What does "best explained" by design mean?

[pitabread]

no according to your own source:

"The central idea of biological evolution is that all life on Earth shares a common ancestor"

so its not just mere changes.

This isn't a debate. Go back and re-read the page because you apparently skipped over most of it:

"Biological evolution, simply put, is descent with modification. This definition encompasses small-scale evolution (changes in gene — or more precisely and technically, allele — frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations). Evolution helps us to understand the history of life."

An introduction to evolution​

 

[Abraxos]

Not really - the ENCODE project paper was a lesson on the dangers of not clearly defining or explaining the terms used and their meaning in the context of the study, and of post-hoc re-scoping.

Their figure for 'functional' DNA referred to DNA that they thought might potentially be transcribed (they were not particularly judicious in their choice of transcription proxies) and might possibly result in biochemical activity (it was already known that there was transcription activity in 'junk' DNA).

Unfortunately, it was taken (read) to mean DNA that was actively transcribed and had biological activity, i.e. contributed to a selective advantage. This misunderstanding of 'functional' caused a strong reaction and criticism from other researchers in the field, particularly as it was clear that active areas involved were not strongly conserved as would be expected of biologically functional sequences.

It was later explained that, as ENCODE was investigating activity potentially relevant to biomedical studies, they were interested in biochemical products whether biologically significant or not (perhaps for possible drug interactions). Subsequent papers from the group no longer mention a 'functional' DNA figure. It is now widely thought that the original lead paper was written knowing that the figure was likely to be misinterpreted, so as to attract publicity.

See The Truth about Encode and The ENCODE Controversy.

I'm not sure if I'm reading this correctly so I'm going to have to mull over on this comment for a bit.

Your characterization of design patterns is a little off the mark. Design patterns are simply proven strategies or template solutions for common tasks or problems; they're useful and effective ideas.

Well yes, strategies and templates that work within our current vernacular, yet there are even better and more efficient strategies and even better templates seen within cells that transcends anything man has achieved.

Error correction is not itself a design pattern, but a particular technique of error correction might be. You can abstract design patterns from any efficient and generalisable utilitarian sequence of operations; i.e. you can pick up good ways of doing things by seeing how things that work well are done.

I'm curious to know what design patterns you see in DNA repair, because IIRC, there are about six repair mechanisms, each of which is pretty specific; can you describe the design pattern or patterns they demonstrate?

I'm actually delving much deeper than that, and without getting too technical, the automated error correction is just one aspect of the whole templated processing system which also contains storage areas designed (or seen) to house a dense population of information, and it does this more efficiently and more effectively compared to what man has ever achieved.
It's basically understanding the design better by using rational design principles and use those principles to model the kind of design patterns we see in nature and use that to our benefit. This is known as biomimetics which uses what's in nature to solve design problems that we face because after all the premise is that nature was designed, life was designed.

​

But how is the possibility of picking up neat tricks from biological processes relevant to Intelligent Design?

With respect, this thesis doesn't seem to hold together or make much sense...

ID theorists such as Stephen Meyer learned from Charles Darwin that when you are trying to reconstruct an event in the remote past, there is the use of a different method of scientific reasoning which you displayed as your own criterion of inferring the best explanation invoking a causality which is known to produce the effect; in this case design patterns portraying "neat tricks."

It's certainly one thing to say we have scientific arguments and we are looking at certain scientific features of the world, and this was what my initial thoughts were on when considering ID as a scientific theory, yet it's really an attempt to classifying arguments or theories. The main point is whether the inference of ID is true or not.
So in terms of whether it can be demonstrated through the scientific method, the short answer would be: Yes. The scientific method goes from: observation -> hypothesis -> experiment -> conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesise that if objects were designed, they will contain CSI. They then seek to find CSI. One easily testable form of CSI is irreducible complexity (IC). ID researchers can then experimentally reverse-engineer biological structures to see if they are IC. If they find them, they can conclude design.

That all said, I am somewhat still uncertain as to what to make of the inference of ID from a scientific perspective. It comes off as the signature to the sophistication of the tools used which denote away from the tools which we call science. There is no level of scientific reasoning to presuppose ID as God or alien or some superhuman which in and of itself is not a signature at all, and cannot be attributed to the designer that we are copying as we cannot know who the designer is. That is beyond the sciences. While I am sympathetic to the arguments and I find some of them intriguing, I prefer to be free of that intelligent design label as it seems to restrict my actual view.

