DanielBoyd

The inconvenient truth about genetics

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4 minutes ago, John Cuthber said:

You didn't.

It's a quote glitch

 

That's what authority is for.

It's to save you the trouble of regurgitating all the stuff you learned during the course of training.

It's so that when the doctor says "take these pills" you don't waste his time asking why.

I suppose after this comment I'll leave it at it or we may need a separate thread for this, but;
A I would always ask my doctor why, and expect him/her to be able to explain why its good for me, B as someone in the field I would then possibly even be able to disagree with my doctor but C this forum isn't the doctor, someone has a (possibly wrong) idea and wants to discuss it. Saying they are wrong without giving any reason is just not helpful.
Yes after many reason have been given and all of them are ignored (as is the case in some other threads where someone has an "theory" and subsequently keeps ignoring everyone or picking only the few things they can counter to respond to), we could say "go learn [insert field] as you clearly have no idea what you are talking about". But if we just do that to everyone we disagree with, there's not going to be many interesting discussions and people won't learn anything.
Let's say I have some fringe idea based on my knowledge of RNA dynamics, and you think its not likely or just plain wrong; how far will we get if I present you the reasons for why I believe said fringe idea, and you just say "welp you got no idea what you are talking about". If it is so obvious, why not respond at least with some amount of detail and use said authority to up lift other people at least a little bit to your level of knowledge.

On a side note, I do definitely get, with the amount of crackpot theories, ideas and ignorant people on these forums, that some people don't feel like answering in detail as its not worth the time, but I just think that everyone should try to be above that, especially when its a new member (assuming this isn't a secondary account of someone) and his points have not been addressed properly and in detail yet.

Anyway if you disagree or if we continue this discussion we should ask the mods if it can be separate thing as otherwise the thread is overtaken (@ mods, no need if this is the end of our discussion or we both agree to (dis)agree).

-Dagl

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!

Moderator Note

Interesting as the diversion is, can we try and stay on topic

 

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I am wondering a bit why DanielBoyd got so many negatives on his OP. I think some people read it as another Intelligent Design posting, but it isn't. But as OP in a new thread, it is a bit long. Flying over it can lead to some wrong conclusions. But of course DanielBoyd is also to blame for this, given the title of the thread, and the, in my opinion, superfluous mentioning of entropy and its provocative title.

For me it is clear that the DNA does not, and cannot, contain all information to build or even identify an organism (except of course by just comparing DNA of known organisms). It needs the complete apparatus of the living cell that the DNA can fulfill its function.  A viewpoint one can use is that of a message and its interpretation. A message can only be interpreted by a correct interpreter. AFAIK the cellular 'interpreter' of DNA is not 'neutral'. Even if we had the complete DNA of some dinosaur, we will not be able to reconstruct how it looked like, because how the information is interpreted depends on what the dinosaur cell did with it. (So the Jurassic Park idea, to exchange  frog DNA with dinosaur-DNA and so let grow a dinosaur, will not work, because the frog-egg has not the correct environment for the DNA to produce a dinosaur.) So I agree with DanielBoyd that DNA contains the design of an organism is not correct, even if DNA of course has a strong influence on what the organism will look like. It is more like a list of ingredients of a recipe. And of course there are all kind of feedback loops in the mechanism, where proteins synthesized according to a gen, has impact on what the cell does (directly or indirectly), and so possibly also on what genes will be read later on.

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37 minutes ago, Eise said:

I am wondering a bit why DanielBoyd got so many negatives on his OP. I think some people read it as another Intelligent Design posting, but it isn't. But as OP in a new thread, it is a bit long. Flying over it can lead to some wrong conclusions. But of course DanielBoyd is also to blame for this, given the title of the thread, and the, in my opinion, superfluous mentioning of entropy and its provocative title.

