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DNA doesn’t even tell teeth what they should look like

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More from the tortured world of gene-centricity.

Further to: How much does DNA influence cell shape (“In short, we don’t know how even these single cells get their shape, and it doesn’t seem to be as simple as “from their DNA, moron!”):

Come all you budding Darwinians, and you will hear the truth about how DNA rules, the selfish gene is the most important concept in science ever, and Darwin’s is the single greatest idea anyone ever had.

For our demonstration, we will use the humble tooth. A friend writes to mention a mouse experiment where developing tooth buds were moved so that the incisors and the molars were switched. The tooth buds became the tooth appropriate to the switched location, not the original one, in direct contrast to what we would expect from a gene’centric view. Apparently, developing tooth cells alter their transcription and development in response to signals from the gum tissue. He thinks this is also why human bicuspids (premolars) look weird. They are getting signals from both tissue locations.

File:Gray1003.png
bicuspids (premolars) in middle

Here is the conclusion from one article:

This study provides the first comprehensive analysis of differential gene expression between developing murine tooth types, leading to new insights into the regulatory mechanisms involved in the ontogenesis of mammalian teeth. Molecules belonging to pathways involved in various aspects of development (such as the Wnt, TGFß/BMP, or FGF pathways) were discovered as potentially carrying information for differential tooth morphogenesis. Of interest is the involvement of the retinoic acid pathway [76], as retinoids have marked effects on molar and incisor morphogenesis [22,77]. Tooth morphology and its evolution in various mammalian species were proven to be related to dosage effect of signaling molecules, like for instance FGF3 being able to modify the cusps pattern [16,78]. Our microarray analysis highlighted molecules more or less strongly expressed in a given tooth type, reinforcing the model of dosage modulating mechanisms. Gene dosage abnormalities are likely to occur in human rare diseases presenting with a tooth family specific dental phenotype [37,38,79]. Some of the corresponding genes were not retrieved in our analysis of differential gene expression in lower incisors versus lower or upper molars, suggesting that other levels of regulation, post-transcriptionally via effectors of a given pathway or via fine tuning of kinase signaling (e.g. ref. [80]), will undoubtedly also participate in the molecular identity leading to specific tooth morphology. Future investigation of differential gene expressions between upper and lower incisors, two similar tooth types formed from neural crest cells of different origins, might also contribute to shed light on specific morphogenesis and its link to individual tooth shape.

See also: Here and here. Thank to David A. DeWitt for citations.

See also: “If DNA really rules, why did THIS happen?”, where human neurons, transplanted into a mouse, had a mouse morphology.

Jonathan Wells: Far from being all-powerful, DNA does not wholly determine biological form (Mutate a fruit fly embryo in every possible way, and observe only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.)

Jonathan Wells: We are far from a good theoretical model of organisms’ development (We are far from having a complete list of the components, as a matter of fact.)

Note:  Mice don’t usually have bicuspids (premolars) between the incisors and molars but they may appear in mice as supernumerary (extra) teeth.

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35 Replies to “DNA doesn’t even tell teeth what they should look like

  1. 1
    nightlight says:

    Not sure why is this a major discovery or novelty of any sort, when mere a glance at any multicellular organisms with all its different cell, tissue and organ types produced from the single ancestor cell and its DNA. That little fact alone makes it perfectly obvious that DNA does not determine shape or function of a cell, or its further aggregations into tissues and organs.

    The final outcome, such as shape or function of cell, is always a result of interaction between DNA, cellular biochemistry and environment in which it develops. Making an ID argument out of such commonplace phenomenon is like marveling at the mystery about how come water comes in so many forms and shapes, yet it is all made of the same molecule H2O.

    Generally, natural laws, such as physics, plus initial state of a system, don’t determine on their own the future behavior of a system. You need also boundary conditions to deduce the specific final result.

    If you use quantum theory laws, then even all three elements, the laws + initial conditions + boundary conditions, don’t determine the outcome or behaviors, but merely determine probabilities of different outcomes. It still practically infinite number of possible, intrinsically unpredictable, outcomes for a large system such as cell (which is astronomically large in terms of number of elementary particles to which one applies quantum theory).

    So, I am not sure, where do these strawman expectations that initial conditions (DNA) + natural laws, determine cell shape or function. This whole series of recent UD posts on this theme reflects ignorance of the most basic science, such as how physical laws work.

