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DanielBoyd

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Posts posted by DanielBoyd


  1. 7 hours ago, Ken Fabian said:

    No, we do not agree. In any case, surely genes only directly determine RNA sequences. And not all of those RNA's are used to pattern proteins from. I provided images of working examples of combinations of RNA and proteins. RNA's have enormous biochemical potential - able to bring proteins together as a catalyst for example, as well as combine directly with them, as well as provide the pattern for making those proteins.

    If you are seeking better understanding then sticking to the belief that DNA only determines proteins when it has been pointed out clearly and repeatedly that is not the case is not a good start. And you still haven't told us your reasoning for concluding that DNA doesn't contain enough information - just repeated that conclusion.

     

    Not a good example perhaps. On consideration, all species share so much DNA that the total is not going to include enormously more than one species has. However I still absolutely depend on the DNA of other species, including for molecules my own body and cells can make. And my mother provided the ovum with all the cellular 'machinery' and epigenetic triggers, patterned from her DNA - which I may well have good copies of, for later.

    I'm not convinced a design specification exists, or more correctly that it is an appropriate conceptual framework for describing what is happening - the structures and their form look like an emergent outcome, not a specification.That may be arguing semantics. But I suspect this whole thread is about semantics.

     

    Hi Ken, you're right, I'm oversimplifying the biochemistry, but there isn't space here to be complete on such complexities. My point is (whether we're talking DNA, RNA or protein), we're still on the molecular level here, and need to transcend that to explain the higher levels of organisation that are what life is really about.

    Your last sentence suggests that we share common ground. This is exactly what I am saying: that an emergent outcome is not the result of specification.

    Some people seem to think I'm making a mountain out of a molehill here: of course there are regulatory processes and stuff which actually determine outcome, but that that is trivial. Because the genome makes the parts it's still in control.

    I think this is more than semantics, and that the conceptual framework (self-assembly vs design as formative explanations for observed structures) is fundamental to the discussion. 

    If you see the cell (and organism) as an emergent outcome, how do you interpret the role of the genome in that context?

    6 minutes ago, John Cuthber said:

    And what you said was that you were not going to answer my point.

    WHERE IS THIS INFORMATION STORED, IF IT IS NOT IN THE GENOME?

    Sorry, I thought I'd answered this question. The point is that self-assembly does not need or use information to create its product. A snowflake does not need some design to create its filligree form: this is simply the result of water molecules interacting. The thermodynamics of this process allow something complex to arise out of something simple (chilly water vapour) without any design information or external mechanism to build it. 

    Proteins are different from snowflakes in this sense. They have a design (the gene) and a construction mechanism (gene transcription).

    My contention is that the cell and the organism are like the snowflake, not the gene. They spontaneously grow without any external source of information to guide them out of the components (genetically-defined proteins, lipids, carbohydrates etc) that are available. We don't see cells or organisms 'crystallising' out of a random mix of molecules or cells like we do with snowflakes: instead growth and formation take place at the same time. But we do see something similar happening in the butterfly crysalis: All of the caterpillar's internal structures are first broken down into a disordered mush, which the re-forms into an entirely different ordered body. This is a classic case of self-assembly.

    Having said this, you are right that there is an 'information gap'. In terms of information theory the entropy of a cell/organism is lower than that of a random collection of molecules/cells, You can see this as: "it requires more information to define it". So where this information come from, if not from the genome, is a good question.

    In thermodynamic terms, this extra information (order) is created by the self-assembly process itself. It creates this order through the metabolic use of external energy sources. So the extra information is not stored but created.

    Does this answer your question?


  2. 10 hours ago, John Cuthber said:

    If I get a bunch of matchsticks and cover them with glue, put them in a box, shake them up into some random arrangement and let the glue dry then they have "self assembled" into that shape.

    But it's almost certainly no use.

    If I want molecules to self assemble into something useful, I need to "choose"- and specify- those molecules very carefully.

    And the way I do that is via the genome.

    You seem to be persistently ignoring all the points I make.

    May I remind you that the rules of the forum say that you have to address them, otherwise you are engaging in soapboxing, rather than discussion.

     

    It's a shame you should feel that way. I must say that I share the feeling: that you are failing to respond to the arguments I present concerning the limited role of the genome, simply repeating your own viewpoint.

    If I step back and try to look at the thread objectively, I see us both responding to what the other is saying, but maybe our mindsets are so far apart that bridging the distance from either side is nigh impossible. 