 

[FrumiousBandersnatch]

...Well yes, strategies and templates that work within our current vernacular, yet there are even better and more efficient strategies and even better templates seen within cells that transcends anything man has achieved.

Such as?

I'm actually delving much deeper than that, and without getting too technical, the automated error correction is just one aspect of the whole templated processing system which also contains storage areas designed (or seen) to house a dense population of information, and it does this more efficiently and more effectively compared to what man has ever achieved.

If you don't want to get 'too technical', how about supplying a citation or reference?

It's basically understanding the design better by using rational design principles and use those principles to model the kind of design patterns we see in nature and use that to our benefit. This is known as biomimetics which uses what's in nature to solve design problems that we face because after all the premise is that nature was designed, life was designed.

I'm well aware of biomimetics - and many people use it daily without realising, for example, in Velcro (other hook & loop products are available).

I'm happy to call the trial & error products of natural selection 'designs', but it's generally frowned on here because of its teleological baggage. But can you explain how abstracting design patterns from nature supports the premise of ID in particular? - is that what you're claiming?

​

ID theorists such as Stephen Meyer learned from Charles Darwin that when you are trying to reconstruct an event in the remote past, there is the use of a different method of scientific reasoning which you displayed as your own criterion of inferring the best explanation invoking a causality which is known to produce the effect; in this case design patterns portraying "neat tricks."

I didn't think it necessary to compare ID against my criteria as it was so obviously inadequate, but let's go through them:

1. Justifiability & fruitfulness: the junk DNA prediction is mistaken; are there any other fruitful predictions?
2. Explanatory power: ID is non-specific and lacks detail (and, as I mentioned previously, it's based on guesswork) so provides little understanding; but fatally, it raises more questions than it answers, and all are unanswerable, so it has no explanatory power. Without an explanatory mechanism or framework, it gives us no understanding of the phenomena it purports to explain, nor does it unify our understanding of wider phenomena.
   
3. Parsimony: ID introduces an unexplained, unjustified assumption - an additional entity, the Designer.
4. Conservatism: ID doesn't cohere with our existing body of knowledge - you could tenuously hypothesise intelligent aliens (for which there is no evidence), but that just raises the question of their origins - is it intelligent aliens all the way down? But specifically, in this example, it contradicts the genetic evidence of progressive lineage diversification with accumulating biologically non-functional weakly conserved DNA.

I surely don't need to do a point-by-point comparison with the ToE; the only hypothesis that could do worse than ID is something even more nebulous, such as 'magic', but only because we can't even begin to guess what magic might be inclined to do, whereas we can make guesses at what we think an intelligent designer might do - but without any way to validate or verify those guesses. Correspondence with the real world doesn't confirm that a guess of what an intelligent designer might do is correct, any more than saying you're going to make it rain and it subsequently raining confirms that you made it rain.

It's certainly one thing to say we have scientific arguments and we are looking at certain scientific features of the world, and this was what my initial thoughts were on when considering ID as a scientific theory, yet it's really an attempt to classifying arguments or theories. The main point is whether the inference of ID is true or not.

The world does not have 'scientific features', just features. ID is not a scientific theory, it is pseudoscience; the argument from design is a teleological argument. It assumes purpose, intent, knowledge, and potency, and is ultimately unfalsifiable (e.g. "God The 'intelligent designer' moves in mysterious ways...").

So in terms of whether it can be demonstrated through the scientific method, the short answer would be: Yes. The scientific method goes from: observation -> hypothesis -> experiment -> conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesise that if objects were designed, they will contain CSI. They then seek to find CSI. One easily testable form of CSI is irreducible complexity (IC). ID researchers can then experimentally reverse-engineer biological structures to see if they are IC. If they find them, they can conclude design.

Sadly, ID falls badly at the hypothesis hurdle, as already explained.

But since you bring up CSI, that too is rather ill-defined - Dembski's mathematics and understanding of probability have been shown to be flawed - and he begs the question by requiring you to calculate the probability of the feature arising naturally in order to calculate its CSI. The proposed instances of irreducible complexity to which it is most applicable have all been refuted, and computer simulations of evolution by natural selection produce high CSI products...