For me it is clear that the DNA does not, and cannot, contain all information to build or even identify an organism (except of course by just comparing DNA of known organisms). It needs the complete apparatus of the living cell that the DNA can fulfill its function.  A viewpoint one can use is that of a message and its interpretation. A message can only be interpreted by a correct interpreter. AFAIK the cellular 'interpreter' of DNA is not 'neutral'. Even if we had the complete DNA of some dinosaur, we will not be able to reconstruct how it looked like, because how the information is interpreted depends on what the dinosaur cell did with it. (So the Jurassic Park idea, to exchange  frog DNA with dinosaur-DNA and so let grow a dinosaur, will not work, because the frog-egg has not the correct environment for the DNA to produce a dinosaur.) So I agree with DanielBoyd that DNA contains the design of an organism is not correct, even if DNA of course has a strong influence on what the organism will look like. It is more like a list of ingredients of a recipe. And of course there are all kind of feedback loops in the mechanism, where proteins synthesized according to a gen, has impact on what the cell does (directly or indirectly), and so possibly also on what genes will be read later on.

While the regulation of the genes, alternative splicing and possibly even the folding and post-translational functions of some proteins may be affected, eventually the dinosaurs DNA will produce a cell which is like that of the original dinosaur. DNA on its own doesn't really do much as you said, and of course if you take a human egg cell with dinosaur DNA you will most likely not get a dinosaur (or a human for that matter). However if you manage to keep said cell alive, then eventually the DNA that is transcribed will most likely replace all the proteins of a human with those of a dinosaur, the issue here being that I am not sure if such a cell could be kept alive at all, seeing as many transcription factors may not have much conservation in there binding motifs. 

But as new cells are produced continuously, wouldn't you say that the apparatus to make new cells is build into the DNA, thereby containing all the information to build or even identify an organism? I feel like my point isn't very... clear right now so I hope its at least clear enough; DNA on its own doesn't do much and requires a functional cell to be interpreted, but within the DNA code is the information to build such a functional cell with which to interpret the DNA, therefor the DNA does contain all the information of an organism. 
Now to be fair though, saying "all the information" may be a bit of a fallacy, we should speak of the chromatin including epigenetic marks and even then there will be some exceptions (there was a paper released a few weeks back showing that microRNA led to transgenerational responses in worms I think, but even then those microRNA's are encoded by the genome). 

-Dagl

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25 minutes ago, Dagl1 said:

But as new cells are produced continuously, wouldn't you say that the apparatus to make new cells is build into the DNA, thereby containing all the information to build or even identify an organism? I feel like my point isn't very... clear right now so I hope its at least clear enough; DNA on its own doesn't do much and requires a functional cell to be interpreted, but within the DNA code is the information to build such a functional cell with which to interpret the DNA, therefor the DNA does contain all the information of an organism. 

I am not so sure. The DNA is part of the fertilized egg, and the egg brings the 'correct interpreter' for the DNA with it. Surely the DNA contains the blueprint for all proteins of the cell, but if that is enough to know when which gene is read, and what happens with the synthesised protein afterwards I am no so sure. It really looks like a a kind of recursive loop, that might change by mutations in DNA, but also by changes in the (direct) environment of the DNA.  So it becomes an egg-chicken (egg-DNA?) question: what was first? 

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On 6/22/2019 at 11:16 PM, Moontanman said:

You are correct, I misread your statement but it comes back to your 10 assertions, can you provide a citation for any of them? They do indeed sound like the ravings of a creationist your claim you are not one is meaningless. We see creationists all the time who try to sneak in their agenda by claiming not to be creationists. You made the assertions, it's not our job to disprove them, it's your job to show they are valid... 

Could you please drop the creationist thing? Since I am arguing for self-assembly over design, all of my objections apply equally well to intelligent design, and I could add a whole list more. Intelligent design is not science; the observations I make about the functional limitations of genetic information are at least valid in the sense that they are rational, even if radical. Rather than just blanket bombing, perhaps you could pick one of my assertions you disagree with? Then we could have a content-based discussion.   

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6 hours ago, DanielBoyd said:

Rather than just blanket bombing, perhaps you could pick one of my assertions you disagree with? Then we could have a content-based discussion. 

Maybe you could pick one of the many objections to your claims and discuss it...

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8 hours ago, Eise said:

It needs the complete apparatus of the living cell that the DNA can fulfill its function. 

Please indicate the parts of the apparatus of the cell that are reproduced, but for which there is no corresponding DNA.

Now, I accept that, for example, water is a major part of cells, and there's no DNA which (meaningfully) makes water, but it's also hard to see that as the "information" needed to make a cell.