    At the same time, I have the feeling that there is common ground that we are failing to find. At least we agree that genes determine proteins, that proteins are the most significant types of molecules in the cell, and that which proteins are present will therefore strongly influence the processes (both formative and functional) taking place in the cell.

    So fas so good?


  3. 2 hours ago, Arete said:

    Strange already explained it, but the opening post sounds an awful lot like an irreducible complexity argument, and the factual errors, lack of citation and flawed analogies are archetypical of such arguments. 

    To clarify, I'm not accusing you of religious motivation - but the opening post sure looks an awful lot like the standard lead up to a creationist pitch, which might explain some of the reaction you're getting. 

    Thanks for the explanation. I'm new to this forum and was expecting, since its a science forum, that I wouldn't need to explain that I'm not some religious zealot in disguise. Are there really such types in abundance here who aren't here for the science but to undermine it?


  4. 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.

     


  5. 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 ;-)


  6. 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. 

     

     


  7. 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?   


  8. 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!

     

        

     


  9. 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?


  10. 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.

     


  11. On 6/27/2019 at 1:54 PM, Strange said:

    So this is an argument about popular science writing / journalism, rather than the actual science?

     

    If only! Typing "A gene for" into Google Scholar produces 245,000 hits. Admittedly, many of these are biochemical studies where there is a direct relationship, but certainly not all. Within the scientific community there is an implicit or explicit assumption that hereditability of traits is synonymous with genetic determinism. Therefore anything that is inherited must be genetically determined. Therefore morphology and physiology are genetically determined. That is the assumption I am challenging with this article.


  12. 5 hours ago, Arete said:

    I appreciate you've though deeply about this issue - however this is incorrect. 

     

    Regulatory genes can, for example, encode silencing mRNA which is used for post-transcriptional regulation of gene expression. 

    RNA secondary structure can act to alter gene expression

    Somatic V(D)J  recombination of existing genes is critical for adaptive immune function. 

    There is an entire field of Developmental Genetics which deals with the mechanisms for differential expression during development - and the vast majority are genetically determined. 

     

    Ultimately, the genome does a lot more than simply encode proteins, and much of its less obvious function is newly and incompletely understood - the term "junk DNA" was coined in 1972 to describe the 98% of the human genome that does not encode proteins. It wasn't until the 1990's that we started to unravel the function of non-coding DNA, but it does a lot more than we originally thought and were are still in the process of determining its function. 

    Great, now we are getting to the meaty stuff!

    Certainly gene activation and transcription is a more complex mechanism than just sticking an amino acid to a codon, with intermediate steps involving RNA. And, absolutely, there are feedback mechanisms involved in activation.

    But if we look at how these actually work, things get trickier. Hox genes have an important role in organismal development and are found across the animal kingdom. However, the same genes have different effects in different species https://www.sciencedirect.com/science/article/pii/S0960982206003216 . Does this not show that they are participants in the organisational processes they take part in, rather than determining it's specific outcome, as would be the case if they constituted a determinative design?


  13. Sorry, people, I come back from my day job and find a whole thread has grown that I have failed to respond to. Gotta earn a living!

    I think the general conclusion is that we don't actually disagree that much: the only direct information present in the genome is for the amino acid sequence, but the amino acid sequences determine how the proteins produced behave in the cell. In this way genetic differences indirectly exert some control over the formation and function of cells, and more indirectly on the interactions between cells that lead to the formation of multicellular organisms.

    My point - that the genome does not literally contain a design for these things - may seem trivial, but it's surprising how often you still read about 'a gene for this' or 'a gene for that', when in fact what is happening is that a genetic/protein variation is only having an indirect effect on the complex, emergent, self-organizing system it is a part of. A logic similar to putting the wrong size spark plug in your car and claiming to have explained how the engine works when it splutters. 

    This is why the discussion of the quantity of information in the genome is relevant. In information theoretical terms, the emergent processes taking place create more information than is present in the genome. This is not just a 'decompression' of hidden content in the genome, or a random expansion, but a highly specific generation of information that is simply not present there. This is where the 'missing information' comes from.

    Re-reading my article, and your responses to it, makes me realise not so much that I am wrong or you are wrong, but that I have spectacularly failed to define the issue sufficiently clearly. So now we're like the two knights meeting at a crossroads arguing about whether the statue is silver or gold (if you know the story).

