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The Origin of Specious Nonsense. Twelve years on. Still going. Answer soon.
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I fully accept that this is not well understood in terms of the mechanism. There is no science to cite because as yet the mechanism is not understood. However, evolutionary biologists, from what I have read, seem agreed that behavior is a mixture of inherited, learned in early development (due to environment) and modifiable. All three involve wiring the brain, and the only thing that can wire the brain is DNA. The unknown is the mechanism.
I am having some trouble following you here...
Yes we all agree that behaviour is a mix of learned and inherited...
Can you link to anywhere an evolutionary biologist has said that learned behaviour can be passed on to offspring by genetic factors?
You seem to be saying that Teaching a dog to fetch changes not just the cells in its brain but also its gonads. ... I think it's more likely that some dogs are easier to train to fetch due to some factor which has some other role such as returning food for pups which we are highjacking... which makes "returning" a satisfaction inducing behaviour...
And now I have to get off the luas and can't address the rest of your post right now.I fully understand the objection here, that the agreed mechanism in genetics currently has no place for events that happen during the lifetime of the organism in terms of phenome development that can impact the genome in terms of inherited characteristics. What I am saying is based on what we observe there must be a mechanism.
There are many observed inheritance traits we have no mechanism for. We know for certain many mental illness conditions are inherited (like schizophrenia), but we have no mechanism for how it happens. If you go on the blog that darjeeling referenced a few posts up you will see very lively debate on this topic.
The main point I am making is that because something is observed in nature or in evolution does not mean we have a mechanism to explain it, but the only possible mechanism is in DNA because that is the only molecule involved in inheritance.
What is instinct if it isn't learned behavior at some point in the organism's evolution? Think about dog breeding. A dog running after a falling pheasant or a stick may be called instinctive, but there are many dog breeds who will not run after anything. A dog that runs after something, fetches it and returns it is behavior that was bred into the dog. The same with chickens roosting. It's easy to say "instinct" but not so easy to explain the mechanism. Clearly at some point in their evolution the behavior of roosting became hardwired into a domestic chicken's brain structure and this behavior is inherited. Yes, you can say from a natural selection standpoint chickens who did not roost all got eaten eventually and only the one's who roost survived to reproduce.. but what is the mechanism? Is there an allene for roosting, for stick fetching?0 -
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I am having some trouble following you here...
Yes we all agree that behaviour is a mix of learned and inherited...
Can you link to anywhere an evolutionary biologist has said that learned behaviour can be passed on to offspring by genetic factors?
The whole field of epigenetics is suggesting this. Epigenetics does not involve a change to the DNA code sequence (A,G,C, etc) but biochemical changes on the bases themselves, methylation for example, that make it through the reproductive cycle.
It likely explains why some evolution proceeds so rapidly. The earlier paper from darjeeling provides data from an epigenetics study on chickens that suggests how we got from a wild animal (red junglefowl) to the domestic chicken so quickly. These rapid changes in morphology, physiology and behavior cannot be explained by random selection/natural selection or random genetic drift. These are adaptive changes where the organism changes during a lifetime and the change is inherited.
Have a read of some of the examples from this general paper on epigenetic inheritance from the University of Utah. I like the water flea example, makes one wonder why the native Irish have not developed something similar to combat the rain
http://learn.genetics.utah.edu/content/epigenetics/inheritance/0 -
Yes...
I have encountered this before in humans with regard to famine survivers and their children (or was it their grand children) and obesity/fat storage.
These things are not learned skills...0 -
The "Discovery" "Institute" is publishing a new "book" and -- lacking the funds and the interest in doing any actual, you know, research -- they grabbed a few suitable-looking photos from the internet and emailed the owner for permission to use them. Unfortunately, the owner was a professional biologist who was familiar with the DI. He published the email exchange:
http://blogs.agu.org/mountainbeltway/2013/02/14/the-discovery-institute-feels-sorry-for-my-students/
Didn't realize that DI supporters were nicknamed "Tooters" -- nice0 -
darjeeling wrote: »The best evidence for inherited epigenetic behavioural changes seems to be the Swedish chicken study, which claims to have found results at odds with Mitchell's view. I haven't fully read the paper yet, but mean to when I get time.