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Posted (edited)

Hi guys, just want to apologise for my tardiness in replying to your posts. I will get round to it, but hadn't anticipated such a response, and I've also got a day job... Which fortunately doesn't involve convincing anyone about wild ideas ;-)

Edited by DanielBoyd
Incomplete

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Posted (edited)
On 6/22/2019 at 3:27 PM, DanielBoyd said:



A claim that flies do rudely in the face of accepted wisdom clearly needs solid substantiation, so here are short descriptions of not one but ten lines of reasoning that support this conclusion:

Reason 1: The genome does not contain enough information. Any design needs to contain all the information necessary to accurately specify the product. For a ball bearing, this is easy: make a steel sphere with diameter x. Now think about how much information is required to define your body: all its different kinds of cells, its tissues and organs, its shape and size. It may seem that the billions of base pairs in your genome contain a lot of information, but they are not used individually: instead long strings of them (genes) are used together to build a protein. The number of different proteins that can be built is a more modest tens of thousands. Variations in these proteins are the only information that the genome actually sends out into the world, and this information is not nearly enough to define and distinguish a man from a mantis and a cat from a caterpillar.

Citation please. 

On 6/22/2019 at 3:27 PM, DanielBoyd said:


Reason 2: The genome only says how to build some parts. The best analogy for the genome is the book of blueprints used in a vehicle factory to make the metal parts it needs. Whenever a particular part is needed, the engineer opens the book at the right page, makes the part, and passes it on to the production line. Building a vehicle also requires all sorts of plastic and rubber parts, which come from other sources and are not based on these blueprints. Similarly, the genome provides the information needed to make proteins, but no designs for the many other essential cellular components such as fats, carbohydrates and minerals. Some of these are built with the help of enzymes (a kind of protein) but this indirect genetic effect does not constitute an end-product design.

Citation please.

On 6/22/2019 at 3:27 PM, DanielBoyd said:


Reason 3: The genome does not determine which of its genes are used and when. Depending on whether the factory is building bicycles or biplanes, some blueprints will be used while others are not, but the instruction book has no say in the matter. Similarly, your genome is a resource that can be used by each of the very different types of cells in your body to produce those proteins they need. Many are only used in specific types of cell. Your genome does not independently determine which of its genes will be called upon. So genetic information does not even determine which parts are available to build each cell.

Citation please. 

On 6/22/2019 at 3:27 PM, DanielBoyd said:


Reason 4: The genome cannot guide its products. Simply sending loose parts to the production line is not going to build a car. Similarly, a functioning cell isn’t just a jumbled bag of molecules: instead it contains a collection of structures that must be built out of proteins and other molecules. After a protein has been constructed on the basis of genetic information, it therefore needs to go to the right place in the cell and join up with other molecules in order to play its part. The genome has no information or mechanism to guide it. 

 

Citation please.

Quote

Reason 5: No way of reaching the next level. A country’s transport systems require the right vehicles to be in the right places. A ship at an airport or a car moored in a harbor are not going to be particularly effective. Factory blueprints for metal parts are clearly far detached from this higher level of organisation. Similarly, our bodies are strictly organised systems created by having the right cells in the right places, and there is no genetic information that says how to build morphological structures like a leg, a heart or an eye. 

 

Citation please.

Quote

Reason 6: The limited role of developmental proteins. Most of a cars parts are designed to help it work as a vehicle. On the other hand, honking horns, flashing headlights and indicators have an external function, allowing interaction with other vehicles to ensure effective and safe traffic flows. A particularly loud horn may be more effective, while a malfunctioning one may lead to an accident. However, this is not to say that the instructions for building the metal parts of cars horns can be considered as an explanation for the transport function of the road network. Like the parts of a car, most of the proteins built on the basis of genetic instructions have a job within the cell, but some have signalling functions between cells that help them to interact and work together to form and operate as an organism. Variations in these proteins will have an effect on the organism’s developmental processes. However, this is not to say that the genome contains information on how cells should be arranged to build organs, or organs should be arranged to build a body. 

 

Citation please.