  2. 2
    JacobyShaddix says:

    Apparently, developing tooth cells alter their transcription and development in response to signals from the gum tissue.

    It must be snowing in hell today. Creationists have realised something that scientists have known all along.

  3. 3
    News says:

    Nightlight, too bad you didn’t think to mention these physical laws when people were toiling away making the basic biological discoveries; you could have got a Nobel.

  4. 4
    JacobyShaddix says:

    “If DNA really rules, why did THIS happen?”, where human neurons, transplanted into a mouse, had a mouse morphology.

    Because genes tell cells how to grow but they are regulated by the environment in which they find themselves which in turn alters how they are expressed.

  5. 5
    jerry says:

    where do these strawman expectations that initial conditions (DNA) + natural laws, determine cell shape or function.

    Anything but a straw man. Meyer spends a couple chapters on these epigenetic codes which determine body plans. In order to get something new what must be changed is the information contained in the “initial conditions” of the cell that is extraneous to the DNA. This information may be just or more complex than the genome and science knows very little about this. These initial conditions produce the same body plan each time but with a different array of parts which give each organism, individuality.

    Hardly a straw man and just more complexity that has to be explained that somehow just shows up. Again I will repeat what the brain video said that I watched. 100 billion nerve cells emanating from a single cell and each knows exactly just where to go. Repeating the old joke about the thermos bottle that keeps hot things hot and cold things cold, “How does it know?”

  6. 6
    wd400 says:

    This new bugbear of yours is verys strange.

    Apparently, developing tooth cells alter their transcription and development in response to signals from the gum tissue

    Those “signals” being proteins, which are encoded by DNA? Even if there are more exotic regulatory methods likes miRNAs and methyl- tags going on, there is still a genetic basis underlying these results.

  7. 7
    jerry says:

    exotic regulatory methods likes miRNAs and methyl- tags

    Ah, another simple explanation for an extremely complex process that just happened somehow. I wonder where all these exotics came from. Selection is really amazing.

  8. 8
    Dionisio says:

    How much of the DNA does correspond to actual genes that code for proteins (yes, after splicing, cut&paste and all that)?
    What happens with the rest of the DNA? what is it for?
    Do the DNA and the other machines within the cell have to be setup in such a way so that it reacts to environmental signals in the right way in order to function and build as it does? How does that operate?
    How does it happen that the zygote goes through several iterations of symmetric cellular divisions until a point, then cells start dividing asymmetrically? What determines the cell fate in those cases? what determines their migration paths?
    the first few days they were all apparently equivalent, weren’t they? so what makes them turn into one or another type, and position themselves in this or that location? how does that work? what part of the DNA is involved in all that? are many parts of the DNA, beyond the genes, involved in a way or another in all that orchestration and choreography?
    Got more questions, but let’s pause at this for now.
    Looking forward to hearing your comments on this. Thank y’all in advance.

  9. 9
    Dionisio says:

    How much of the DNA does correspond to actual genes that code for proteins (yes, after splicing, cut&paste and all that)?
    What happens with the rest of the DNA? what is it for?
    Do the DNA and the other machines within the cell have to be setup in such a way so that it reacts to environmental signals in the right way in order to function and build as it does? How does that operate?
    How does it happen that the zygote goes through several iterations of symmetric cellular divisions until a point, then cells start dividing asymmetrically? What determines the cell fate in those cases? what determines their migration paths?
    the first few days they were all apparently equivalent, weren’t they? so what makes them turn into one or another type, and position themselves in this or that location? how does that work? what part of the DNA is involved in all that? are many parts of the DNA, beyond the genes, involved in a way or another in all that orchestration and choreography?
    Got more questions, but let’s pause at this for now.
    Looking forward to hearing your comments on this. Thank y’all in advance.

  10. 10
    bornagain77 says:

    Of related note:

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,
    http://www.thenewatlantis.com/.....nisms-mean

    The futility of what the reductive materialism is up against in trying to explain the ‘form’ of a organism is perhaps most easily understood by the following example:

    A Meaningful World: How the Arts and Sciences Reveal the Genius of Nature – Wiker and Witt
    Excerpt: They focus instead on what “Methinks it is like a weasel” really means. In isolation, in fact, it means almost nothing. Who said it? Why? What does the “it” refer to? What does it reveal about the characters? How does it advance the plot? In the context of the entire play, and of Elizabethan culture, this brief line takes on significance of surprising depth. The whole is required to give meaning to the part.
    http://www.thinkingchristian.n.....821202417/

    In the same way that “Methinks it is like a weasel” means almost nothing without overall context to give it meaning, the reductive materialist is without the overall context to give his protein ‘parts’ meaning towards a coherent, and meaningful, whole.

