The inconvenient truth about genetics

[DanielBoyd]

11 hours ago, Arete said:

 

From your own citation: "Evidence in support of this last hypothesis has come from recent studies which document the overlapping function of different Hox genes [18], [19], and comparative studies of expression patterns in a number of crustaceans and insects [13], [14], [20] which support the idea that changes in Hox gene regulation may be responsible for the diversification of body plans and the generation of new segment types."

Substantial research over the last 20 years has elucidated that spatio-temporal variation in Hox gene regulation and protein plasticity allows for an extraordinary array of body plans from the same ancestral set of homeobox genes. e.g.  

"A considerable body of evidence suggests that evolutionary changes in developmental gene regulation have shaped large-scale changes in animal body plans and body parts. In particular, many comparative analyses of Hox gene expression in arthropods, annelids, and vertebrates have revealed a consistent correlation between major differences in axial morphology and differences in the spatial regulation of Hox genes." https://www.cell.com/fulltext/S0092-8674(00)80868-5

https://onlinelibrary.wiley.com/doi/full/10.1002/bies.201600246

 

So, no, it supports the idea that developmental genetics underlies morphological diversity in the animal kingdom. 

 

Thanks for bringing in the serious science, Arete. What I am saying is actually supplementary rather than contrary to what you write. Certainly developmental genetics is an important factor in morphological development. But does this equate to sufficient causative explanation for the existence of complex morphological structures?

The products of Hox genes are transcription factors that influence the expression of other genes. In other words, they determine how much of some other protein should be produced by the cell. This secondary protein then goes on to play a role in cellular or intercellular processes, along with a whole load of other molecular components. The Hox gene does not define the secondary protein that is produced (that is the task of the gene it activates), nor the way in which it all works together in an organised fashion to determine how the cell functions in its environment, let alone how millions of cells with different patterns of gene expression work together to create a morphological structure. All it does is say: let's send this much of this protein into the mix. 

The outcome of any self-organising process will obviously be determined by the participating components. In so far as a Hox gene influences how much of a particular component is present, it will therefore have an effect on the outcome. However, this is most certainly not the same as saying that the Hox gene (or even all of the Hox genes together) provides sufficient determinative explanation for the outcome. 

Furthermore, we have the question of the regulation of the expression of Hox genes: who directs the director? Hox genes cannot cause their own expression, so even they are only players in the greater scheme of things. 

To explain such a small part of this immensely complex system and deem this as sufficient explanation for the whole is surely to overstate your claim.

 

[Strange]

It has been known for a long time that self-organisation plays a role in biological development. For example, in the 19050s Turing wrote about how this can determine the patterns in animal skin can arise from the interaction of different process: https://en.wikipedia.org/wiki/The_Chemical_Basis_of_Morphogenesis

I think this has now been extended to explain the development of larger structures (eg limbs).

 

[Arete]

10 hours ago, DanielBoyd said:

Certainly developmental genetics is an important factor in morphological development. But does this equate to sufficient causative explanation for the existence of complex morphological structures?

On its own - no. You brought up Hox genes in the context that the diversity of Hox genes did not account for the diversity of observed body plans. I simply presented the considerable body of empirical evidence which demonstrates that they do explain that variation. 

10 hours ago, DanielBoyd said:

The Hox gene does not define the secondary protein that is produced (that is the task of the gene it activates), nor the way in which it all works together in an organised fashion to determine how the cell functions in its environment, let alone how millions of cells with different patterns of gene expression work together to create a morphological structure. All it does is say: let's send this much of this protein into the mix. 

I hope this stems from a lack of understanding rather than disingenuity - but  the proximity of a regulator to other coding genes dictates its effect in a regulatory cascade - no one should expect the Hox gene, or any other regulatory gene to self determine its regulatory function - genomic architecture dictates the genes downstream of a regulator. 

Hox genes are part of a regulatory cascade that does determine which proteins are expressed in cells, and how they differentiate spatio-temporally. They are part of the genetic system that governs "how millions of cells with different patterns of gene expression work together to create a morphological structure". I certainly did not state that Hox, or homeobox genes in general explain everything - that's a considerable strawman. 