    This could partly be explained by the fact that the article was originally longer, more complete and more formal, but I reduced it down and made it a little more playful in the hope of at least getting it read. I think this particular reduction in information didn't help: the emergent processes that followed created a bit of a monster!

    What the solution is I'm not sure, but I would like to thank particularly Eise, John, SharonY,  Ken and Dag1 for your feedback (sorry that I didn't get round to responding to your extensive post on the first page). 

     


  14. This is quite wonderful: the examples of cellular processes and structures being presented all demonstrated the 'incompleteness' of genetic information as a determining explanation for the functional cell.

    With respect to Brownian motion, certainly this may (partly) solve the 'transport problem' of how to move proteins from where they are made to some other place in the cell, but the cell is far from a mixed bag of molecules all zipping around randomly and bumping into each other. It contains many stable structures (usually built out of lipid membranes with specific proteins embedded in them). So getting (and keeping) proteins and other molecules in the right place is essential (and, of course, not genetically determined).

    It may have occured to you that up to now, we are still inside the cell: the molecular environment in which the genome still plays a fairly direct and dominant role. Even here, we are encountering the importance of self-assembly in addition to genetic information to get things done. The original article, however,  is primarily about the (massive!) step to the next level of organisation: that of the cellular differentiation and organisation involved in creating a multicellular organism. 

    What are your ideas on the relationship between genetic information and. say, the structure of the kidney, of the layers of cells that make up skin tissue?

    cell.jpg


  15. 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.


  16. 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.


  17. 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.


  18. 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.


  19. 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 ;-)


  20. 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.   


  21. 3 minutes ago, Moontanman said:

    Actually you are so far off on all of them your not even close enough for why your wrong to be explained. You make completely off thew wall, and i suspect a dishonest creationist source, assumptions at the beginning of each point that are not close enough to even be wrong.

    The Earth and it's biosphere is not a closed system.. 

    I find it odd to suspect a creationist source, when in an opening paragraph I actually denounce intelligent design. 

    Nowhere do I claim that the Earth/biosphere is a closed system, nor is that relevant to this discussion. 

    I really would be interested in your argument against any one of my reasons. Simply saying they are 'not close enough to even be wrong' is not a worthy rebuttal. 

     


  22. 20 minutes ago, swansont said:

    For me it starts with “There’s still a lot of energy about that can create interesting structures in defiance of the Second Law.

    Nothing going on here is in defiance of the laws of thermodynamics 

    The Second Law states that entropy can only increase or remain constant (in a closed system). The creation of complex structures constitutes a decrease in entropy. 'Defiance' may be a rather emotive word for a physical process, but it is in any case locally contrary to the Second Law. Of course, entropy in the total system does not decrease, but that's one of the main characteristics of life: the creation of order through the consumption of free energy from the environment. Just like us building cars (though in the end they rust on the scrap heap, so the Second Law has the last laugh).


  23. It’s safe to say that most people – not just the (wo)man in the street but also biologists – work on the assumption that genetics explains what we are, or at least our bodies. There is, of course, a nature-nurture debate concerning many of our mental functions. Clearly, genetics doesn’t explain which language we speak. And there’s a thing called epigenetics: the influence of our environment on how we develop. If you eat too much you get fat, work out in the gym and your muscles grow. But the fact that we’ve got two arms and two legs, a heart that beats, eyes that see – that’s all genetics, right? Wrong. 

    To explain why, we’re going to have to go pretty deep, but I’ll do my best to keep it as simple as possible. So stick with me!

    The first thing we need to consider is how complicated things can exist at all. There’s this thing you might of heard of called the Second Law of Thermodynamics: order decays into chaos. To take a simple example, if you put your hot mug of tea down briskly then before long the tea will stop sloshing, and before much longer it will have cooled to room temperature. It’s not just your tea that the Second Law wants to ‘level out’. Physicists tell us that in the end the whole universe will settle into a cold, flat and featureless state. Fortunately, we’re nowhere near that point now. There’s still a lot of energy about that can create interesting structures in defiance of the Second Law. And (making things simple again) there are just two ways of doing this. The first is design and construction: what we people are great at. From farming to pharmaceuticals, we use our brains to think up what we want and how to get it and then use our hands to make it. The second is self-assembly. This is how everything else in the physical universe comes to exist, from round planets to delicate snowflakes and from craggy mountains to rippled sandy beaches. There’s no design behind these things, just the laws of physics acting on material substances. 

