Is there (or are there) a DI-affiliated anthropologist that you and your co-authors consulted in conducting research for your work? 2 points of note, with questions: First, Wesley J. Smith (affiliated with DI) speaks of ‘human exceptionalism.’ Do you promote this term with Douglas and Casey in your book? Second, do you in the book make the claim that ‘human origins’ are/were ‘intelligently designed’ or that ‘intelligent design’ was required to produce human beings as we know ourselves today? Thanks for your answers to these questions, Gregory Gregory

Most interesting. We are hoping to hear from people who have actually read what Gauger has said in toto. News

gauger: "You can’t gauge an argument from snippets, or sentences taken in isolation." With all due respect: Yes, I can. Certainly not for everything, but enough. If the argument requires a time machine to allow it to satisfy the criterion of falsifiability? It's wrong, full stop. If it's hindcasting or making future predictions about a non-linear system with feedbacks? It's wrong, full stop. You can get back to me when economists, brokers, and weathermen can actually make muster on this. Because until then the *mathematics* isn't valid for doing such. The theory and any pretense to falsifiability criterion doesn't even come on the radar until the math is sound. If it requires the porn-test -- "I know it when I see t" -- then it's wrong. Sniffing out the homology between the works of Flint, Michaelangelo, God, Darwin, or Dice is best lest to the cultists. If it ever even *pretends* to affirm the consequent. It's wrong. This is a ground rule of logic and science. You cannot *prove* your pet pablum. But you sure can disprove someone else's. If it makes a large claim on a small isolated factor? It's wrong. I don't care if you're playing Texas Sharpshooter by correlating a couple few base pairs out of 4 billion or if you're talking MV=PQ, or the absorpta bands of plant food. If you don't slap a big honkin' "Ceteris Paribus" on it then you're off in the weeds. If it's possible that it might that it could in some possible world potentially be feasible in some perhaps past or future time on the basis of some theoretically knowable contingents? Yeh, that's right: It's wrong. It's so wrong it isn't even a claim. You will find that every contentious bit of life runs afoul of these most meager notions of sound reason and evidence. You'll find it in every soft-science, politics, quantum nonsense, cosmology, evolution, global warming, etc. In short anything that is Philosophy and held or presented as a Really Real True Fact of the universe. It's all Jonestown Koolaid Kult nonsense. Now I mean absolutely no disrespect here and there's nothing wrong with you putting forward a rebuttal to notions *held, put forward or believed* by others on their own terms. Quite the contrary, it is absolutely the right way to go with any proper rebuttal. But any of the above short-list of bovine excrement detection can make itself plainly known in a sentence *fragment*. Damn the sentence, the paragraph, the monologue, anthology, or voluminous repetitions of credentialed True Believers loudly selling their religion as science. Maus

Quite true, evilsnack, but lastyearon is simply trying to misdirect a discussion around a technical issue that he has avoided by the expedient of jumping in without having read the book. If he comes back here without having read it, we will ban him. News

lastyearon, we have zero interest in snarks from people who don't, won't, and maybe can't read the book. Do so, or don't show up in this discussion again. News

It's safer not to read the book if all the person wants to do is tilt at straw men. Once you know the actual argument, you have to respond to that. Some knowledge of the actual question at issue (how wide must the bottleneck be?) is required. News

Anne, Thanks for your efforts in writing this latest book! I've already bought a copy and can't wait to read it. I also love the work you've done with Douglas Axe on Metamorphosis and other projects. Anyway, my question is this. Are you familiar with the study on wild horses referenced here: http://www.sciencedaily.com/releases/2011/09/110907163921.htm I heard a pod cast from Reasons To Believe released on 9/13/2011 entitled "Wild horses, high genetic diversity, and the case for a literal Adam" which you can listen to here: http://www.reasons.org/podcasts/science-news-flash/wild-horses-high-genetic-diversity-and-the-case-for-a-literal-adam It discusses population bottlenecks and examines the situation of a special breed of wild horse which was reduced to a population of 12 but has rebounded to a population of 2,000. At any rate, the genetic diversity within this population far exceeds what was predicted with evolutionary population genetic models. I was wondering what your reaction was to this study and how it might impact the research in your recent book? Thanks! wgbutler

lastyearon: I daresay that an entity capable of fabricating the body of one life form out of a portion of the body of another is quite capable of making any other desired modifications along the way, including genetic ones. No reliable inference on this question can be drawn from present-day genetic observations. And the only eyewitness account of those times informs us that the snake in question was no ordinary snake. No reliable inference on this question can be drawn from the capabilites of modern-day reptiles. EvilSnack

No, but I am learning something about snake pits. gauger

I haven't read the book, so a couple questions... Anne, do you explore the possibility that the first human female was made from the rib of the first human male? I'm interested to know what genetic evidence you might have found regarding that. Also, were you able to uncover any evidence suggesting linguistic capabilities of snakes at or around the time of the first humans? Thanks. lastyearon

Guys, you really should read the book. You can’t gauge an argument from snippets, or sentences taken in isolation. And if you do read the book, my viewpoint (based on the scientific evidence) will be clear.