    Pastor Joe Boot puts the insurmountable ‘context’ problem for reductive materialism this way:

    “If you have no God, then you have no design plan for the universe. You have no prexisting structure to the universe.,, As the ancient Greeks held, like Democritus and others, the universe is flux. It’s just matter in motion. Now on that basis all you are confronted with is innumerable brute facts that are unrelated pieces of data. They have no meaningful connection to each other because there is no overall structure. There’s no design plan. It’s like my kids do ‘join the dots’ puzzles. It’s just dots, but when you join the dots there is a structure, and a picture emerges. Well, the atheists is without that (final picture). There is no preestablished pattern (to connect the facts given atheism).”
    Pastor Joe Boot – Defending the Christian Faith – 13:20 minute mark of video
    http://www.youtube.com/watch?v=wqE5_ZOAnKo

    Verse and Music:

    Jeremiah 29:11
    For I know the plans I have for you,” declares the LORD, “plans to prosper you and not to harm you, plans to give you hope and a future.

    Steven Curtis Chapman – Lord of the Dance (Live)
    http://www.youtube.com/watch?v=hDXbvMcMbU0

  11. 11
    wd400 says:

    I didn’t say development was simple – it’s just silly to point at gene-regulation as the weakness of DNA as if the molecules doing the regulation weren’t themselves encoded by DNA

  12. 12
    bornagain77 says:

    wd400, the weakness is in the absurd belief that fantastically complex integrated complexity we find in life can be had by a ‘bottom up’ trial and error process:

    it is increasingly clear that the long-reigning neo-Darwinian paradigm is collapsing – and despite many efforts to deny what is obvious – clearly “the emperor has no clothes.” The extremely sophisticated hardware and software systems that enable life simply cannot be built by any trial and error system. In particular – it is very clear that software can never be developed one binary bit at a time. Apart from a fully functional pre-existing hardware/software system, a single bit has absolutely no meaning. I feel that if we are to preserve our scientific integrity, we must acknowledge that we have a major explanatory problem, and we need to go back to the drawing board in terms of understanding the origin of biological information.
    John Sanford
    http://www.uncommondescent.com.....integrity/

  13. 13
    wd400 says:

    How much of the DNA does correspond to actual genes that code for proteins (yes, after splicing, cut&paste and all that)?

    In humans, about 1.5%.

    Do the DNA and the other machines within the cell have to be setup in such a way so that it reacts to environmental signals in the right way in order to function and build as it does? How does that operate?

    More or less. There are regulatory nerworks – some genes encode products that ‘react’ to environmental cues and drive the expression of other genes. Developmenal Biology and Molecular Biology are the general fields you want to research to get to understand how these networks work.

    How does it happen that the zygote goes through several iterations of symmetric cellular divisions until a point, then cells start dividing asymmetrically

    In vertebrates the short answer is ‘nodal flow’ – small projections (cillia) along the midling of the zygote wave to create a directoinal flow that specifies left from right – other genes react to this signal and new reguatory networks are set off.


    the first few days they were all apparently equivalent, weren’t they? so what makes them turn into one or another type, and position themselves in this or that location? how does that work? what part of the DNA is involved in all that? are many parts of the DNA, beyond the genes, involved in a way or another in all that orchestration and choreography?

    The most important parts are “transcription factors” (proteins encoded by DNA) that bind to specific ‘cis-regulatory’ regions (non-genic regions fo DNA) to drive expression fo particuarly genes (protein coding or not). There are many other levels of regulation, all the way from DNA packaging to the production mRNA to protein translation and export of proteins from the cell. It’s ceratainly isn’t a simply topic, but there are plenty of resources out that explain some of what’s going on.

  14. 14
    bornagain77 says:

    wd400, translation

    ‘You just don’t understand evolution!” 🙂

  15. 15
    jerry says:

    it’s just silly to point at gene-regulation as the weakness of DNA as if the molecules doing the regulation weren’t themselves encoded by DNA

    But this is Meyer and Wells’ point. The DNA creates the parts but what tells the parts where to assemble is such a precise way and in such an exact sequence that allows so very little deviation. Such a program must be quite complex and where is it? And how did it appear where ever it is.