 

10 hours ago, DanielBoyd said:

Furthermore, we have the question of the regulation of the expression of Hox genes: who directs the director? Hox genes cannot cause their own expression, so even they are only players in the greater scheme of things. 

"A diverse range of mechanisms, including nuclear dynamics, RNA processing, microRNA and translational regulation, all concur to control Hox gene outputs." https://dev.biologists.org/content/140/19/3951.abstract

10 hours ago, DanielBoyd said:

To explain such a small part of this immensely complex system and deem this as sufficient explanation for the whole is surely to overstate your claim.

And here we go down the rabbit hole of shifting goalposts and argumentum ad ignorantiam.  No one ever claimed that Hox genes in isolation explain the diversity of the tree of life, all of developmental genetics and the entirety of tissue differentiation. They are adequate to explain animal body plan variation, as shown by significant, already cited empirical evidence. The claim that they demonstrate a gap that genetics cannot explain was therefore false.  

[John Cuthber]

10 hours ago, Strange said:

It has been known for a long time that self-organisation plays a role in biological development. For example, in the 19050s Turing wrote about how this can determine the patterns in animal skin can arise from the interaction of different process: https://en.wikipedia.org/wiki/The_Chemical_Basis_of_Morphogenesis

I think this has now been extended to explain the development of larger structures (eg limbs).

 

And the thing that "knows how" to make the bits which self-organise (whether it's at the level of lipid bilayers or limbs) is DNA.

The information is essentially encoded into the genome.

 

[Strange]

12 minutes ago, John Cuthber said:

And the thing that "knows how" to make the bits which self-organise (whether it's at the level of lipid bilayers or limbs) is DNA.

I thought that went without saying! (but perhaps not...)

The OP's argument seems to be:

1. Genes are (relatively) simple: they just encode proteins

2. The systems that cause morphological development are incredibly complex.

3. Therefore 2 can't just be caused by 1.

There are several fairly obvious reasons why 3 doesn't follow.

[John Cuthber]

1 hour ago, Strange said:

I thought that went without saying! (but perhaps not...)

The OP's argument seems to be:

1. Genes are (relatively) simple: they just encode proteins

2. The systems that cause morphological development are incredibly complex.

3. Therefore 2 can't just be caused by 1.

There are several fairly obvious reasons why 3 doesn't follow.

Yep, that's part A of his problem- it's a non sequitur.

Part B is that he's unable to say where the information is stored (since he says' it's not in the genome).

If he ever gets us beyond that, we can look at the other strange/ impossible claims he's made.

I am not holding my breath.

 

 

[DanielBoyd]

9 hours ago, John Cuthber said:

Yep, that's part A of his problem- it's a non sequitur.

Part B is that he's unable to say where the information is stored (since he says' it's not in the genome).

If he ever gets us beyond that, we can look at the other strange/ impossible claims he's made.

I am not holding my breath.

 

 

Your assumption seems to be that any system must be the product of the expression of some source of stored external information. Therefore, if I say the genome does not contain enough information I need to provide an additional source.

This assumption, however, is false. No self-assembling system is defined by external information: that is the very definition of self-assembly.  There is no instruction for building a snowflake, and there is no instruction for building an eyeball. Both are the result of inherent interactions between their component parts. So no need to hold your breath ;-) I'm not going to tell you where this information is stored, because it doesn't exist. Instead, self-assembling systems create their own information (thermodynamically: use external sources of energy to decrease their entropy).

21 hours ago, Strange said:

It has been known for a long time that self-organisation plays a role in biological development. For example, in the 19050s Turing wrote about how this can determine the patterns in animal skin can arise from the interaction of different process: https://en.wikipedia.org/wiki/The_Chemical_Basis_of_Morphogenesis

I think this has now been extended to explain the development of larger structures (eg limbs).

 

So you would agree with me that the morphogenesis is a form of self-organisation, and therefore not genetically defined?  After all, the definition of self-organisation is that it is not defined by some external influence or instruction, but arises directly through the interactions between components.

11 hours ago, John Cuthber said:

And the thing that "knows how" to make the bits which self-organise (whether it's at the level of lipid bilayers or limbs) is DNA.

The information is essentially encoded into the genome.