So no - as it stands, the scientific method would take a barge-pole to ID, and CSI is sciency hand-waving for an uncritical (gullible?) audience. In other words, more pseudoscience.

That all said, I am somewhat still uncertain as to what to make of the inference of ID from a scientific perspective.

See above

... I am sympathetic to the arguments and I find some of them intriguing, I prefer to be free of that intelligent design label as it seems to restrict my actual view.

In that case, you're pointing in the right direction; scepticism and critical thinking is the path to take, but it does take more work than the alternative routes.

 

[pitabread]

ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesise that if objects were designed, they will contain CSI. They then seek to find CSI. One easily testable form of CSI is irreducible complexity (IC). ID researchers can then experimentally reverse-engineer biological structures to see if they are IC.

Do you have any citations that show that this is the case?

In all the ID literature I've read, I've never seen cases where either CSI or ID were ever used in a meaningful fashion. Or for that matter, where those concepts have even been validated as biologically relevant to begin with.

Right now, CSI and ID sit as failed attempts at methods to try to detect artificial design. To the best of my knowledge, nobody actually uses them for anything even though there are arguably applications for design detection in biology (i.e. GM sequences/products).

 

[xianghua]

This isn't a debate. Go back and re-read the page because you apparently skipped over most of it:

"Biological evolution, simply put, is descent with modification. This definition encompasses small-scale evolution (changes in gene — or more precisely and technically, allele — frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations). Evolution helps us to understand the history of life."

An introduction to evolution​

again: "and large-scale evolution". if they include that part then evolution must deal with "macro evolution" too.

 

[pitabread]

again: "and large-scale evolution". if they include that part then evolution must deal with "macro evolution" too.

In this context, "macro evolution" is simply referring to patterns of evolution that arise from the process of evolution occurring over time.

I'm not sure where you are going with any of this.

 

[Abraxos]

Such as?

If you don't want to get 'too technical', how about supplying a citation or reference?

I'm well aware of biomimetics - and many people use it daily without realising, for example, in Velcro (other hook & loop products are available).

It's painfully technical, but let me put it this way, it's basically allowing us to model off pre-existing designs that are proven to function which scientists are currently using as the foundation to build nanomachines that can exclusively attach to cancer cells to inject medicine or to further drill into the cancer cell's membrane to kill it.
You can continue to watch the video provided in the OP as your reference and introduction on what modern biologists are discovering inside a cell. He starts describing these design patterns at 43:30 minutes into the video. Let me know if this is like velcro in your honest opinion.

I'm happy to call the trial & error products of natural selection 'designs', but it's generally frowned on here because of its teleological baggage. But can you explain how abstracting design patterns from nature supports the premise of ID in particular? - is that what you're claiming?

​

There would most probably be a tendency to discredit rather than investigate, but if we are to be critical thinkers, one should owe it to themselves to differentiate between the philosophical (teleological ) and the scientific (inference). It's that inference to the best explanation which is that the creation of new information is habitually associated with conscious activity. What goes on after that by trying to ascertain the reason of why there is design becomes a philosophical argument.

The main point here is the origin can be accounted for on these issues of phenotypic complexities and anatomical novelties that cannot be explained by the evolutionary processes I touched upon in post #30. These problems were outlined by prominent evolutionary thinkers such as Professor Gerd Muller at the Royal Society of London, and he made a list of the explanatory deficits of modern synthesis. (modern synthesis is another name for neo-Darwinism.) And almost all of which had to do with the lack of creative power surrounding the famed natural selection and random mutation mechanism.

I didn't think it necessary to compare ID against my criteria as it was so obviously inadequate, but let's go through them:

1. Justifiability & fruitfulness: the junk DNA prediction is mistaken; are there any other fruitful predictions?
2. Explanatory power: ID is non-specific and lacks detail (and, as I mentioned previously, it's based on guesswork) so provides little understanding; but fatally, it raises more questions than it answers, and all are unanswerable, so it has no explanatory power. Without an explanatory mechanism or framework, it gives us no understanding of the phenomena it purports to explain, nor does it unify our understanding of wider phenomena.
   
