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GP on the Origin of Body Plans [OoBP] challenge

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. . . here (at 194) in his amazing engineering thread as he responds to Dionisio:

>>Dionisio:

Thank you for summarizing that interesting discussion.

I will summarize it even more.

1) Nobody knows how morphogenesis is controlled and guided.

2) Moran is no exception to that.

3) “Experts” are no exception to that.

4) However, according to Moran (and, unfortunately, he is probably quite right): “experts do not see a need to encode body plans and brain in our genome”

5) You and I, and probably some more sensible people, do see that need.

6) So, it seems, the problem is not about what we know, but about what we see as a need.

Now, I notice that Moran says:

“experts do not see a need to encode body plans and brain in our genome” (emphasis mine)

OK, that can mean two very different things:

a) Experts do not see a need to encode body plans and brain in our genome, but they think that body plans and the brain are encoded elsewhere

OR

b) Experts do not see a need to encode body plans and brain anywhere.

I will not ask Moran what he really meant, because I think it unlikely that he would respond. So, I can only guess.

I would say that he means b). Why? Because, if he means a), I could probably partially agree, and that is a rather unlikely situation, IMO.

Now, a) just means that the procedures are encoded elsewhere. That is probably true, at least in part. That “elsewhere can still mean two different things:

a1) At some epigenetic level, that we can imagine

a2) In some other way, that at present we cannot even imagine

Well, I believe that all of that is true. The procedures are encoded in the genome, both at the level of proteome (see my OP here, for that) and at the level of non coding DNA (Ouch! Moran will not like that). And they are also encoded at many epigenetic levels. And they are also encoded at other levels that at present we cannot imagine.

But there is one certainty, for me: they are encoded somewhere.

Because, you see, most neo darwinists would rather go with b): they really believe that those things are not encoded anywhere.

Now, while you and I certainly find that idea completely absurd, let’s try to understand what they think.

The best, and most honest, admission about that, in my memory, was made by Piotr, some time ago, in a discussion that was exactly about the procedures for cell (and tissue, and organ, and body) development. He said, if I remember well:

“I think it’s just the memory of what worked”.

OK, that’s a very honest statement of a neo darwinian perspective. But, as it is honest, it includes a precious little word: memory.

Now, you and I, having some love for informatics and programming, know all too well that “memory” is not a vague concept.

Memory of information must be stored to survive and be available. And that requires, in our human experience, some storage medium. Usually some physical (and often expensive) storage medium.

IOWs, no memory storage medium, no party.

So, I would like to ask Piotr (if he still reads this blog, that is unlikely), or Moran (if he likes to answer, that is unlikely), or anyone else:

Where and how are the procedure for cell (and tissue, and organ, and body) development stored?

Because, you see, they are certainly available in some way, otherwise how could the embryo of any organism generate the full body?

I suppose that the most likely argument of any neo darwinist, at this point, would be that those procedures must, after all, be very simple. A few HARs, a few hundred, at best a few thousand, nucleotides, and the deed is done.

Done? The human body plan? The human brain and nervous system? The whole immunology network? And so on, and so on?

You and I, having some love for informatics and programming, know all too well a very basic truth: very simple programs require some limited memory to be stored, but very complex programs require a lot of memory.

So, is the information for human brain really so simple? Is it like squeezing, say, Windows 10 in 1-2 KB at most?

OK, we know that the biological designer must be very good, but so good?

Ah, but I forgot: neo darwinian evolution can do practically anything: even miracles, provided we don’t call them miracles! >>

He goes on, in 201:

>>By the way, let’s comment some more on this interesting issue of development, always in the light of the results presented in this OP.

Vertebrates are considered as a subphylum of chordates: chordates with backbones.

So, in a sense, the basic body plan is set up in chordates, with the appearance of the notochord, and other features.

As we know, phyla correspond to basic body plans. But, strangely enough, they all appear very “suddenly”, during the so called “Cambrian explosion” (approximately 541 – 520 million years ago).

We know well all the debates about that amazing event. Of course, neo darwinist have tried their best to hypothesize that the explosion is not an explosion at all, and that the true information for all those new body plans was being “manufactured” more gradually during the previous times. And so on.