Quote

Reason 7: Lack of construction endpoint. A design-and-construction process starts off with raw materials and works towards the endpoint described in the design. The result is therefore only functional at the end of construction: a car can only drive at the end of the production line; a protein can only do its thing when it is complete. This is a luxury that living organisms do not have. They need to be viable from the first moment, all the way through embryonic, foetal and infant stages to adulthood. For this reason organisms cannot be the product of endpoint design.

Citation please.

Quote

Reason 8: Diversity from the same genome. It is not only the many different kinds of cell in an organism that share the same genetic instruction book. The same applies to entirely different organisms. Vertebrates are unusual in having the same body plan throughout their lives, and even here infants are not just scaled down versions of adults. More commonly, an organism goes through radically different stages in its life cycle. A butterfly, for instance, starts out life as a caterpillar before breaking down all its organs in the chrysalis to develop into something completely different. Each of these forms contains identical genetic information. Logically, then, this information cannot determine which form to build. Furthermore, if the genome were to contain a design for each of these creatures it would need to be twice the size as the genome of an animal without such different stages. This is not the case. 

Citation please.

Quote

Reason 9: Designed systems can’t repair themselves. Systems that are created by design and construction, both of which are external to the system, cannot repair themselves. Get a dent in your car and you need a garage to fix it; a damaged protein also can’t mend itself. Yet if you cut your finger it quickly restores itself to its initial state. This inherent, corrective stability is characteristic of all bodily components, and is firm evidence that they are not the products of design.
 

Quote

Reason 10: Development is not construction. Design-based construction involves choosing the right parts and bringing them together in the right configuration. This is what happens on our factory production lines, and how proteins are built from amino acids on the basis of genetic instructions. It is not the way organisms come to exist. Instead they grow and develop, a process fundamentally different from construction that cannot use design-type information to reach its endpoint.
 

Citation please.

Quote

As Sherlock Holmes famously said: “Once you eliminate the impossible, whatever remains, however improbable, must be the truth”.

Sherlock Holmes was wrong, this is nothing but a argument from ignorance, if you don't know then you don't know no matter how many things you think you've eliminated deciding something is the truth with no supporting evidence is not valid. 

Would you say there are no white swans because you've never seen one? Until Australia was discovered there were no white swans as far as anyone knew but there they were. 

Quote

The alternative, after all, is mind-blowing. Going back to the start of this article, we saw that there are just two ways of making complex systems: design and self-assembly. If there is no design for living organisms, then they must self-assemble. In other words, starting from a single fertilized cell every cell division, the differentiation into different types, the layering of cells into tissues, the twisting and wrapping involved in creating organs, each in just the right place in the body and functioning like a well-oiled machine: all that must just be the result of inherent interactions between component parts, starting at the molecular level with proteins and other compounds harmoniously moving and working together; moving up to cells exchanging information, nudging and jostling into just the right places; the whole thing growing and blossoming, while at every stage being a viable, vibrant, living entity interacting with its environment to obtain the resources it needs to grow; and eventually finding a mate with which to join germ cells to start the whole cycle anew. All this without any kind of design or plan? Ok, we can see how a filigree snowflake can grow without a plan, but a living organism? Surely this is absurd?

 The only thing absurd is using an argument from ignorance, I see no reason to think the "plan" in not contained in the genome just because you can't see it.. 

Edited by Moontanman

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2 hours ago, John Cuthber said:

Please indicate the parts of the apparatus of the cell that are reproduced, but for which there is no corresponding DNA.

Well there are a variety of metabolites and co-factors that are enmeshed in the regulatory circuits required for proper functioning. And there is of course the perhaps trivial point that we need the proteins to interact with the DNA to actually read out information from the DNA (I thought that might what Eise mentioned with the hen and egg issue, but I may be wrong). 

In my mind there is much less hierarchy in the involved machinery but it is dependent on definition to some degree. None of which making the assertions in OP any less absurd, of course.

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On 6/22/2019 at 11:16 PM, Moontanman said:

You are correct, I misread your statement but it comes back to your 10 assertions, can you provide a citation for any of them? They do indeed sound like the ravings of a creationist your claim you are not one is meaningless. We see creationists all the time who try to sneak in their agenda by claiming not to be creationists. You made the assertions, it's not our job to disprove them, it's your job to show they are valid... 