Finally - in part due to this thread! - I have. There are several papers now, dating from 2007 on, and I think I've gone through the main three.
In paper 1 and paper 2, Swedish scientists took domestic chickens and (in paper 1) some of their wild ancestors: red jungle fowl. They let some lead stress-free lives, and spooked others by randomly turning the lights on and off so they never knew when they'd get to feed (chickens don't eat in the dark). They then tested behaviour and brain gene activity, both on the birds themselves and their offspring (all unspooked).
Domestic chickens born to spooked parents showed poor spatial recall, and tended to eat more and compete more for food. Effects, though, weren't consistent, and weren't always strong. The genetic evidence is weaker. A noisy experimental system was used for gene analyses, and the first paper also used small sample sizes. In paper 1, very few genes were be consistently altered in activity in both generations, reproducibility wasn't great, and some artefactual explanations weren't considered. Paper 2 found almost no difference in gene activity in parent birds, never mind trans-generational effects.
Paper 3 is a bit different. The same scientists looked for epigenetic (DNA methylation) and gene activity differences between jungle fowl and domestic chickens. Quite a lot of genes showed both, though the methylation and gene activity levels didn't correlate. Breeding multiple generations showed the epigenetic modifications were stable and inherited along with genotype. A handful of the genes were in areas of the genome shown to have undergone recent Darwinian selection. Taken together, this suggests that the 8,000 years of farming that brought about domestic chickens may have selected for genetic changes that manifest through epigenetic effects.
Paper 3 also looked at differences between birds scoring high vs low in 'fear' tests, and found no evidence that the difference was inherited epigenetically.
I think I want to see something a lot more convincing than these data to persuade me that neo-Lamarckian epigenetic inheritance is a reality. First, better reproducibility is needed. If that were achieved, we'd need to break the system down into stages to track epigenetic change at each crucial stage of reproduction and development to understand what might be going on.
If you read this far, thanks!0 -
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darjeeling wrote: »I think I want to see something a lot more convincing than these data to persuade me that neo-Lamarckian epigenetic inheritance is a reality. First, better reproducibility is needed. If that were achieved, we'd need to break the system down into stages to track epigenetic change at each crucial stage of reproduction and development to understand what might be going on.
If you read this far, thanks!
I agree that it is very early days, but it is such an exciting area of research. Although I have only started to read into the detail, what is fascinating to me is the mechanism involved in how the epigenome controls gene expression throughout the lifetime of the organism, not just in fetal and early childhood development. The fact that the epigenome learns from its experience of its environment and that this may be inherited is quite mindboggling.
The attached recent article from the NIH is a good summary of the work to date in epigenetic inheritance with lots of references. It doesn't mention the Swedish study, maybe that was too recent.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2989988/0 -
I agree that it is very early days, but it is such an exciting area of research.
Yes, it is a new and fast-developing field, and the more I read, I see there's now quite a stream of studies looking for this trans-generation epigenetic inheritance (metabolism in mice, rats, humans; depression in mice; cocaine response in rats; ...)
Research is now weeding out effects due to more mundane causes and beginning to dissect the processes, for instance looking directly for chemical changes to germline DNA that then pass from males to offspring. The recent coke and rats work does this nicely, and it's the kind of effort that will show what's going on in the black box. I expect some effects will disappear when retested, and some will turn out to be environmental. Some, though, may be true epigenetic inheritance - perhaps with a fairly simple epigenetic switch turning on a genetic pathway. We will have to wait to see if any of these might turn out to be advantageous.
I feel I've probably wandered off from what this thread was about and into Biology forum territory. Where were we again?0 -
darjeeling wrote: »Yes, it is a new and fast-developing field, and the more I read, I see there's now quite a stream of studies looking for this trans-generation epigenetic inheritance (metabolism in mice, rats, humans; depression in mice; cocaine response in rats; ...)
Research is now weeding out effects due to more mundane causes and beginning to dissect the processes, for instance looking directly for chemical changes to germline DNA that then pass from males to offspring. The recent coke and rats work does this nicely, and it's the kind of effort that will show what's going on in the black box. I expect some effects will disappear when retested, and some will turn out to be environmental. Some, though, may be true epigenetic inheritance - perhaps with a fairly simple epigenetic switch turning on a genetic pathway. We will have to wait to see if any of these might turn out to be advantageous.