But the evidence of the fossils remains what it is, and I don’t think that our “polite dissenters” have succeeded in explaining away the “almost miracle” of the Cambrian events.

However, with vertebrates we are apparently observing an event slightly later than the Cambrian explosion itself. The emergence of a very important (for future developments) subphylum in the well established phylum of chordata.

That allows to localize better the emergence of the new information, to somewhat later than the Cambrian, but anyway well more than 400 million years ago.

Now, if we judge from the following natural history, it seems that the emergence of vertebrates was a very successful innovation: indeed, chordates not vertebrates are a rather small bunch of organisms today, while vertebrates are, in comparison, one of the main representative groups of animals, from many points of view, even if we don’t consider the side aspect that we, as humans, are part of it.

So, it is rather interesting to observe, according to the data presented in the OP, that the transition to vertebrates was a very exceptional “jump” from the point of view of some specific functional information in the proteome, certainly the biggest step we can observe in the accumulation of human conserved protein information. In that sense, it is a much bigger step than the simple appearance of the phylum chordata, with the appearence of more than twice human conserved information (3,708,977 bits vs 1,685,550, not corrected for redundancy).

If we want to make hypotheses about that interesting fact, we could probably reason that the new body plan of vertebrates includes at least two major innovations that will be very important in all the future natural history of that branch:

1) Cephalization, and in particular the gradual development of the brain, and therefore of all new functiona connected to that

2) Adaptive immunity, which appears for the first time in jawed vertebrates.

Both these innovations have a common denominator: they are linked to the appearance and development of two very complex regulatory systems, both aimed to a very complex and nuanced interaction with the outer environment.

IOWs, they are both, in different ways, complex systems that process information from the outer world.

That is an important concept, because it bears a fundamental implication:

If the bulk of the huge informational jump that appears in the vertebrate proteome is really linked to the premises for the development of the central nervous system and the brain and of the adaptive immune system, then it is perfectly reasonable to think that much of that new information must be strongly connected, as one can expect in any big and complex system that mainly processes information and reacts to it in very complex and nuanced modalities.

Another way to say it is that, in that huge informational jump, a great part of the total information can be expected to be irreducibly complex.>>

Sobering issues, well worth headlining and inviting further discussion. Let’s see if objectors to design thought have a good, cogent and plausible counter-case that is suitably empirically well-grounded in actual observations rather than ideologically loadesd reconstructions of the inherently unobservable remote past of origins. END

PS: I have been very busy RW.

140 Replies to “GP on the Origin of Body Plans [OoBP] challenge

  1. 1
    kairosfocus says:

    GP, I think your summary of a summary and onward comments are far too good not to be headlined separately, so pardon my doing so! KF

  2. 2
    Dionisio says:

    KF,

    I agree with your decision! Well done!

  3. 3
    Dionisio says:

    We hear some politely-dissenting folks popping up here and there claiming that there’s little or no science in the ID paradigm.
    Well, here’s an opportunity offered by KF for the politely-dissenting folks to come and challenge the presented arguments.
    Anybody out there?

  4. 4
    gpuccio says:

    KF:

    Thank you for giving attention to my reasonings! I am really honored. 🙂

    I hope that some interesting discussion may arise about these important points. Of course, I will be happy to participate.

  5. 5
    kairosfocus says:

    Folks,

    a note or three of my own.

    1: OoL as we know it — cell based — likely implies a genome size of 100 – 1,000 k bases, about 100 – 1,000 times the FSCO/I threshold. Where, every additional bit DOUBLES config space to be searched.

    2: For OoBP, dozens of times over (and with an eye to the Cambrian life manifestations as an indicator) we are looking at more like 10 – 100+ mn new base pairs to account for cell types, tissues, organs and networks etc. The low end is from a simplistic calc, the upper end is based on what we observe. 10 – 100 thousand times the FSCO/I threshold.