Actually, disproof (rather than proof) is the way science works. I have presented 10 arguments that are logically consistent and based on observable facts. The next step in the process is exactly that: to show why they are incorrect. I look forward to your disproof of any one of my reasons.

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On 6/23/2019 at 3:15 PM, Dagl1 said:

Let's say I have some fringe idea based on my knowledge of RNA dynamics, and you think its not likely or just plain wrong; how far will we get if I present you the reasons for why I believe said fringe idea, and you just say "welp you got no idea what you are talking about". If it is so obvious, why not respond at least with some amount of detail and use said authority to up lift other people at least a little bit to your level of knowledge.

Full ack. With 'authority' comes responsibility. In this case, to show where somebody is wrong. If the person in question does not react on that, then OK, leave him/her with his/hers ideas. So this is pretty useless:

9 hours ago, Moontanman said:

Citation please. 

Citation please.

Citation please. 

Citation please.

Citation please.

Citation please.

Citation please.

Citation please.

Citation please.

This neither advances discussion, nor teaches anybody anything. 'Citation please' can be useful when somebody claims that 'science has shown that...' followed by a crackpot idea. But I do not think the OP did that. He pretty clearly shows his ideas, and the experts between us can look if these ideas match present science, and when not, can show this (with citations, if necessary). Citations are necessary when we do not agree on the facts; on theories, i.e. interpretations of facts,  we must discuss. Above has nothing to do with any advancement in insight from anybody, but only about 'winning a discussion'.

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On 6/23/2019 at 1:15 AM, Strange said:

You would need to provide some evidence to support this. (Given your apparent lack of understanding, I don’t expect that to be forthcoming.)

That is a truly terrible analogy. It would imply there was “a gene for” every part and every variant of the body. Do you really think there is a specific gene for the 2nd joint on the third finger of the left hand?

This ignorance probably explains why you believe the previous point was sensible. 

It very obviously does. Because, as you say, some genes “are only used in specific types of cell” (and often only in specific circumstances). This activation of specific genes is, ultimately, under the control of ... the genome. (I assume you think it is a god that turns the genes on and off as required.)

I can’t be bothered to read more of this ignorant drivel. 

I do not believe that insults are appropriate in in a science forum, and would kindly request you to refrain.

With respect to your counterarguments:

- If you had read the article completely you would see that my conclusion is precisely that there is no specific gene for the 2nd joint of the third finger of the left hand. Apparently you at least agree with me on that point.

- The activation of genes is a far too complex process to be brushed off as 'under control of the genome'. There are many more factors involved, as you should know if you are as knowledgeable as you claim.

- Why you bring god into the equation is entirely unclear to me. Nowhere to I indicate any supernatural causal element.

20 hours ago, Eise said:

I am wondering a bit why DanielBoyd got so many negatives on his OP. I think some people read it as another Intelligent Design posting, but it isn't. But as OP in a new thread, it is a bit long. Flying over it can lead to some wrong conclusions. But of course DanielBoyd is also to blame for this, given the title of the thread, and the, in my opinion, superfluous mentioning of entropy and its provocative title.

For me it is clear that the DNA does not, and cannot, contain all information to build or even identify an organism (except of course by just comparing DNA of known organisms). It needs the complete apparatus of the living cell that the DNA can fulfill its function.  A viewpoint one can use is that of a message and its interpretation. A message can only be interpreted by a correct interpreter. AFAIK the cellular 'interpreter' of DNA is not 'neutral'. Even if we had the complete DNA of some dinosaur, we will not be able to reconstruct how it looked like, because how the information is interpreted depends on what the dinosaur cell did with it. (So the Jurassic Park idea, to exchange  frog DNA with dinosaur-DNA and so let grow a dinosaur, will not work, because the frog-egg has not the correct environment for the DNA to produce a dinosaur.) So I agree with DanielBoyd that DNA contains the design of an organism is not correct, even if DNA of course has a strong influence on what the organism will look like. It is more like a list of ingredients of a recipe. And of course there are all kind of feedback loops in the mechanism, where proteins synthesized according to a gen, has impact on what the cell does (directly or indirectly), and so possibly also on what genes will be read later on.