I feel I've probably wandered off from what this thread was about and into Biology forum territory. Where were we again?
nagirrac was explaining how guessing is valid science, lol :P0 -
The "Discovery" "Institute" is publishing a new "book" and -- lacking the funds and the interest in doing any actual, you know, research -- they grabbed a few suitable-looking photos from the internet and emailed the owner for permission to use them. Unfortunately, the owner was a professional biologist who was familiar with the DI. He published the email exchange:
http://blogs.agu.org/mountainbeltway/2013/02/14/the-discovery-institute-feels-sorry-for-my-students/
Didn't realize that DI supporters were nicknamed "Tooters" -- nice
This is a great quote
It’s a funny idea: to cling to the idea of a Creator, they imply that he did a job that was (a) almost completely indistinguishable from an evolved system but (b) just sloppy enough that we can find his fingerprints hidden in life’s unexamined details.0 -
nagirrac was explaining how guessing is valid science, lol :P
Now that its been explained to you that there actually is another mechanism for inheritance, shouldn't you be printing out the past several pages and eating them?
You clearly had never heard of epigenetics or epigenetics inheritance nor had any idea of what their likely implications are for evolution. You might want to get up to speed and rejoin the conversation, rather than just hurling personal insults.0 -
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darjeeling wrote: »I feel I've probably wandered off from what this thread was about and into Biology forum territory. Where were we again?
It's highly relevant though as it highlights the "scientism" thinking of many atheists on this thread. The thinking that goes; "evolution is just a messy, blind process and this conclusion is backed up by genetics". The scism that is occuring between evolutionary biologists and epigeneticists is highlighting the fallacy of this conclusion. If you don't believe there is a scism, read the comments on Jerry Coyne's blog about leading epigenetics researchers. Even Dawkins has a pop: "I can't wait for this epigenetics bandwagon to be replaced by the next one". The last stings of a dying wasp.
In your prior post you used the term "black box". This is very accurate and highlights the most common misconception regarding genetics in general. What many people do not grasp is we may understand the structure of DNA but we are still dabbling at understanding the function of DNA, and the function of the epigenome. There is a huge paradox in genetics which is barely known outside the biological community. The accepted genetic mechanism is that DNA transcribes to RNA which then translates to proteins. However, what are the mechanisms whereby 1) the same DNA molecule in one cell gives rise to a neuron and in another gives rise to a skin cell and another a kidney cell, and 2) the same DNA molecule contains all the instructions to build a complete organism. The answer to both appears to be that the genome does not do this, that is the function of the epigenome.
It even goes further than that when you just scratch the surface of evolution. We share 98% of our coding DNA with a mouse. Mice and humans have a common ancestor that is estimated to be from ~100 million years ago. So, in 100 million years all of the evolution from that mouse-like mammal to a modern day human is supposed to be in 2% of our coded DNA? Forget about similarities to a chimp, we are 98% the same as a mouse in terms of our coded DNA.
As we unearth more of the detail in the mechanisms involved (the black box) it is hard to escape the conclusion that DNA represents the "lego" pieces that can be arranged with literally infinite variety to give rise to various species. The epigenome is what does the arranging, much of it appears pre-programmed and much of it in response to its environment. This results in a phenotype which is highly adaptable during its lifetime, and some of these adaptions appear to be inheritable. The observed evidence for this conclusion is everywhere we look, but it is a conclusion that overturns the predominent "gene-centric" view of science and the "blind" evolution view of atheists.0 -
Therefore magic?0
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Therefore magic?
No, therefore much more complex than we had imagined. A bit like quantum physics, classical physics was relatively easy to understand until we came across the anomalies of QM (which we still can't interpret 100 years later).
Genetics and DNA seemed easy to understand until we actually had the tools to dig into the mechanisms involved. I have a sinking feeling biology is headed the same way as physics.0 -
Now that its been explained to you that there actually is another mechanism for inheritance, shouldn't you be printing out the past several pages and eating them?