3. Parsimony: ID introduces an unexplained, unjustified assumption - an additional entity, the Designer.
4. Conservatism: ID doesn't cohere with our existing body of knowledge - you could tenuously hypothesise intelligent aliens (for which there is no evidence), but that just raises the question of their origins - is it intelligent aliens all the way down? But specifically, in this example, it contradicts the genetic evidence of progressive lineage diversification with accumulating biologically non-functional weakly conserved DNA.

I surely don't need to do a point-by-point comparison with the ToE; the only hypothesis that could do worse than ID is something even more nebulous, such as 'magic', but only because we can't even begin to guess what magic might be inclined to do, whereas we can make guesses at what we think an intelligent designer might do - but without any way to validate or verify those guesses. Correspondence with the real world doesn't confirm that a guess of what an intelligent designer might do is correct, any more than saying you're going to make it rain and it subsequently raining confirms that you made it rain.

The world does not have 'scientific features', just features. ID is not a scientific theory, it is pseudoscience; the argument from design is a teleological argument. It assumes purpose, intent, knowledge, and potency, and is ultimately unfalsifiable (e.g. "God The 'intelligent designer' moves in mysterious ways...").

Sadly, ID falls badly at the hypothesis hurdle, as already explained.

But since you bring up CSI, that too is rather ill-defined - Dembski's mathematics and understanding of probability have been shown to be flawed - and he begs the question by requiring you to calculate the probability of the feature arising naturally in order to calculate its CSI. The proposed instances of irreducible complexity to which it is most applicable have all been refuted, and computer simulations of evolution by natural selection produce high CSI products...

So no - as it stands, the scientific method would take a barge-pole to ID, and CSI is sciency hand-waving for an uncritical (gullible?) audience. In other words, more pseudoscience.

See above

TBH I find these statements unwarranted as it is based on conjecture and a misrepresentation of the arguments. I also can't help but see a bit of double standard being placed upon the same method of reasoning used by Charles Darwin himself. You are welcome to go point by point using neo-Darwinism as a comparison, but you may surprise yourself on realising that the scientific method debunks neo-Darwinism. If prominent evolutionary scientists pointed this out in the Royal Society of London, I think it is only a matter of time before it is slowly made aware of gently to the broader community.

One issue which I will address:

Junk DNA
When the genome was decoded back in 2000 it was discovered that only 2% of the genome coded for proteins and the other 98% was dismissed as junk. This lead to the premise that this was attributed attributed to molecular accidents that have accumulated through the course of gradual evolution. Well known biologists such as Richard Dawkins and Francis Collins have used the term "junk DNA" as evidence for neo-Darwinism and it had certainly resonated with many evolutionary enthusiasts as a running talking point. But when the results of over 1,600 experiments by 450 scientists from 32 different institutions discovered that the 98% that people thought were junk, wasn't junk at all, but absolutely essential for the maintenance of life. The opinion pieces you provided seem to suggest that prominent scientific journals "misrepresented the position of junk DNA" which I find no evidence of, rather a display of a shifting of the goal posts - yet for whatever reason, the goals here are not in favour toward neo-Darwinian ideas.

In that case, you're pointing in the right direction; scepticism and critical thinking is the path to take, but it does take more work than the alternative routes.

I don't think there is a whole lot of luxury in rigorously investigating the matter of a thing, but it is required if you want to understand something thoroughly enough to shape an objective opinion. Many may seem to announce they're critical in their thoughts, but more often than not they appear more interested in dissecting appearances rather than the substrate.

 

[pitabread]

When the genome was decoded back in 2000 it was discovered that only 2% of the genome coded for proteins and the other 98% was dismissed as junk.

[Citation Needed]

(I find it odd that when trying to look up this claim, the only thing I can find are ID/creationist sources.)

 

[xianghua]

In this context, "macro evolution" is simply referring to patterns of evolution that arise from the process of evolution occurring over time.

I'm not sure where you are going with any of this.

so evolution by definition isnt just mere changes but specific changes.

 

[pitabread]

so evolution by definition isnt just mere changes but specific changes.

What do you mean by "specific" changes?

The process of evolution is just hereditary changes in populations over time. Or, more specifically a change in the gene pool (of a population) over time.

And yes, the science of evolution also encompasses studying the results of those changes.

What's your point again?

 

[FrumiousBandersnatch]

It's painfully technical...

OK, well stop if it hurts too much, we wouldn't want you to injure yourself...