 

I agree (almost) entirely. To be a bit more exact about it: DNA knows how to build polypeptides, which form the basis for the self-assembly of proteins through the creation of secondary and tertiary structures, which constitute a significant part of the collections of molecules that self-organise to form organelles, with self-organise to form cells, which self-organise to form tissues, which self-organise to form organs, which self-organise to form organisms.

You proposition is that nothing more than the DNA sequence is necessary to define and determine the outcome of all these self-organisational processes?

[Strange]

1 hour ago, DanielBoyd said:

Your assumption seems to be that any system must be the product of the expression of some source of stored external information. Therefore, if I say the genome does not contain enough information I need to provide an additional source.

This assumption, however, is false. No self-assembling system is defined by external information: that is the very definition of self-assembly.  There is no instruction for building a snowflake, and there is no instruction for building an eyeball. Both are the result of inherent interactions between their component parts. So no need to hold your breath ;-) I'm not going to tell you where this information is stored, because it doesn't exist. Instead, self-assembling systems create their own information (thermodynamically: use external sources of energy to decrease their entropy).

So you agree that there is no additional source of information, and therefore all the information is in the genome?

1 hour ago, DanielBoyd said:

So you would agree with me that the morphogenesis is a form of self-organisation, and therefore not genetically defined?

Of course it is genetically defined. Where else does the information to create the biochemical reactions that create these patterns come from? 

You just said there is no other source.

Unless you are using "genetically defined" in a ridiculously narrow way to mean that the genes should encode the shape an position of every spot on the leopards skin.

Quote

After all, the definition of self-organisation is that it is not defined by some external influence or instruction, but arises directly through the interactions between components.

And where are those components defined?

1 hour ago, DanielBoyd said:

You proposition is that nothing more than the DNA sequence is necessary to define and determine the outcome of all these self-organisational processes?

Oh look, another straw man.

[Essay]

7 hours ago, DanielBoyd said:

....self-assembling systems create their own information (thermodynamically: use external sources of energy to decrease their entropy).

So you would agree with me that the morphogenesis is a form of self-organisation, and therefore not genetically defined?  After all, the definition of self-organisation is that it is not defined by some external influence or instruction, but arises directly through the interactions between components.

I agree (almost) entirely. To be a bit more exact about it: DNA knows how to build polypeptides, which form the basis for the self-assembly of proteins through the creation of secondary and tertiary structures, which constitute a significant part of the collections of molecules that self-organise to form organelles, with self-organise to form cells, which self-organise to form tissues, which self-organise to form organs, which self-organise to form organisms.

You proposition is that nothing more than the DNA sequence is necessary to define and determine the outcome of all these self-organisational processes?

It’s been pointed out earlier in the thread, and you yourself seem to grasp, how the basic physical principles (such as diffusion, the forces that fold molecules, lock and key binding, Brownian motion, etc.) of “self-organization” do explain morphology.  So why are you looking for something else or something more?  Perhaps it is simply that ‘self-assembly’ is more varied and pervasive and powerful than you currently perceive.

When a virus inserts its DNA into a cell, the products from that message don’t get incorporated into the morphology of the host, because they aren’t designed (by the DNA) to ‘self-assemble’ with the host.  The viral products within the cell are designed (by the DNA) to self-assemble, within the cell, into some viral morphology.  I’m amazed ‘self-assembly’ can discriminate that well, with odd or sticky proteins, but it seems to.

You ask about "[The] proposition is that nothing more than the DNA sequence is necessary to define and determine the outcome of all these self-organisational processes?"  Yes, doesn't this seems obvious when you think about how it is the DNA that provides the "self" for those self organization processes.  As with the virus example, that seems to be the answer you seek.

[Arete]

11 hours ago, DanielBoyd said:

I agree (almost) entirely. To be a bit more exact about it: DNA knows how to build polypeptides, which form the basis for the self-assembly of proteins through the creation of secondary and tertiary structures, which constitute a significant part of the collections of molecules that self-organise to form organelles, with self-organise to form cells, which self-organise to form tissues, which self-organise to form organs, which self-organise to form organisms.

Correct me if I'm wrong, but it seems like you're saying the "missing" information is that gene products conform to the scientific laws of nature in order to form biological structures... or are you implying that some unknown, supernatural other organizing force is necessary? 