  16. 16
    wd400 says:

    How do we know it allows such little deviation?

  17. 17
    Dionisio says:

    wd400 @ 13
    Thank you for looking into my questions.
    The genotype-phenotype association and the cell fate determination are some of the interesting issues to dig in.
    I’m taking online classes offered by some universities. Switching from engineering apps software development to systems biology ain’t easy at all for me. But it’s very exciting. I can’t think of another field of science more fascinating than developmental biology, specially for information technology professionals that worked on engineering design apps.

  18. 18
    bornagain77 says:

    of trivia to ‘form’:

    Da Vinci Vitruve Luc Viatour – interactive image
    http://upload.wikimedia.org/wi.....iatour.jpg

    “Speaking as one who has examined the original Vitruvian Man drawing, I can say that Leonardo was looking for a numerical design scheme that informs the proportions of the human body.
    The drawing began as an illustration from Vitruvius’ book, De Architectura where Vitruvius justifies the use of the square and circle as design elements because those shapes are integral to the human body: a man’s height is equal to his width (with arms outstretched) as a square, and a circle drawn with the navel as center and feet as radius is coincident with the hands’ reach.
    Leonardo also notes the other proportional relationships from Vitruvius such as the head height measures to the whole as well as the arms and hand sections.
    Leonardo then continued measuring (from the evidence of pin point indentations made by walking dividers, especially along the left vertical edge) to find more proportional relationships. He would take a measure of a part of the figure with the dividers and walk that measure along the height to see if the measure would fit an even number of times.
    From this drawing and others where Leonardo was working on the same type of problem it is evident that Leonardo believed there was a something like a unified field theory of design where everything in nature was related by numerical and geometrical design systems.
    He was one of the original ID thinkers.”
    – Dr. Ford
    Of note: The Vitruvian Man is a world-renowned drawing created by Leonardo da Vinci c. 1487. It is the one commonly associated with the science of physiology

    Ring Acrobat – video
    http://www.youtube.com/watch?v=IbEVXNfGS2k

    One Body – animation – video
    http://www.youtube.com/watch?v=pDMLq6eqEM4

    Alexander Tsiaras: Conception to birth — visualized – video
    http://www.youtube.com/watch?v=fKyljukBE70

    Mathematician Alexander Tsiaras on Human Development: “It’s a Mystery, It’s Magic, It’s Divinity” – March 2012
    Excerpt: ‘The magic of the mechanisms inside each genetic structure saying exactly where that nerve cell should go, the complexity of these, the mathematical models on how these things are indeed done, are beyond human comprehension. Even though I am a mathematician, I look at this with the marvel of how do these instruction sets not make these mistakes as they build what is us. It’s a mystery, it’s magic, it’s divinity.’
    http://www.evolutionnews.org/2.....57741.html

    “Can it be by accident that all birds, beasts, and men have their right side and left side alike shaped, (except in their bowels,) and just two eyes, and no more, on either side of the face; and just two ears on either side of the head, and a nose with two holes; and either two fore- legs, or two wings, or two arms on the shoulders, and two legs on the hips, and no more? Whence arises this uniformity in all their outward shapes but from the counsel and contrivances of an Author? Whence is it that the eyes of all sorts of living creatures are transparent to the very bottom, and the only transparent members in the body, having on the outside a hard transparent skin, and within transparent humours, with a crystalline lens in the middle, and a pupil before the lens, all of them so finely shaped and fitted for vision, that no artist can mend them? Did blind chance know that there was light, and what was its refraction, and fit the eyes of all creatures, after the most curious manner, to make use of it? These, and suchlike considerations, always have, and ever will prevail with mankind, to believe that there is a Being who made all things, and has all things in his power, and who is therefore to be feared.”
    (Sir Isaac Newton, A Short Scheme of the True Religion)

    Sir Isaac Newton – Of Atheism – video
    https://www.youtube.com/watch?v=XAMCgWV3PVI

  19. 19
    jerry says:

    How do we know it allows such little deviation?

    Because we do not observe it. Our eyes and our scientific instruments tell us. The body plans for every species are incredibly precise. If you believe otherwise, then provide examples.

  20. 20
    wd400 says:

    We mainly know what ‘deviations’ are tolerated (more than you might think, btw) but seeing seeing want can’t be tolerated, which is mostly (but not exclusively) via genetic mutation…

  21. 21
    jerry says:

    which is mostly (but not exclusively) via genetic mutation

    You should read Meyer’s book and follow the references. Meyer is talking about body plans and they are not contained in the genome. Mutations provide bad parts so the body plan cannot work but the genome again is not the source of the body plan.