Why? When did I ever object to epigenetics?
You claimed that animals intelligently and creatively learn to adapt to their environment, that evolution is an intelligent and creative process. Perhaps you should read up on what epigenetics or epigenetics inheritance actually says, because it ain't what you think.
Stop making ridiculous claims and then searching around for science you think you can tenaciously attach to your far out ideas.0 -
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No, therefore much more complex than we had imagined.
Meh. Another layer of complexity ain't no thang. Certainly doesn't suggest creative intelligence. Just makes things a bit messier. I'm not surprised if there's a bit more to it than straightforward genetics. Certainly neither are any of the folks I work with in UCC's microbiology department.0 -
No, therefore much more complex than we had imagined. A bit like quantum physics, classical physics was relatively easy to understand until we came across the anomalies of QM (which we still can't interpret 100 years later).
Genetics and DNA seemed easy to understand until we actually had the tools to dig into the mechanisms involved. I have a sinking feeling biology is headed the same way as physics.
I have to start by saying I really don't understand the inclusion of the highlighted word. Well, not meaning any offense nagirrac, I can understand why you have a sinking feeling but I'm not sure why anyone else should have.
I don't mind the idea of biology going down the road of quantum physics. Not knowing is cool. It means there's some really weird **** and some seriously exciting discoveries up ahead.
It's like what Richard Feynman says here:
It could be that there is a simple explanation as to why evolution (for example) proceeds in the way that it does or it could be that it's like the layers of an onion and the deeper we get the more complex it becomes. But whatever way it turns out that's the way it is.
In the end the take home message from Feynman, which is particularly relevant IMO regarding epigenetics and junk DNA, is this:
"I can live with doubt and uncertainty and not knowing. I think it is much more interesting to live not knowing than to have answers which might be wrong."
That is a pretty neat summary of my attitude towards science and religion. To me, religion and theism and deism is a crutch for the weak. There are gaps in our knowledge, sure. But plugging that gap by saying that it must have been Yahwheh or a deity or "an intelligence" is a weak argument. It is a deduction from a lack of knowledge not positive knowledge. What's wrong with leaving the gap there and saying I don't know.0 -
Meh. Another layer of complexity ain't no thang. I'm not surprised if there's a bit more to it than straightforward genetics. Certainly neither are any of the folks I work with in UCC's microbiology department.
I agree, that's what makes science fun. I just think there's more to it than "a bit more to it" though. I think we are at the beginning of a paradigm shift in biology, exciting times ahead.
Microbiology is one of the disciplines that would lead you to the conclusion there is more to it than straightforward genetics. Those microbes are damn smart:)0 -
Meh, we've known that life has been associated with quantum physics for decades. Thinking there's more to it has no bearing on what there IS to it. I see epigenetics as just another subset of biology, along with molecular biology, genetics, systems biology, biochemistry, immunology, bioinformatics and however many more there are. If it comes up with more evidence than it currently has all well and good, it'll have plenty of company. If it doesn't, nobody will miss it. Hardly the earth-shattering revolution that proves God or whatever.0
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It's highly relevant though as it highlights the "scientism" thinking of many atheists on this thread. The thinking that goes; "evolution is just a messy, blind process and this conclusion is backed up by genetics".
[...]
The observed evidence for this conclusion is everywhere we look, but it is a conclusion that overturns the predominent "gene-centric" view of science and the "blind" evolution view of atheists.
I think you are looking at some exploratory science and wanting to see a pattern that supports a view of the world in which there is design and purpose rather than aimless radomness. The science is asking 'how?' and you want it to tell us 'why'. I don't think it can.
As for biology and evolution, I don't see any prospect or need of a paradigm shift. What's going on now is the unveiling of what was possible, suspected or actually predicted within an evolutionary framework, but hitherto technologically inaccessible.It's like what Richard Feynman says here:0 -
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I have to start by saying I really don't understand the inclusion of the highlighted word. Well, not meaning any offense nagirrac, I can understand why you have a sinking feeling but I'm not sure why anyone else should have.
In the end the take home message from Feynman, which is particularly relevant IMO regarding epigenetics and junk DNA, is this:
"I can live with doubt and uncertainty and not knowing. I think it is much more interesting to live not knowing than to have answers which might be wrong."