...it's basically allowing us to model off pre-existing designs that are proven to function which scientists are currently using as the foundation to build nanomachines that can exclusively attach to cancer cells to inject medicine or to further drill into the cancer cell's membrane to kill it.

My understanding is that rather build nanomachines from scratch, they're using modified bacterial mechanisms such as CRISPR Cas9, but I'd be interested to see a link or reference to what you describe.

...You can continue to watch the video provided in the OP as your reference and introduction on what modern biologists are discovering inside a cell. He starts describing these design patterns at 43:30 minutes into the video. Let me know if this is like velcro in your honest opinion.

OK, I watched that part of the video - and I can see you just used Meyers' misleading description of design patterns verbatim. Dixon's discovery of the complexity of generic code transcription is nothing new, and a major factor in its efficiency and 'elegance' is that it doesn't really function like computer code (whatever Bill Gates may have said) but more like an industrial demand economy...

I asked you what particular design patterns we could use because, to my knowledge (I've used design patterns in software development for 20+ years), we already have our own implementations of automated error correction (as I said, not in itself a design pattern), hierarchical filing, and nested coding, that are well suited to our computer architectures and resources.

As for overlapping reading frames, overlapping code sequences were experimented with at the dawn of computer programming, but are pretty much unmaintainable. Self-modifying code is still used in special circumstances, so it's possible some overlapping code is in use, but without the storage restrictions of early computing systems, there's generally no good reason to use it. As it happens, overlapping reading frames are expected to have evolved in the genome because of the way transcription (assembly of mRNA) control differs from translation (protein assembly) control - see Start & Stop Codons for an overview.

As I explained previously, Velcro is the commonest biomimetic in everyday use, and hook & loop is a design pattern, so it has 'being a design pattern' in common with other design patterns. You suggested that we could make biomimetic use of the genomic design patterns, but you haven't yet given an example - I'm sceptical because of the major differences between genome processing and computer processing architectures, but I'm interested to hear your suggestions.

... It's that inference to the best explanation which is that the creation of new information is habitually associated with conscious activity.

If you're suggesting that a claim of 'habitual association' somehow makes a testable hypothesis, you'll have to explain how you reach that conclusion. But in any case, new information is only associated with consciousness by people who don't understand information.

Information is inherent in the arrangement of matter - if the arrangement changes, the information changes; if the arrangement is new the information is new; new information is produced continually in nature. This is why it's so fundamentally related to entropy. If you were instead referring to Dembsky's hokey 'Complex Specified Information', that too has been shown to be produced by natural processes, so consciousness is not a requirement.

The main point here is the origin can be accounted for on these issues of phenotypic complexities and anatomical novelties that cannot be explained by the evolutionary processes I touched upon in post #30. These problems were outlined by prominent evolutionary thinkers such as Professor Gerd Muller at the Royal Society of London, and he made a list of the explanatory deficits of modern synthesis. (modern synthesis is another name for neo-Darwinism.) And almost all of which had to do with the lack of creative power surrounding the famed natural selection and random mutation mechanism.

You didn't supply any references, so I don't know what specific problems were raised, but if you're referring to Shapiro's work, he's arguing that known processes (e.g. epigenetics, genome doubling & restructuring, symbiogenesis, HGT, inter-specific hybridization) play a larger role in cellular evolution than the neo-Darwinian synthesis suggests. His views are more extreme and so more controversial than most, but it's clear these processes have some influence, it's a matter of establishing the degree; it's early days. But the underlying principle of evolution by natural selection still applies.

TBH I find these statements unwarranted as it is based on conjecture and a misrepresentation of the arguments. I also can't help but see a bit of double standard being placed upon the same method of reasoning used by Charles Darwin himself. You are welcome to go point by point using neo-Darwinism as a comparison, but you may surprise yourself on realising that the scientific method debunks neo-Darwinism.

Expressing dissatisfaction is not an argument. You're quite welcome to show your own abductive analysis, or counter mine. If you think I'm misrepresenting the argument, by all means show how I'm doing so.

Junk DNA
When the genome was decoded back in 2000 it was discovered that only 2% of the genome coded for proteins and the other 98% was dismissed as junk.

Citation? You do realise that the term 'junk DNA' was coined in the 1960's, and formalized in 1972 ?