[John Cuthber]

14 hours ago, DanielBoyd said:

Your assumption seems to be that any system must be the product of the expression of some source of stored external information.

That's pretty much the opposite of what I said.
I'm saying a tadpole is the expression of information that is internal to the egg and that the place where that information is stored is the genome. It can't get access to any external information. As I said; it hasn't got an instruction book.

 

14 hours ago, DanielBoyd said:

No self-assembling system is defined by external information: that is the very definition of self-assembly.  There is no instruction for building a snowflake,

True, but if I want to specify making a hexagonal structure the instruction I might give is "burn hydrogen and cool the reaction product until it freezes".
If I wanted a cubical structure I would say " burn sodium in an atmosphere of chlorine then carefully cool the product."

The ice or salt crystals self-assemble, but it's the instruction which defines what shape you get.
If you make the wrong molecule, it doesn't work, because it doesn't self assemble into the right thing.

14 hours ago, DanielBoyd said:

Both are the result of inherent interactions between their component parts.

How did the body know to produce component parts that would assemble into an eye?

It's possible, in principle, to screw up the DNA and get a "mutant" eye. 

How would that be possible if the DNA didn't control the production of the eye?
Shortsightedness is, to a fair degree, heritable.

How could that happen without the information being carried from parent to child?

Are you saying the mother's eyes wander off to the womb for a bit "to show the foetus how it's done"?
And the father's contribution?

Your idea just doesn't stand up to serious consideration in its own right.

And you still need to say where you think the information about, for example, an eye is stored for the growing offspring if it's not stored as part of the genome.

15 hours ago, DanielBoyd said:

 I'm not going to tell you where this information is stored, because it doesn't exist.

That's not going to cut it on a science  page.

 

[Ken Fabian]

DanielBoyd - it isn't just one individual's DNA involved in this - from edible plants and animals to gut flora, an individual's DNA operates with access to - making use of - the biochemical products of a complex biological community, based around more DNA than any discreet, single organism ever contains. My DNA doesn't have to have the combinations that will make every component that goes into assembling me. I don't need the DNA combinations for getting cells to make gluten for example, that I need; DNA of plants have those.

I think the ability of DNA - of individual, parents and associated species - to determine which specific molecules are made (including molecules that, when put together will assemble into more complex biochemical structures) hasn't been actually been shown to require more DNA than is present. You really need to move beyond claiming there is not enough information to quantifying what is available compared to what is required. I think you need to be showing much more of the reasoning you are using for seeing a cell structure like eg a microtubule and a molecular motor and concluding DNA can't have determined the precise molecules used - which includes those that are downstream products made by structures that were made from DNA determined parts.

Of course there is no 'design' specification in that DNA - that has always been just an analogy; the cascading, branching, interacting flow of biochemical processes that is Life only need for the resultant biochemical structures to work, not for the DNA to contain any descriptions of the end results.

 

 

Edited July 3, 2019 by Ken Fabian
clarity

[John Cuthber]

5 hours ago, Ken Fabian said:

I don't need the DNA combinations for getting cells to make gluten for example, that I need

You don't need gluten.
What you need is food.

Your DNA (albeit helped by gut bacteria) knows how to make the enzymes that break down the food to components that get reorganised into "you".
However, it's true that we need, but lack the  enzyme(s) to make, vitamin C.

We also can't photosynthesise.

5 hours ago, Ken Fabian said:

Of course there is no 'design' specification in that DNA

Well, where is it then?

[DanielBoyd]

Reading all your comments, it strikes me that we seem to agree on the fact that genes only directly determine protein amino acid sequences, and that the rest is self-assembly or self-organisation. Where we seem to differ is in the significance we ascribe to what happens between the polypeptide sequence and the organism.

You seem to be saying that by defining the protein components, DNA is completely responsible and in control of everything that happens in all the levels of organisation that are built above the molecular. In essence, this is an ultimately reductionistic explanation of life: define the components and you have defined life.

This is to ignore the principles of emergence, which tell us that the whole can be more than the sum of the parts, and the parts therefore cannot explain the whole. The discussion of information quantity is important in this context, since emergence results in the existence of structures (information) at higher levels of organisation that cannot be derived from the parts. 