That is a pretty neat summary of my attitude towards science and religion. To me, religion and theism and deism is a crutch for the weak.
What's wrong with leaving the gap there and saying I don't know.
Of course it's offensive oldnwiser but it is the predominently athiest forum so one gets used to it
You say you don't understand why I used the term "sinking feeling" but you can conclude why I used it and even make a judgement on me based on that interpretation? Wow, just wow!
I will explain my use of the word later.
I absoloutely love Richard Feynman as a teacher. I would say most of everything I have learned about physics came from multiple readings of "six easy pieces" and "six not so easy pieces" and watching his lectures on line. It's a tragedy he was taken from us while he still had a brilliant mind.
The interview posted though is mainly describing his atheist worldview. It's how he looked at the world. It has nothing to do with science or the pursuit of science per se. Science is the pursuit of knowledge about the observed universe we live in, nothing more, nothing less. There is no necessity to draw any conclusions about the meaning or lack of meaning in the universe from science, this is the mistake creationists and atheists alike make.
Back to my use of "sinking feeling". What quantum physics tells us is that the universe is non-local. Most people do not understand what non-local means (not what non-local is, what non-local means) as our observed universe at the macro level appears local and determinate. Although we can describe non-local mathematically, we simply cannot interpret what non-local means if we only follow reductionist science. The universe is holistic and indeterminate, and until we adopt a holistic approach involving multipe disciplines we are going to get stuck and stay stuck in chasing rabbits down endless burrows. My "sinking feeling" is due to the realisation that we are, in my humble opinion, close to conclusive evidence indicating life at the molecular level is non-local, and off we will go again trying to break it into smaller pieces to understand it.
As for theism and deism being a "crutch for the weak", that's hardly worthy of comment given the great numbers of scientists who were or are. I am sure Einstein would be interested in your opinion of him, but I am also sure he would be inoffensive in his response as he was a very humble man (as most deist and theist scientists tend to be, unlike many of their atheist colleagues).0 -
darjeeling wrote: »I think you are looking at some exploratory science and wanting to see a pattern that supports a view of the world in which there is design and purpose rather than aimless radomness. The science is asking 'how?' and you want it to tell us 'why'. I don't think it can.
As for biology and evolution, I don't see any prospect or need of a paradigm shift. What's going on now is the unveiling of what was possible, suspected or actually predicted within an evolutionary framework, but hitherto technologically inaccessible.
You mean in the same sense that atheists look at exploratory science and want to see a pattern that supports a view of the world in which there is aimless randomness? Then, yes, I would agree, not so much that I "want" it though but that I "observe" it.
I would have to disagree with your second paragraph and it has nothing to do with worldview. Our standard model for evolution is that random genetic mutation introducing new physical traits at the individual level leads (over long periods of time) to natural selection at a population level, ultimately leading to new species.
How well does this fit with the fact that humans and mice have 98% similarity in coding DNA? If evolution was solely due to mutation of coding DNA (including random drift), wouldn't you expect a bit more divergence in said coding DNA over 100 million years?0 -
You mean in the same sense that atheists look at exploratory science and want to see a pattern that supports a view of the world in which there is aimless randomness? Then, yes, I would agree, not so much that I "want" it though but that I "observe" it.
I think science can spot randomness, but aimlessness is outside its remit. That's why we find people with quite different religious outlooks being able to agree on scientific theory. For what it's worth, I'm not in favour of trying to use science to argue for 'strong atheism', though it can be used to disprove the odd Flood here or there.I would have to disagree with your second paragraph and it has nothing to do with worldview. Our standard model for evolution is that random genetic mutation introducing new physical traits at the individual level leads (over long periods of time) to natural selection at a population level, ultimately leading to new species.
How well does this fit with the fact that humans and mice have 98% similarity in coding DNA? If evolution was solely due to mutation of coding DNA (including random drift), wouldn't you expect a bit more divergence in said coding DNA over 100 million years?