Well said. It's more than a little disturbing, to see certain evolutionists take issue with a claim prior to reading the full argument/context of what is being said. This knee-jerk, negative response to something posted by I.D proponents comes across as desperate, irrational and illogical. Blue_Savannah

Guys, you really should read the book. You can't gauge an argument from snippets, or sentences taken in isolation. And if you do read the book, my viewpoint (based on the scientific evidence) will be clear. Sorry Greg, I can't remember injuring my leg in the recent past. Maybe you have me confused with someone else. I think there is a real possibility of two original parents. Not all the facts are available concerning how our genome works, and what is required to make a human being rather than an ape. I am deeply suspicious of retrospective calculations from population genetics when so many variables are at play. I think as we learn more it will be clearer. I personally accept an old earth, but I don't know when or where to place those first two parents. Not being dodgy, there are just too many unknowns. I do not know when to place true sapience, and our present DNA certainly can't tell us. Casey Luskin does a good job on the fossil record in the book. But choosing when we first appeared on the planet all depends on what criteria you choose to define "human". gauger

Nick: "If incomplete lineage sorting isn’t discussed here, the discussion is worthless." That's a mighty fancy way to state that phylogeny is wrong. Bookquote: "Currently, neo-Darwinism is the accepted explanation for our origin. " It is because it is what is currently taught to children. No more or less and still no replicable experimental proof on offer. Nor, I submit, will there be until we're able to hang out and sink a few tubes with the Morlocks and Eloi. Maus

Hi again Ann, We've met in person before. Last time you had an injured leg. I'm not a biologist, so I have no comment or say about the main point you're making. What I'd like to ask is this: Are you saying 'Young Earth' or 'Young Human' ideas are wrong, according to your interpretation/understanding? You speak of millions of years. I haven't read your book. Do you believe/in or accept a 'real, historical' Adam and Eve? If so, in what time period do you place them? Thanks, Gregory Gregory

As to the common complaint I've heard from Darwinists that two parents would not have enough genetic diversity to found a population: Yet: Evolution of adaptive phenotypic traits without positive Darwinian selection - A L Hughes - November 2011 Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity–relaxation–mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201197a.html A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html Cichlid Fish - Evolution or Variation Within Kind? - Dr. Arthur Jones - video http://www.metacafe.com/watch/4036852 African cichlid fish: a model system in adaptive radiation research: "The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory(of evolution).----surprising implication of the study?---- the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages" http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16846905 Single male and female sheep maintain genetic diversity. A mouflon population (considered an ancient "parent" lineage of sheep), bred over dozens of generations from a single male and female pair transplanted to Haute Island from a Parisian zoo, has maintained the genetic diversity of its founding parents.This finding challenges the widely accepted theory of genetic drift, which states the genetic diversity of an inbred population will decrease over time. "What is amazing is that models of genetic drift predict the genetic diversity of these animals should have been lost over time, but we've found that it has been maintained," Dr. David Coltman, an evolutionary geneticist at the University of Alberta Allozyme evidence for crane systematics and polymorphisms within populations of sandhill, sarus, Siberian and whooping cranes. "This is contrary to expectations of genetic loss due to a population bottleneck of some 15 individuals in the 1940s. The possibility should be explored that some mechanism exists for rapidly restoring genetic variability after population bottlenecks." Molecular Phylogenetics and Evolution 1:279-288- Dessauer, H. C., G. F. Gee, and J. S. Rogers. 1992. Children of the Corn: A Reader Objects - April 2012 Excerpt: As John Doebley put the point in 2004, "The critical genetic variants involved in maize evolution were pre-existing in teosinte populations" (p. 46). http://www.evolutionnews.org/2012/04/children_of_the058251.html etc.. etc.. etc.. bornagain77

"If it were true that we share thirty-two separate lineages of HLA-DRB1 with chimps, it would indeed cause difficulties for an original couple. But as we have seen, the data indicate that it is possible for us to have come from just two first parents." Although I like the conclusion, I have a problem with the assumptions on which this research was based. It seems like from what she writes here that common descent is simply assumed. So her conclusion means very little if one does not believe in common descent. Plus, if I understand it right, her conclusion only shows that it could be a possibility, right? I just have a problem with the idea of common descent personally. tjguy

Talk to me when you have read the chapter, Nick. I sincerely want to know if there is a way to demonstrate a purely natural explanation for the pattern of HLA polymorphisms. But so far I have found no model that can preserve multiple polymorphisms across multiple speciation events that date back more than 30 million years. Especially when those trans-species polymorphisms are embedded in species-specific introns in a region of suppressed recombination. gauger

I discuss it under the term trans-species polymorphism, which is the term used by Klein in discussing HLA polymorphism. Incomplete lineage sorting is usually applied to situations of recently diverged species, and doesn't involve balancing or over-dominant selection, as would be the case for HLA. gauger

NickMatzke-UD, are you saying that it isn't? Do you know? Have you read the book? The chapter? Anything? It's quite possible Discovery Institute Press would send you a free copy. News

If incomplete lineage sorting isn't discussed here, the discussion is worthless. NickMatzke_UD