But when the results of over 1,600 experiments by 450 scientists from 32 different institutions discovered that the 98% that people thought were junk, wasn't junk at all, but absolutely essential for the maintenance of life. The opinion pieces you provided seem to suggest that prominent scientific journals "misrepresented the position of junk DNA" which I find no evidence of, rather a display of a shifting of the goal posts - yet for whatever reason, the goals here are not in favour toward neo-Darwinian ideas.

Perhaps I didn't explain clearly enough. ENCODE study identified that much 'junk DNA' is transcribed and translated; but the products are not biologically functional, i.e. it produces harmless junk. They say their concern was to identify products that might affect medical treatments, e.g. drug interactions.

'Junk DNA' is not 'absolutely essential for the maintenance of life' - experiments have shown that at least 3% can be deleted with no noticeable effects. Some parts of it are known to have undergone exaptation to acquire biological functionality, but deleterious mutations set a limit for the number of functional loci in non-conserved areas.

Some non-coding junk DNA, the 'satellite DNA', does appear to have a structural role in packaging chromosomes in the nucleus, which explains why it is more highly conserved than the rest.

 

[xianghua]

What do you mean by "specific" changes?

The process of evolution is just hereditary changes in populations over time. Or, more specifically a change in the gene pool (of a population) over time.

And yes, the science of evolution also encompasses studying the results of those changes.

What's your point again?

so evolution by definition most include "macro evolution". means evolution at the familiy level.

 

[pitabread]

so evolution by definition most include "macro evolution". means evolution at the familiy level.

That's not what "macro evolution" means.

You really need to spend more time studying the subject and less time trying to argue it.

 

[DogmaHunter]

Though your criteria are accurate to a T, and I too did not initially see any quantifiable aspects to the ID theory or where it could lead in advancing our scientific endeavours, but, it seemed ID theory has had some gradual progression last I looked into it.

Predictive Power of ID

For example, the ID theory can actually be predictive which was the case back in recent years that concerned "junk DNA" as false. It was for many years that big sections of the genome didn't appear to code for proteins, and therefore neo-Darwinism was correct in the view that 97% of the genome was non-functional; and this would be expected evidence of the non-functional parts of the genome being the byproduct of that trail and error process consistent with the neo-Darwinian theory, the accumulation of mutations gradually over time.
It is apparent that mutations and natural selection are real processes, but are they really the mechanism for neo-Darwinism to be functional and evident in molecular biology? Yet if the genome was designed then we wouldn't expect to find 97% of the genome as being junk and only 3% being functional, and it was the ID theory that predicted that non-coding regions of the DNA would turn out to be importantly functional.
At the forefront of the work of "junk DNA," an evolutionary biologist Richard Sternberg predicted on the basis of ID that the non-coding regions are going to have a function. This was a major study that came out of the National Institutes of Health called the Encode Project, and in 2011 it confirmed what Sternberg and evolutionary biologist James Shapiro had been working on, that at least 85% of the genome is transcribed into various RNA's and have many important regulatory functions that are not just dealt with the DNA, but it's a whole complex hierarchically organised informational processing system. James Shapiro acknowledged Sternburg as the first one to have the insight that the non-coding regions would be functional.

Unfortuately, there was controversy surrounding his decision being he is an evolutionary biologist coming to conclusions that invoked intelligent design, and it led to his dismissal from a well established career in molecular evolution.

How could ID be used to advance?

One of the scientific applications of ID is what's called Design Patterns, and programmers will know what that means as it pertains to the function of the digital information within a computer and how it is processed, and design patterns is an established method of storing or processing information.
One such design pattern that could further our scientific advancement is that within a molecular cell there is a mechanised application of correcting errors. Basically, it is like our version of spellcheck on our computing devices, only much more efficient while hierarchically filing millions if not billions of information in a much more compact and dense storage area. By looking for design patterns within other areas of molecular frameworks other than cells, there is room for advancement in human progression and an understanding of the universe.

Certainly an advancement in design principles in computer science and potentially benefit other fields such as increasing the efficiency in medical or weaponised applications.

As a senior software engineer who also takes interns under his wing and grades them at the end of the internship, I'll go ahead and give your "definition" of what design patterns are, an F--

 

[Abraxos]

OK, well stop if it hurts too much, we wouldn't want you to injure yourself...