I think we would all agree that what I might expect from gut common sense is very different from the predictions of a mathematical model of evolution. I don't see that our models have a problem with the similarities we see, though I think I will pass on delving into the numbers for everyone's sake.0 -
darjeeling wrote: »I think we would all agree that what I might expect from gut common sense is very different from the predictions of a mathematical model of evolution. I don't see that our models have a problem with the similarities we see, though I think I will pass on delving into the numbers for everyone's sake.
Would you agree that the differences between mice and humans has essentially nothing to do with their coding DNA, but is due to divergence between the non-coding regulatory regions of DNA and their respective epigenomes?
Tim Hubbard of the Sanger Institute thinks that human and mice coding DNA is the same and all differences are due to non-coding regions. I know, appeal to authority, but they are the one's that produced the most extensive mouse data we have.0 -
Would you agree that the differences between mice and humans has essentially nothing to do with their coding DNA, but is due to divergence between the non-coding regulatory regions of DNA and their respective epigenomes?
No...Tim Hubbard of the Sanger Institute thinks that human and mice coding DNA is the same and all differences are due to non-coding regions. I know, appeal to authority, but they are the one's that produced the most extensive mouse data we have.
Does he? Would you be able to link to somewhere he talks about that?0 -
Does he? Would you be able to link to somewhere he talks about that?
I don't have a direct link where he said it, but these two sources quote him. I am as sceptical of a lot of what is written in the popular science publications as anyone, but don't believe they would misquote him on such a fundamental statement. If you go to the www.yourgenome.org website and listen to his interviews he clearly puts the emphasis on non coding DNA.
http://www.newscientist.com/article/dn2352-just-25-of-dna-turns-mice-into-men.html
http://www.askabiologist.org.uk/answers/viewtopic.php?id=7413
As an aside, I am not saying at all that Darwinian or neo-Darwinian evolution does not occur, of course it does. I am saying we do not understand the functionality of the genome/epigenome well enough to make conclusions about the underlying mechanisms. Saying it's all random mutation of genes (as in coded sections of DNA) is to me highly questionable.What we can say, I believe conclusively, is that changes at the molecular level of the genome/epigenome give rise to different traits that are inherited and result in variation, leading to natural selection.0 -
Would you agree that the differences between mice and humans has essentially nothing to do with their coding DNA, but is due to divergence between the non-coding regulatory regions of DNA and their respective epigenomes?
Tim Hubbard of the Sanger Institute thinks that human and mice coding DNA is the same and all differences are due to non-coding regions. I know, appeal to authority, but they are the one's that produced the most extensive mouse data we have.
We could discuss what he means and how true it is, given the evidence. But given the way this thread has gone, I'm not sure that would be the best idea.
With the current technological revolution happening in biology, there are a lot of new things being discovered. To understand what they mean and how important they are, we need to see how they fit with established facts and theory. If we lose sight of that and instead try to see if each new finding can be made to fit with some preconceived metaphysical idea we have about the universe, we're going to end up with a very skewed picture. Unfortunately when evolution is constantly being discussed in an atheism vs religion context, this is what happens.0 -
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There's zero evidence for abiogenesis, yet it's accepted by many as what must have happened. I'd call it wishful thinking.
* http://www.nasa.gov/topics/solarsystem/features/life-components.html
^ http://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experimentMy mammy does this despite the fact she knows I'm an atheist...
Haven't lived at home since I was 17.....I've been renting and move a lot so it's easier to get sh*t sent there....No, you're not.
Humans seem as if designed, ergo designer.
Earth seems designed as it supports human life, ergo designer.
The designer(s) of Earth and humans also seem designed (because humans are).
The universe must be designed to support the Earth-designers.
And so on, ad infinitaum. You're kicking the can down the road. At some point you have to have life that arose without a designer. Otherwise, you're putting forward "God did it".0 -
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Isn't it your position, as a christian (I assume), that the entire universe moves exactly to gods plan, that literally everything is designed. So what frame of reference would you have to recognise something that isn't designed? If all you have is a hammer, everything looks like a nail.
No, I'm not a Christian or a member of any other religion.
I just think it's reasonable to infer intelligence as the best explanation for the appearance of design in life forms. This inference doesn't give the creative intelligence any other attributes normally associated with God, although it raises further questions and the cosmological and fine tuning arguments take on a greater significance.0
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