Thanks, Else, for getting this discussion back on track and introducing the nuance above the gut reactions. My idea with the title was to link with Al Gore rather than creationists, but I appreciate how it may have worked like a red flag for some, who then approached the article with such expectations that they didn't actually onboard what I an saying. Misjudged that one!

I like your argument as an addition to my list: could you reconstruct an organism on the basis of it's genetic information? Clearly not. In itself this is a bit short-shrifted because the question is how you use the available information. The cell reads/uses it in very specific ways. One issue here is that this highly specific 'reading system' is taken as 'given'. The genome cannot independenly create a cell even provided with an aqueous solution of all cellular components, so apparently some other organisational mechanism is required.

My suggestion is that the only remaining option is for this to be an incredibly advanced form of self-assembly.

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9 hours ago, CharonY said:

And there is of course the perhaps trivial point that we need the proteins to interact with the DNA to actually read out information from the DNA

And, every time the cell reproduces, more of those proteins are made, following instructions coded in DNA.

There might be a problem here for abiogenesis, but it's not a problem for evolution and, more importantly, it's not support for the OP's claim that there's not enough information stored in the genome.

 

 

29 minutes ago, DanielBoyd said:

but I appreciate how it may have worked like a red flag for some

The red flag was posting lots of things that you can't show are true. Asking us to take them all on faith is equivalent to starting your own religion (regardless of what your intention may have been).

 

 

30 minutes ago, DanielBoyd said:

I like your argument as an addition to my list: could you reconstruct an organism on the basis of it's genetic information? Clearly not. 

You may like it, but it's wrong.
 As I said, you can watch a frog egg construct a frog without needing to search wiki for the instructions.
If you say the information isn't in the DNA, you need to say why you think that, and you need to explain where you think it is.

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11 hours ago, John Cuthber said:

Please indicate the parts of the apparatus of the cell that are reproduced, but for which there is no corresponding DNA.

Already answered by CharonY:

9 hours ago, CharonY said:

Well there are a variety of metabolites and co-factors that are enmeshed in the regulatory circuits required for proper functioning. And there is of course the perhaps trivial point that we need the proteins to interact with the DNA to actually read out information from the DNA (I thought that might what Eise mentioned with the hen and egg issue, but I may be wrong). 

Yep, that is what I meant. A change in the mechanism that activates reading of a gene, or the mechanism that synthesises proteins, will change the organism, just as mutations in DNA do.

Say we have a extremely reduced juke box. It reads tones from a medium, and plays them. Take the very short melody C, A, G, E. Now imagine we want to hear the melody B,A,C,H (in German b-moll is called 'H'). We can do 2 things: change the medium with the tones we want; or change the reader of the juke box so that it interprets the same medium as B,A,C,H. The message, or if you want the code, only gets its meaning in the relationship between the medium and its interpreter. With DNA it is similar. 

And as just an argument from authority: Dawkins also says that DNA is more like a recipe, than a design of an organism.

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Just now, Eise said:

Already answered by CharonY:

Not really. See above.

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3 minutes ago, John Cuthber said:

You may like it, but it's wrong.
 As I said, you can watch a frog egg construct a frog without needing to search wiki for the instructions.
If you say the information isn't in the DNA, you need to say why you think that, and you need to explain where you think it is.

You answered it yourself. Made it bold for you.

5 minutes ago, John Cuthber said:

And, every time the cell reproduces, more of those proteins are made, following instructions coded in DNA.

Idem.

Say I have a small gen: AAGCTTTCCAAAATCCCC. I can read it as a melody, just interpreting the 'T' as 'F'. Without the machinery of the cell that determines which genes are read, and how to interpret them, the DNA code means nothing. And if this machinery changes, the results change. 

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19 hours ago, Dagl1 said:

While the regulation of the genes, alternative splicing and possibly even the folding and post-translational functions of some proteins may be affected, eventually the dinosaurs DNA will produce a cell which is like that of the original dinosaur. DNA on its own doesn't really do much as you said, and of course if you take a human egg cell with dinosaur DNA you will most likely not get a dinosaur (or a human for that matter). However if you manage to keep said cell alive, then eventually the DNA that is transcribed will most likely replace all the proteins of a human with those of a dinosaur, the issue here being that I am not sure if such a cell could be kept alive at all, seeing as many transcription factors may not have much conservation in there binding motifs. 