My understanding is that rather build nanomachines from scratch, they're using modified bacterial mechanisms such as CRISPR Cas9, but I'd be interested to see a link or reference to what you describe.

OK, I watched that part of the video - and I can see you just used Meyers' misleading description of design patterns verbatim. Dixon's discovery of the complexity of generic code transcription is nothing new, and a major factor in its efficiency and 'elegance' is that it doesn't really function like computer code (whatever Bill Gates may have said) but more like an industrial demand economy...

I asked you what particular design patterns we could use because, to my knowledge (I've used design patterns in software development for 20+ years), we already have our own implementations of automated error correction (as I said, not in itself a design pattern), hierarchical filing, and nested coding, that are well suited to our computer architectures and resources.

As for overlapping reading frames, overlapping code sequences were experimented with at the dawn of computer programming, but are pretty much unmaintainable. Self-modifying code is still used in special circumstances, so it's possible some overlapping code is in use, but without the storage restrictions of early computing systems, there's generally no good reason to use it. As it happens, overlapping reading frames are expected to have evolved in the genome because of the way transcription (assembly of mRNA) control differs from translation (protein assembly) control - see Start & Stop Codons for an overview.

As I explained previously, Velcro is the commonest biomimetic in everyday use, and hook & loop is a design pattern, so it has 'being a design pattern' in common with other design patterns. You suggested that we could make biomimetic use of the genomic design patterns, but you haven't yet given an example - I'm sceptical because of the major differences between genome processing and computer processing architectures, but I'm interested to hear your suggestions.

Yes well, it's one thing to understand it but another to explain it in simple terms (but you seemed to have grasped the nature of the technicalities better than I could have), but it is really beside the point as the take away is that the template for processing information and storing information is better than ours which you seem to agree with. To analogise, it is like you made an Atari 2000 and along comes a PS4; the same functionality is applied but is formatted differently with a few more innovations.
Biomimetics in the field of molecular biology is indeed nothing new but is emerging. I'm sure many have a belief that within certain parts of a cells molecular structure would be too complex to be copied — which is okay to believe, but discoveries are currently being made which have exciting proposals and potentials limited only by one's attitude.

If you're suggesting that a claim of 'habitual association' somehow makes a testable hypothesis, you'll have to explain how you reach that conclusion. But in any case, new information is only associated with consciousness by people who don't understand information.

Information is inherent in the arrangement of matter - if the arrangement changes, the information changes; if the arrangement is new the information is new; new information is produced continually in nature. This is why it's so fundamentally related to entropy. If you were instead referring to Dembsky's hokey 'Complex Specified Information', that too has been shown to be produced by natural processes, so consciousness is not a requirement.

From our knowledge and experience, we understand that conscious activity derives or is synonymous with a mind, and that is as far as science will allow us to follow. To some that may be enough and move on and to others it may not be enough and may lead them to delve into the metaphysical — which is fine, but the issue here is understanding this from a scientific perspective which is that the causality of consciousness is mind. An interesting prospect, and if you require a reference, look into Information Theory in biology.

Also, information NEVER associates with the material. The material may house the information, but it is not inherent to it. I won't ask you to demonstrate it as we both know you cannot substantiate that claim. Data is abstract, not material. You can write data on a piece of paper and then transfer it to your computer where it is now in some server form, and then transfer it by printing it onto multiple papers and so on. The matter can change, but the information remains the same. If you alter the material, then the data becomes altered. For example, if the information on the piece of paper becomes scrunched up, then the data has "devolved" as it is difficult to read. It has lost its actual meaning. There was no "new" information added but a loss of information. Again, problematic for neo-Darwinian mechanisms, but consistent with intelligence being the cause of knowledge.

I'm more than happy to flesh this out on why matter is a crummy candidate for being the originator of information if you want.

You didn't supply any references, so I don't know what specific problems were raised, but if you're referring to Shapiro's work, he's arguing that known processes (e.g. epigenetics, genome doubling & restructuring, symbiogenesis, HGT, inter-specific hybridization) play a larger role in cellular evolution than the neo-Darwinian synthesis suggests. His views are more extreme and so more controversial than most, but it's clear these processes have some influence, it's a matter of establishing the degree; it's early days. But the underlying principle of evolution by natural selection still applies.