This goes far beyond the trivialisation of "sure, then they go on and do what they were designed to do". Living systems could not exist or survive without the kinds of powerful emergent top-down control that have been discovered in the course of the evolutionary process.

This is acknowledged in homoeostatic systems: for instance our thermoregulatory processes determining whether brown adipose tissue cells are switched on to generate heat. However, before life can start controlling things it needs to create control systems. I see less evidence of appreciation of the determinative role of emergent top-down control in this even greater challenge. For instance, understanding how the brain works is pretty tough. Explaining how the brain (which has been quantified as the most complex structure in the known universe) comes to exist is next level.

As I say in my opening sentence, many people see DNA as complete and sufficient explanation for the organism. Yet if any degree of emergence is involved then this is simply not true - and if there's one thing evolution is good at it's building powerfully emergent systems.

That is why I wrote this article, and this discussion seems to confirm the necessity. Here, too, I hear people voicing the reductionistic explanation based on the sufficiency of genetic information, and trivialising the determinative emergent processes that actually create the massively improbable living structures we see.

Clearly, my article spectacularly failed to transfer this meme! But your comments certainly help me underrstand why, so thanks for that!

 

    

 

[Arete]

8 minutes ago, DanielBoyd said:

Reading all your comments, it strikes me that we seem to agree on the fact that genes only directly determine protein amino acid sequences, and that the rest is self-assembly or self-organisation.

You mean aside from the extensive discussion of regulatory function. Most of the eukaryotic genome does not encode amino acids. 

11 minutes ago, DanielBoyd said:

learly, my article spectacularly failed to transfer this meme! But your comments certainly help me underrstand why, so thanks for that

The original post failed spectacularly because it was riddled with factual errors and stank of religiously motivated creationist tropes. 

[Strange]

2 hours ago, DanielBoyd said:

Reading all your comments, it strikes me that we seem to agree on the fact that genes only directly determine protein amino acid sequences

Nope. 

2 hours ago, DanielBoyd said:

You seem to be saying that by defining the protein components, DNA is completely responsible and in control of everything that happens in all the levels of organisation that are built above the molecular.

Nope. Have you actually read any of the responses? Or are you just ignoring them so you can continue with this straw man argument?

2 hours ago, DanielBoyd said:

This is to ignore the principles of emergence, which tell us that the whole can be more than the sum of the parts, and the parts therefore cannot explain the whole. The discussion of information quantity is important in this context, since emergence results in the existence of structures (information) at higher levels of organisation that cannot be derived from the parts. 

This has not been ignored at all.

2 hours ago, DanielBoyd said:

Here, too, I hear people voicing the reductionistic explanation based on the sufficiency of genetic information, and trivialising the determinative emergent processes that actually create the massively improbable living structures we see.

You are not, as far as I can tell, hearing that from anyone here. You seem to be deliberately misunderstanding what is said in order to support your prejudices.

2 hours ago, DanielBoyd said:

Clearly, my article spectacularly failed to transfer this meme! But your comments certainly help me underrstand why, so thanks for that!

That would be a great conclusion, if it weren't for the fact you seem to have wilfully misunderstood all the patient attempts to explain your errors and misrepresentations.

[DanielBoyd]

7 hours ago, Arete said:

You mean aside from the extensive discussion of regulatory function. Most of the eukaryotic genome does not encode amino acids. 

The original post failed spectacularly because it was riddled with factual errors and stank of religiously motivated creationist tropes. 

I have been a staunch atheist all my life, so it completely flummoxes me to be accused of religious motivation. I really am curious: what text in the original article leads you to this conclusion?   

[Strange]

7 minutes ago, DanielBoyd said:

I have been a staunch atheist all my life, so it completely flummoxes me to be accused of religious motivation. I really am curious: what text in the original article leads you to this conclusion?

Simply the claim that genes can't explain everything so there must be "something else". This "something else" is most commonly promoted by proponents of Creationism and ID (the latter like to pretend they are not talking about a god, but that is just further dishonesty on their part). If you don't want to sound like a religious nutter, don't use the same language. (This is just another example of your inability to explain what you mean, coupled with unnecessary hyperbole.)