But as new cells are produced continuously, wouldn't you say that the apparatus to make new cells is build into the DNA, thereby containing all the information to build or even identify an organism? I feel like my point isn't very... clear right now so I hope its at least clear enough; DNA on its own doesn't do much and requires a functional cell to be interpreted, but within the DNA code is the information to build such a functional cell with which to interpret the DNA, therefor the DNA does contain all the information of an organism. 
Now to be fair though, saying "all the information" may be a bit of a fallacy, we should speak of the chromatin including epigenetic marks and even then there will be some exceptions (there was a paper released a few weeks back showing that microRNA led to transgenerational responses in worms I think, but even then those microRNA's are encoded by the genome). 

-Dagl

Thanks for picking this up Dag1.  Please don't take the impression from my article that I don't think the genome plays a very essential role. The proteins that it provides direct instructions for are the most important molecular components in the cell. As you say, the apparatus required to replicate cells (and most other functions) is proteinaceous and its function is therefore gentically determined. My point is that this is the exact and only information that the genome provides. Know exactly what's in a toolbox and how it is made does not tell you what will be made using the tools. Therefore any other form of cellular and organismal organisation requires another explanation.  

12 hours ago, John Cuthber said:

Please indicate the parts of the apparatus of the cell that are reproduced, but for which there is no corresponding DNA.

Now, I accept that, for example, water is a major part of cells, and there's no DNA which (meaningfully) makes water, but it's also hard to see that as the "information" needed to make a cell.

An instruction for water would indeed appear superfluous! But proteins only constitute about 50% of the dry mass of the cell. My lipids lecturer at university could get quite heated at the lack of attention paid to 'his' essential cellular component. Carbonydrates are another essential category, along with various inorganic molecules (as a small example, where would hemaglobin be without its iron?). Of all these components, DNA only has direct control over the proteins.

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45 minutes ago, DanielBoyd said:

Thanks for picking this up Dag1.  Please don't take the impression from my article that I don't think the genome plays a very essential role. The proteins that it provides direct instructions for are the most important molecular components in the cell. As you say, the apparatus required to replicate cells (and most other functions) is proteinaceous and its function is therefore gentically determined. My point is that this is the exact and only information that the genome provides. Know exactly what's in a toolbox and how it is made does not tell you what will be made using the tools. Therefore any other form of cellular and organismal organisation requires another explanation.  

An instruction for water would indeed appear superfluous! But proteins only constitute about 50% of the dry mass of the cell. My lipids lecturer at university could get quite heated at the lack of attention paid to 'his' essential cellular component. Carbonydrates are another essential category, along with various inorganic molecules (as a small example, where would hemaglobin be without its iron?). Of all these components, DNA only has direct control over the proteins.

On the first page, I posted arguments towards each "Reason", maybe that is a good start.

In regards to Eise, Daniel and maybe someone else, deepzero the machine learning artificial intelligence has last been able to show how a protein folds based on its sequence, thus I would argue if we can predict protein folding based on sequence, then from just the genomic information we SHOULD be able to produce a fully functioning cell, with the only feedback still required being correct chromatin epigenetic status, post-translational modifications (but I am having the feeling (no real evidence here) that most proteins will function well enough when all proteins are present and over time the post-translational modifications will be added by, for example, kinases) and lastly microRNA feedback loops. 

Scrap what I said above, you would also need several membranes (Cell membrane, nuclear membrane, mitochondrial membranes and such) and vitamins/essential amino acids etc. 

Either way, I think that we can say: given that sufficient nutrients are available, and a lipid-like container is present, the DNA contains possibly (with some feedback loops that need some type of start excluded) all the information to produce a living/functioning cell.

-Dagl

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8 hours ago, DanielBoyd said:

Actually, disproof (rather than proof) is the way science works. I have presented 10 arguments that are logically consistent and based on observable facts. The next step in the process is exactly that: to show why they are incorrect. I look forward to your disproof of any one of my reasons.