I'm referring to Professor Gerd Muller, and he summarises the main problems with modern synthesis. He noted five problems, but I'll list three of them as it pertains to the discussion.

Deficits of the Modern Synthesis:

• Origin of phenotypic complexity: the origin of eyes, ears, body plans, i.e., the anatomical and structural features of living creatures).
• Origin of anatomical novelty: i.e., the origin of new forms throughout the history of life (for example, the mammalian radiation of some 66 million years ago, in which the major orders of mammals, such as cetaceans, bats, carnivores, enter the fossil record, or even more dramatically, the Cambrian explosion, with most animal body plans appearing more or less without antecedents).
• Non-gradual forms or modes of transition: where you see abrupt discontinuities in the fossil record between different types.

For further information, look into Professor Gerd Muller's article and speech at the Royal Society website.
Reference: | Royal Society

dissatisfaction is not an argument. You're quite welcome to show your own abductive analysis, or counter mine. If you think I'm misrepresenting the argument, by all means show how I'm doing so.

I think my dissatisfaction comes from the lack of scientific reasoning behind your statements. There are many claims but no substance to them. Besides, what's to address that hasn't already been discussed throughout our discourse?

Citation? You do realise that the term 'junk DNA' was coined in the 1960's, and formalized in 1972 ?

Perhaps I didn't explain clearly enough. ENCODE study identified that much 'junk DNA' is transcribed and translated; but the products are not biologically functional, i.e. it produces harmless junk. They say their concern was to identify products that might affect medical treatments, e.g. drug interactions.

'Junk DNA' is not 'absolutely essential for the maintenance of life' - experiments have shown that at least 3% can be deleted with no noticeable effects. Some parts of it are known to have undergone exaptation to acquire biological functionality, but deleterious mutations set a limit for the number of functional loci in non-conserved areas.

Some non-coding junk DNA, the 'satellite DNA', does appear to have a structural role in packaging chromosomes in the nucleus, which explains why it is more highly conserved than the rest.

The term "junk DNA" goes back almost 50 years for sure, but when the Human Genome Project began in the '90s and finished in 2003, the first draft of the human genome was announced in 2000 — it was kind of a big deal. You can use the Human Genome Project as your reference, though I thought this was common knowledge among science enthusiasts evolution/creation alike.
The views of junk DNA from Francis Collins, the director of the National Institutes of Health, showed just how much that the consensus has moved. Despite the backlash from other evolutionary scientists, he said that he no longer uses the term and that it was a simple case of hubris to believe that they knew enough to say it wasn't functional.

The discussion has noticeably changed ever since the ENCODE Project finished its study. I'm sure people will continue to debate this, but in my opinion, it will only continue to dwindle until "junk DNA" has become nothing more than a myth.

 

[pitabread]

There was no "new" information added but a loss of information. Again, problematic for neo-Darwinian mechanisms, but consistent with intelligence being the cause of knowledge.

In order to make claims about gaining or losing information with respect to genomes, one needs to first have a consistent, applicable definition of information as it applies to genetics.

This is something the ID or creationist crowd has never successfully provided at least insofar as any of their claims regarding information.

 

[pitabread]

Citation? You do realise that the term 'junk DNA' was coined in the 1960's, and formalized in 1972 ?

Out of curiosity I tried searching for this and the only thing that consistently came up was ID literature referencing Collins referring to "genetic flotsam and jetsam".

Seems like the ID crowd is a bit desperate over this one.

 

[Eight Foot Manchild]

What does "best explained" by design mean?

It means 'prepare to hear a bunch of vacuous creationist bilge'.

 

[TagliatelliMonster]

(I find it odd that when trying to look up this claim, the only thing I can find are ID/creationist sources.)

Obviously, that is because of the massive world-wide conspiracy among academia to cover this up.

 

[TagliatelliMonster]

so evolution by definition most include "macro evolution". means evolution at the familiy level.

The model of evolution deals with what you call "macro evolution" in the exact same way as physics models of gravity deal with gravity of a massive star and also with the gravity exerted by something much smaller in mass.

It's just gravity.
Just like it's just evolution.

There aren't any "special" gravity models required to explain the enormous gravity of the sun.
Just like there aren't any "special" evolution models required to explain a large accumulation of mutations over long periods.