[DanielBoyd]

On 7/3/2019 at 3:32 PM, Essay said:

It’s been pointed out earlier in the thread, and you yourself seem to grasp, how the basic physical principles (such as diffusion, the forces that fold molecules, lock and key binding, Brownian motion, etc.) of “self-organization” do explain morphology.  So why are you looking for something else or something more?  Perhaps it is simply that ‘self-assembly’ is more varied and pervasive and powerful than you currently perceive.

When a virus inserts its DNA into a cell, the products from that message don’t get incorporated into the morphology of the host, because they aren’t designed (by the DNA) to ‘self-assemble’ with the host.  The viral products within the cell are designed (by the DNA) to self-assemble, within the cell, into some viral morphology.  I’m amazed ‘self-assembly’ can discriminate that well, with odd or sticky proteins, but it seems to.

You ask about "[The] proposition is that nothing more than the DNA sequence is necessary to define and determine the outcome of all these self-organisational processes?"  Yes, doesn't this seems obvious when you think about how it is the DNA that provides the "self" for those self organization processes.  As with the virus example, that seems to be the answer you seek.

"So why are you looking for something else or something more?  Perhaps it is simply that ‘self-assembly’ is more varied and pervasive and powerful than you currently perceive."

I am not looking for anything more than self-assembly, and I certainly don't underestimate its power, quite the contrary, that amazes me too! The explicit proposition of the article is that it is nothing more and nothing less than highly advanced forms of self-assembly that creates biological structure. That is why I am arguing against the absolute, reductionistic, causative role of the genome.

You say that DNA provides the self for the self-organising processes. If we ignore the non-proteinaceous components for a moment, this is true. But in an emergent, self-organising system knowledge of parts is not sufficient to determine the outcome. Living systems necessarily exert downward causation, in which the whole determines the behaviour of the parts. When they do, the parts loose control over the outcome.

To take a different example, millions of termites work together to build termite mounds. This is not because there is some hidden or even implicit design of a mound in every termite (let alone in the termite's DNA!), Instead, it is the colony that determines the behaviour of the individual termite, resulting in it contributing to building the mound. 

 

 

[Strange]

2 minutes ago, DanielBoyd said:

The explicit proposition of the article is that it is nothing more and nothing less than highly advanced forms of self-assembly that creates biological structure.

It can't be "nothing more" or biological structures would randomly appear out of nowhere all over the place. 

3 minutes ago, DanielBoyd said:

But in an emergent, self-organising system knowledge of parts is not sufficient to determine the outcome.

And yet, the genome is able to exploit the fact that proteins do in fact fold in predictable ways, that reaction-diffusion systems create spots (in leopards) and stripes (in tigers), and so on. So the outcome is not completely arbitrary. It can be determined. Otherwise morphogenesis and evolution would not work.

5 minutes ago, DanielBoyd said:

To take a different example, millions of termites work together to build termite mounds. This is not because there is some hidden or even implicit design of a mound in every termite (let alone in the termite's DNA!), Instead, it is the colony that determines the behaviour of the individual termite, resulting in it contributing to building the mound. 

And what determines the behaviour of the individual termite? Do you need a clue?

6 minutes ago, DanielBoyd said:

That is why I am arguing against the absolute, reductionistic, causative role of the genome.

Which is a straw man argument.

I guess you are largely stating the obvious (with a few misunderstandings of how genes function) but you seem to think you are providing some novel insight that has never occurred to anyone before.

[DanielBoyd]

45 minutes ago, Strange said:

Simply the claim that genes can't explain everything so there must be "something else". This "something else" is most commonly promoted by proponents of Creationism and ID (the latter like to pretend they are not talking about a god, but that is just further dishonesty on their part). If you don't want to sound like a religious nutter, don't use the same language. (This is just another example of your inability to explain what you mean, coupled with unnecessary hyperbole.)

I very explicity indicate what I propose as this 'something else', and that is not supernatural. It is the all-too natural processes of self-assembly that shape most of the natural world.

Perhaps my article was too long to read thoroughly (mea culpa) but I make this very clear. In the second paragraph I state that there are just two ways of creating things: design and self-assembly. God is not on the list. I also explain why design is not a systemic option for living systems: divine, genetic or otherwise. Any creationist should therefore be even more disgruntled than you ;-)

[Strange]

11 minutes ago, DanielBoyd said:

I very explicity indicate what I propose as this 'something else', and that is not supernatural. It is the all-too natural processes of self-assembly that shape most of the natural world.