I look forward to something other than baseless assertions. You must provide something other than your own assertions. I can assert anything in that manner and disproof? You are mistaken, you must provide some support for your assertions other than your assertions. Teapot in orbit around Uranus anyone? 

8 hours ago, Eise said:

Full ack. With 'authority' comes responsibility. In this case, to show where somebody is wrong. If the person in question does not react on that, then OK, leave him/her with his/hers ideas. So this is pretty useless:

This neither advances discussion, nor teaches anybody anything. 'Citation please' can be useful when somebody claims that 'science has shown that...' followed by a crackpot idea. But I do not think the OP did that. He pretty clearly shows his ideas, and the experts between us can look if these ideas match present science, and when not, can show this (with citations, if necessary). Citations are necessary when we do not agree on the facts; on theories, i.e. interpretations of facts,  we must discuss. Above has nothing to do with any advancement in insight from anybody, but only about 'winning a discussion'.

I am responding to what is little more than a gish gallop of baseless assertions, he does not really provide anything that can be called evidence and his logic is at best cartoonish, Sherlock Holmes? Really? 

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Centrosome and Mitochondria are both inherited in humans.

Somewhat logically though you'll need preexisting elements of some sort to continue the chain.

Still generally nuclear DNA contains the bulk of what we might consider meaningful code. If anything it contains much more information than strictly required for a functioning organism.

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On 6/23/2019 at 4:45 AM, Ken Fabian said:

DanielBoyd - you are not going to get much joy (from people rushing to agree with you) by claiming the mainstream science based understanding of DNA's role is so wrong as to be unworkable. Not here anyway, and especially not objections based on some personal insight into theoretical constraints that somehow make what is happening in your body right now impossible.You've dropped a whole lot of arguments all together on us, each capable of inducing people with varying degrees of understanding of it to disagree with you. Seems like the objections you have are mostly those of incredulity - your not understanding how DNA could perform a particular function seems to be taken to be evidence that it cannot. I suggest that analogies, as useful as they can be to aid understanding, can be misleading and suggest something that can be shown to occur is not possible; DNA is not a blueprint or design as we usually think of them but the parts life is made of - even to individuals and different species as well as specialised cells and organs - are made of multifunctional components; they share more in common than they have differences. Perhaps DNA and associated biochemistry is akin to recipe (which you do mention) or perhaps a string of coded instructions, with a lot of "if-then" branches but it not a recipe either. I don't think every biochemical step along the way is anywhere close to being understood - and for abiogenesis and early evolution, may never be known with certainty - but currently some of the questions you ask (differently framed) are on the way to getting answered.

If you are not seeing divine intervention, do you have any better alternatives for how living biochemistry does what it does? Or are you saying that not only do you not know, it is not possible for anyone to know?

Hi Ken, Good questions for clarification. I'm not actually saying that mainstream genetics is unworkable: mainstream genetics typically doesn't concern itself with this broader question, but with the many (very relevant and useful) details of what genetics actually does do. I in no way intend to belittle the importance of this research.

As to my incredulity, the thing about the genome is that in it's basic working it is actually very simple: there's not much to understand. It's a string of codes that are used directly to zip amino acids together in a particular order. This has been known for a long time, and is so clear that it allows us to also clearly conclude what it isn't. Since geneticists are busy enough investigating what what it does do, this question is seldom addressed. In the 80's Susan Oyama started a line of research called developmental systems theory that took a step beyond the classical genetics/epigenetics framework, but this didn't really take off in spite of much interest at the time. Perhaps I'm just trying to revive her legacy!

As to how cells and organisms form if it is not through genetic design, I think any god who did exist would be smart enough not to burden him/herself with such tasks! No, I'm a staunch atheist, so that is most definitely not the direction I am heading.

My proposed alternative to genetic design is not some other form of design but self-assembly.

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Posted (edited)

 

I'm still waiting for someone to answer my question.

If the data's not in the DNA, where is it? (for extra credit, how is it encoded and transmitted to the next generation?)

 

The OP claimed that 

On 6/22/2019 at 8:27 PM, DanielBoyd said:

Reason 1: The genome does not contain enough information. 

Edited by John Cuthber

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