    3: As for FSCO/I, I just remarked to RVB8 as follows in another thread:

    When it comes to the core design inference, even to object you had to create yet another example on top of the trillions already existing, as to how functionally specific complex organisation and/or associated information, are only seen to come from intelligently directed configuration. A config space, search challenge analysis readily shows that blind, chance and necessity-driven search of such a space beyond 500 – 1000 bits, is only capable of sampling so negligible a fraction that we can disregard it as a credible explanation of such FSCO/I. In short, we have here a very strong causal inference on sign backed up by analysis of the search challenge implied by attempted blind search. Where, random document generation exercises [monkeys at keyboards on steroids] show that so far we are a factor of 10^100 short of the bottom end of the threshold zone, precisely as expected. So, when we for example look at the text in the DNA of the cell, and the associated co-ordinated molecular nanotech machinery that allows it to function as communication in controlled processes, we find that this is a strong example of FSCO/I and is therefore best explained by design. On that, we then see that OoL and Oo body plans up to our own, [are] then best explained on the same basis. to date, we find no good, empirically warranted, demonstrated causally sufficient reason to infer otherwise to blind mechanisms.

    KF

  6. 6
    Origenes says:

    Some relevant quotes:

    I posed the question:

    If most of our genome is junk, then where is the information stored for the (adult) body plan? Where is the information stored for e.g. the brain? And where is the information stored for how to build all this?

    Here are the answers by Larry Moran and WD400:

    Larry Moran: …. experts do not see a need to encode body plans and brain in our genome …

    WD400: If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on.

    Unfortunately VJTorley has bought into this incoherent mat evo narrative:

    VJTorley: I believe about 10% of our DNA is functional – maybe 20% at a stretch. I used to think otherwise, but Moran’s posts on junk DNA have convinced me otherwise. He always manages to trounce his critics.

    Eric Anderson: Do you [VJTorley] seriously think 340 beneficial mutations in DNA could turn an ape-like creature into a human, and 3000 beneficial mutations in DNA could turn a land animal into a whale?

    VJTorley: I have to say (reluctantly) that I haven’t seen any rigorous quantitative argument yet as to why this could not be the case. ….
    For human evolution, I’m guessing that 30 to 50 separate organs (or systems) underwent transformation, and that there were 10 mutations per organ, with these mutations occurring more or less in sync (due to intelligent guidance), making 300 to 500 mutations. But I could be wrong, of course.

    Eric Anderson summarized the mat evo position as follows:

    Eric Anderson: … this thread may have uncovered at least one aspect of the simplistic thinking that leads a person to believe that most DNA is junk.
    After all, the thinking goes, all we need to do is specify some parts in the DNA and the machine will build itself all by chemistry. It’s easy! No plan needed. No program required. Just specify some gene products and we’re done. Everything else is probably just junk.
    Amazing what chemistry can do.

  7. 7
    Dionisio says:

    gpuccio asked:

    Where and how are the procedures for cell (and tissue, and organ, and body) development stored?

    Here’s the brilliant response he got from the politely-dissenting interlocutors:

    deafening silence…

    Hello! Anybody out there?

    crickets chirp

    🙂

  8. 8
    Dionisio says:

    What’s going on?

    Where are the debaters, the objectors?

    Did they run out of arguments?

    Did they run for the exit door?

    🙂

  9. 9
    Dionisio says:

    Unlike me, gpuccio does ask honest questions.
    Note that he did not ask “where exactly and how exactly…?”
    He just asked “where and how…?”
    He lowered the bar to no avail… still the objectors are not seen around. Their conspicuous absence seems suspicious.
    I’m sure gpuccio would bold any tricky word like “exactly”, but the fact is that he didn’t even use that word.
    Such a nice guy and look at the response he gets back.

    🙂

  10. 10
    Dionisio says:

    KF:

    Sobering issues, well worth headlining and inviting further discussion.

    Yes, indeed.

  11. 11
    Dionisio says:

    KF:

    Let’s see if objectors to design thought have a good, cogent and plausible counter-case that is suitably empirically well-grounded in actual observations […]

    where are those objectors?

    🙂

  12. 12
    kairosfocus says:

    D, after years and years we wait. Especially after several dozen attempts at counter-examples crashed in flames over the course of several years. Try Martian Canals and a simulation world that assembles clocks (failing to understand what is implicit in say a gear train! . . . I think that one never had to do a ‘shop course or the like), not to mention Dawkins’ Weasel. etc. KF

  13. 13
    kairosfocus says:

    A key principle: a result that requires complex, functionally specific information-rich organisation [and that’s a description, FYI] — including, of course, assembly or construction or composition — cannot credibly be obtained without both the information and adequate means of putting it to work; where the only empirically and analytically warranted source* of such FSCO/I is intelligently directed configuration. So, watch out for the gap where info plus means should be, or the smuggling in of same by the back-door.