    What tells the 100 billion neuron cells where to go? Where is that in the genome? What tells the order of the cell division and turns on and off the gene expression? They do not know.

  22. 22
    wd400 says:

    If DNA doesn’t “tell neurons where to go” how can mutations produce errors in neuronal migration?

  23. 23
    gpuccio says:

    wd400:

    A mutation in a final effector can certainly block an information pathway. In no way does that mean that the final effector is the originator of the outcomes of the pathway.

    That should be simple enough to understand.

  24. 24
    jerry says:

    That should be simple enough to understand.

    It should be for someone who claims to be knowledgeable of evolutionary biology.

  25. 25
    wd400 says:

    Of course – but I don’t see the reason for this mysticism and desire to exclude genes from development. Genes (including those of maternal effect)drive the gene expression networks that underly devlopment.

  26. 26
    gpuccio says:

    wd400:

    Nobody wants to “exclude genes”. Genes are important. But it is really a mystery how genes are regulated.

    We acknowledge that, because mysteries are the clues to new, unexpected knowledge.

    On the other hand, many scientists today, often posing as self-made philosophers, are too proud of what they think they have explained, while they have not explained those things at all.

  27. 27
    wd400 says:

    Well, You’d have to provide examples because I don’t think gene regulation is a mystery.

  28. 28
    gpuccio says:

    wd400:

    So, I suppose that you know how, from the same genome, different transcriptomes arise in order and sequence, at the right time, in the right place.

    Where is the transcriptome for an hepatic cell written? What tells a B lymphocyte what genes must be transcripted at each moment of its ontogenesis? And so on.

    No mysteries? You give the answers, please.

  29. 29
    AVS says:

    We know a lot about gene regulation. There is a huge diversity in both the mechanisms that regulate gene transcription and the variations of these mechanisms. I would venture a guess that we know a good amount about what makes a liver cell a liver cell and B cell a B cell. But we in no way understand every single protein interaction of this process.

  30. 30
    Joe says:

    PMS:

    We know a lot about gene regulation.

    And it is beyond incredulous to say blind processes produced it.

  31. 31
    AVS says:

    That’s a lovely opinion Joe, unfortunately the people who actually study gene regulation would disagree with you….hmmm who should I believe, the people who study gene regulation or the internet half-wit who has demonstrated his lack of scientific literacy and knowledge in biology?

  32. 32
    Joe says:

    PMS:

    That’s a lovely opinion Joe, unfortunately the people who actually study gene regulation would disagree with you

    Until they get it in peer-review I don’t care what they disagree with. And if I am a half-wit you don’t have any wits and actually are in a deficit.

    So stuff your pompous assholiness

  33. 33
    AVS says:

    “Until they get it in peer-review”?
    Are you kidding me Joe? It’s long past that point. It’s already gone through peer review and into the textbooks.
    Open any college level biology book; immunology, gene expression, animal development, every single I guarantee will mention the evolution of some of the topics it covers.

  34. 34
    gpuccio says:

    AVS:

    We know a lot about gene regulation. There is a huge diversity in both the mechanisms that regulate gene transcription and the variations of these mechanisms. I would venture a guess that we know a good amount about what makes a liver cell a liver cell and B cell a B cell. But we in no way understand every single protein interaction of this process.

    No. It’s the other way round.

    We know a lot about final details, like protein interactions. But we have no idea about what governs the whole process.

    Remember, the problem is as simple as completely unsolved:

    How can cells which have the same genome develop complex individual transcriptomes which make them completely different, both morphologically and functionally? What part of the genome, or other, controls that? IOWs, where are the procedures written?

    You “venture a guess” which is rather arrogant. Please, give details of what you know, or believe you know.

  35. 35
    Joe says:

    PMS spewing lies:

    Are you kidding me Joe? It’s long past that point. It’s already gone through peer review and into the textbooks.

    Liar. There isn’t anything in peer-review nor textbooks that supports blind processes producing regulatory networks.

    Open any college level biology book; immunology, gene expression, animal development, every single I guarantee will mention the evolution of some of the topics it covers.

    I have done so and you are a liar. No one knows how nor if blind processes can produce regulatory networks. You are a bluffing liar and a coward.

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