    When faced with the challenge of explaining our existence, most religions quite reasonably concluded that we must be designed. After all, surely it’s ridiculous to suppose that such wonderfully complex things could exist without a design? A design required a designer, the designer was God: problem solved? Unfortunately not. 

    As biology taught us ever more about just how complex the inner workings of animals and plants are, how these structures are built of invisibly tiny cells – and how complicated the inner workings of these cells are – the idea of ‘breathing life into clay’ became woefully insufficient. How an intelligent designer could cause each fertilized egg or seed to grow into a man or a oak tree became a bit of a thing.

    Then science came up with an alternative explanation. Biologists found a set of instructions encoded in DNA that is present in each fertilized egg cell: the genome. Conveniently, this turned out to be a mash-up of the genomes of the parents with a dash of random mutation, which neatly mirrors the inheritance visible between parents and children. If you add natural selection to this combination of inheritance and variation then evolution is inevitable. And given evolution we can explain the entire branching tree of life all the way back to the first simple cell that somehow formed in the primeval soup billions of years ago. Case closed? Not quite.

    Certainly, the genome is an instruction kit. Actually a remarkably simple one: a string of codes that is used to determine which amino acid building blocks to string together into the chains that form the basis for all of the cell’s proteins. Not something complicated like the autoCAD designs that you need a degree in engineering to interpret when building a car. It is this simplicity that allows us to clearly conclude just what the genome does – and what it doesn’t. Unfortunately, it tells us that the genome cannot act as a design for the organism.

    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.

    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.

    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.

    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. 

    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. 

    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. 

    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.

    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. 

    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.

    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.

    This final reason brings us to one last loophole that the genome might creep through to still claim its omnipotent role. Alongside design-based construction there is a second way of creating things to order: the recipe. This is not a description of the end product, but of the steps to be taken to create it. Perhaps, in addition to coding for proteins, the genome also contains a recipe for building the organism. Unfortunately, this fails to avoid most of the above objections, and introduces an even bigger one: how and where are these steps coded in the genome, and how are the instructions read and followed? Loophole closed. 

    With so much simple yet damning evidence against it, why are people still so attached to the idea of the genome as design for the body? One reason is that the genome is, of course, a design. It is also present in every cell and has a visible effect on the body. The most obvious examples are genes for pigment proteins, such as those that determine eye color. Your genes provide a design for your eye pigments, and in doing so determine what color your eyes are. However, this does not mean that the whole complex structure of your eye is determined by genes.

    There are, of course, genes that have an effect on development. Meddle with the genes of a fruit fly and you can make legs grow out of their head. Hey presto! But again, let’s not overstate what is happening here. This is not like introducing a new complex feature on the basis of a necessarily equally complex new design. It is simply a matter of causing one of the existing complex features to be in the wrong place. It tells us nothing about how legs are built. 

    A second reason is undoubtedly wishful thinking. How nice it would be if there was a design that explained the complex structures of the body! How satisfying to replace some vague divine scheme with a neat scientific physical blueprint. How pleasingly recognizable it would be if organisms, like the artifacts we make, were based on design and construction. 

    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?

    As Sherlock Holmes famously said: “Once you eliminate the impossible, whatever remains, however improbable, must be the truth”. We have seen that it is impossible for the genome to constitute a design for the organism, and there is no other design available. Therefore the immense improbability of self-assembly must be the truth. And let’s not forget: this didn’t happen overnight. Our planet was a billion years old before the first self-replicating cells appeared. Even then, with the power of evolution unleashed, it took another two billion years before even the simplest of organisms arose, and another billion before it found ways of building structured bodies with demarcated organs. 

    We may marvel at the functional complexity of modern animals and plants, but we can design and build pumps and cameras that work better than our hearts and eyes. The real miracle of life is not the way we work but the fact that our bodies develop and grow from a single cell without needing a design to tell them how to do so. No wonder it took evolution billions of years to learn this trick!

    Certainly, the genome has an essential role to play in this process. The cell and the organism depend on it to provide templates for the construction of specific templates where and when these are required. But the inconvenient truth is that this is the only role that the genome has to play. It does not mold living creatures out of the inanimate clay; just sits on the shelf of the metal parts factory, waiting for the next order to come in.

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