    *PS: And no, we ourselves are contingent and our bodies are shaped through FSCO/I, we are not ultimate sources of design, we are secondary designers, similar to but more sophisticated than, say, beavers.

  14. 14
    Dionisio says:

    KF,

    Does the second part of the first chapter of the first letter of Paul to the Corinthians imply that God could let some of His children sweep and mop the floor with the best pseudo-scientific arguments the PhDs of this world could ever present against Him, though by now we know they have none?

  15. 15
    Dionisio says:

    KF,

    Shouldn’t science get back to where it once belonged, when Copernicus, Newton, and others could think freely, with open-mindedness, out of wrongly preconceived boxes?

  16. 16
    gpuccio says:

    Dionisio:

    “deafening silence…”

    So it seems… 🙂

  17. 17
    kairosfocus says:

    GP & D, mebbe they are marshalling their resources to reply, perhaps overnight or thereabouts. KF

  18. 18
    mike1962 says:

    gpuccio

    Write a book

    You are a force to be reckoned with

    Larry Moran wishes he was a smart you

    Just do it

    What are you waiting for?

  19. 19
    Dionisio says:

    KF,

    The could be getting ready to launch a fulminating blitzkrieg-style attack to destroy all the arguments presented here.

    Yeah, right. Not even in their wildest daydreaming after many sleepless nights.
    They lack what’s required to do so.

  20. 20
    Dionisio says:

    mike1962 @18:

    Yes, that’s an interesting idea.
    I think so too.

  21. 21
    Dionisio says:

    gpuccio wrote:

    Nobody knows how morphogenesis is controlled and guided.

    That’s a very hard statement.

    I’ll soften it a little:

    Biologists do know something about it, but what is known points doubtlessly to intelligent design.
    What will be revealed tomorrow will keep pointing in that direction, even more.

    No objections out there?

    …deafening silence…

    Hello! Anybody out there?

    …crickets chirp…

  22. 22
    rvb8 says:

    The article on, ‘Evollutionary development biology’,in Wikipedia would be a convenient non-threatening place for you ostriches to start with. Again, you won’t like it. It’s full of clear evidence based theories, with elegant hypotheses explaining likely routes, and even predictive possible futures.

    The chapters 5, ‘Getting a Head’; 6, ‘The Best-Laid (Body) Plans; and 7, ‘Adventures in Bodybuilding’, from Neil Shubin’s ‘Your Inner Fish’, could also be of use for understanding where CURRENT research is at, on this question.

    Also Coyne’s ‘WEIT’, chapter 3, ‘Remnants: Vestiges, Embryos, and Bad Design’, also delves into body plans, and their building.

    Feel free however to declare the non-argument won, and to watch the clouds float over that very deep well you find youselves in.

    Dionosio,

    the silence eminates from the ID side. With Irreducible Complexity, and Specified Complexity, (along of course, with the utterly unknown non-concept, FSCO/I), the only partially defined (with zero experimentation, and evidence) ideas, it is ID that is home to those crickets.

  23. 23
    LocalMinimum says:

    RVB8:
    The article on, ‘Evollutionary[sic] development biology’,in Wikipedia would be a convenient non-threatening place for you ostriches to start with. Again, you won’t like it. It’s full of clear evidence based theories, with elegant hypotheses explaining likely routes, and even predictive possible futures.

    What I see is what would be a decent little blurb on developmental biology, padded out with pretty standard and not particularly inspiring or useful evolutionary speculation. Could you explain precisely what it is that I should be finding here? Perhaps list the best/strongest examples of your statement?

  24. 24
    gpuccio says:

    rvb8 at #22:

    Is that an attempt at “discussion”?

    Because, you know, it really doesn’t look that way. Not at all.

    Maybe you are only trying to remind us that you exist.

    OK, you exist.

    But are you capable of personal thinking, ideas, intellectual confrontation, debate, and similar human activities?