Not in your opening post, which was all full of hyperbole and suggestions that genes don't do anything (or enough).

Given where most people with these sorts of claims end up, it was a reasonable assumption. (They also often start off denying that there is anything religious or supernatural.)

11 minutes ago, DanielBoyd said:

Perhaps my article was too long to read thoroughly

I would say the problem was more with the content, than the length. Full of errors and bogus claims. (Which you are still repeating, four pages later.)

[DanielBoyd]

21 minutes ago, Strange said:

It can't be "nothing more" or biological structures would randomly appear out of nowhere all over the place. 

And yet, the genome is able to exploit the fact that proteins do in fact fold in predictable ways, that reaction-diffusion systems create spots (in leopards) and stripes (in tigers), and so on. So the outcome is not completely arbitrary. It can be determined. Otherwise morphogenesis and evolution would not work.

And what determines the behaviour of the individual termite? Do you need a clue?

Which is a straw man argument.

I guess you are largely stating the obvious (with a few misunderstandings of how genes function) but you seem to think you are providing some novel insight that has never occurred to anyone before.

As long as I read things like "the genome is able to exploit the fact that proteins do in fact fold in predictable ways" I think that the man is not entirely made of straw. I think a more accurate formulation would be "The cell is able to exploit the fact that it has a gene at its disposal that creates proteins that fold in predictable ways".

If you can comply with that, then maybe the man is made of straw and I'm just stating the obvious.

 

[CharonY]

5 minutes ago, Strange said:

Not in your opening post, which was all full of hyperbole and suggestions that genes don't do anything (or enough).

Given where most people with these sorts of claims end up, it was a reasonable assumption. (They also often start off denying that there is anything religious or supernatural.)

I would say the problem was more with the content, than the length. Full of errors and bogus claims. (Which you are still repeating, four pages later.)

I think OP had (among other things) trouble with distinguishing between DNA and genes (the latter being the part of the DNA that are responsible for the production of RNA and ultimately proteins). Quite a bit is down to semantics to various degrees. The DNA does not proximately control all of these processes. However, from an information perspective, the DNA does integrate cellular signals (via regulatory networks formed by proteins and metabolites) and modulates cellular function by adjusting protein levels according to this information. As such it is accurate to say that ultimately control is exerted via the DNA. However, I am not sure how useful such a view is (except for providing simple narratives for students). That being said the OP makes the whole simplification even worse by adding woo to the mix.

[Strange]

5 minutes ago, DanielBoyd said:

As long as I read things like "the genome is able to exploit the fact that proteins do in fact fold in predictable ways" I think that the man is not entirely made of straw. I think a more accurate formulation would be "The cell is able to exploit the fact that it has a gene at its disposal that creates proteins that fold in predictable ways".

I honestly can't see any significant difference in meaning added by the extra words. (I would criticise both, equally, for ascribing agency to the genome/cell.) The point is that the genes contain information about the protein, not how the protein folds. But the protein is functional and useful because of the way it folds (among other things) and that is why the genes are there to create it. (Ditto more complex things like reaction-diffusion processes, morphogenesis, etc.) 

There is nothing novel or insightful about that. It is widely known and understood. Your claim to be the only person who can see this is, well, very silly.

There is an interesting (maybe) analogy with god possible here. (As the topic has been brought up already!)

There are literalists who think that god explicitly created life, and then humans, and perhaps intervenes in daily life. This is analogous to the people you say think that every detail is dictated by the genes. (I don't think there are any such "gene fundamentalists", certainly not among scientists. Maybe among Daily Mail journalists. But that is another discussion.)

On the other hand, there are believers who accept the Big Bang model for the evolution of the universe, accept the roles of biological evolution in creating mankind, etc. They think that a god could have put all the rules of chemistry and physics in place, and created fundamental particles, knowing that it would eventually result in the creation of mankind by natural processes. That is sort of analogous to the role that the genome has: it puts the processes and components in place that eventually lead to the formation of tiger stripes, fingers, the brain, etc.