    Just to know…

  25. 25
    Dionisio says:

    @22:

    The article on, ‘Evollutionary development biology’,in Wikipedia would be a convenient non-threatening place […]

    Does the word “evollution” (with double ‘L’) refer to the Neo-Darwinian stuff?

    Do they write it with double ‘L’ to indicate that it’s wrong or that it doesn’t exist?

    🙂

  26. 26
    Dionisio says:

    KF,

    Sorry, the jellyfish (@22) got in the net. Please, would you mind removing it so that it leaves room for better quality fish?

    🙂

  27. 27
    rvb8 says:

    LocalM,

    No! If you can’t, or won’t read it I can’t and won’t make you. But these two parts are full of links you can and, no doubt with the curiosity inherrant in ID folk, will ignore.

    2.)The control of body structure.
    3.)The origins of novelty.

    The two other scientists and their books that I mention, you should also avoid, being full of facts, and research etc.

    You should keep reading Jonathan Wells’s earth shattering ‘Icons of Evolution’. To be followed by ‘More Icons of Evolution’, and most recently ‘Zombie Science: More Icons of Evolution’. (Zombie Science? Really? This man who is perrenially ignored, is getting annoyed and irritated, and it shows in this childish tantrum title.) Perhaps in a few years we’ll get, ‘Icons 3’, maybe ‘Icons Rebooted’.

    Seriously? Talk about flogging a dead horse. I leave it to Christopher Hitchens to describe the impact on science of this man and these tomes;

    “Mr Wells’s book is unlikely to merit even a footnote in the history of piffle.” The man was indeed a word smith.

    Dionosio,

    no I made a mistake. It shoud be one ‘l’. I don’t mind admitting my errors and failures in syntax and style; you?

  28. 28
    Dionisio says:

    LocalMinimum @23:

    I see your valid point, but you may want to consider not taking that senseless post @22 seriously. Save your precious time for better things. Don’t squander it.

  29. 29
    gpuccio says:

    Dionisio:

    OK, it’s a very hard statement. But maybe I will retain it.

    Please, note that I have said:

    “Nobody knows how morphogenesis is controlled and guided.”

    Not:

    Nobody knows how morphogenesis is implemented.

    IOWs, we certainly know a lot about pathways that are implied in morphogenesis.

    For example, we know that in many steps there is a role for some morphogens.

    But, as you have kindly reminded to Moran and to us, how is a morphogen gradient generated in each specific case?

    IOWs, what initiates, controls and guides the generation of a specific morphogen gradient in each specific context?

    My impression is that all knowledge we have about morphogenesis is descriptive: OK, we see that when a cell differentiates in this way this and that happen.

    But my question is different:

    What kind of information is necessary in a cell so that it can differentiate along some pathway or some other pathway in different conditions?

    I will try to be even more clear with a generic example.

    Let’s say that we have a simple multicellular organism A where a cell “a” generates 30 cells that are all similar:

    aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa.

    That’s all, in the development of that organism.

    Now, let’s say that from that organism derives a more complex, but still rather simple, multicellular organism B where an original cell “b” generates three different layers of cells, each with very different features and functionalities, and specific spatial arrangements:

    ccccccccccddddddddddeeeeeeeeee

    OK, now let’s say that the second organism B derives, by common descent, from the older organism A.

    Now, the simple question is:

    What has to change in the original cell “a” so that it becomes the new original cell “b”, with the new potential to generate three different types of cells?

    Whatever it is, that is exactly the information necessary for the cell differentiation that we observe in the organism B, and that was not present in organism A.

    That information must exist, and must be, in principle, quantifiable.

    It must include not only the effectors (proteins like transcription factors, promoters, enhancers, epigenetic tools, and so on), but also the specific configuration of those effectors, and very likely of other components that we still don’t understand, that initiate, control and guide the processes we observe.

    That’s what I call the functional information linked to the procedure.

    Because, of course, if I need to make a specific change to something to generate a new functionality in that object, what I am doing is simply that: I am adding functional information.

    Each change that is necessary to implement a new functionality is functional information linked to that function

    Now, the myth of darwinists is that such “functional information linked to the procedures” may be very simple.

    They believe, with the simple and sometimes aggressive faith of a new enthusiastic religious adept, that certainly a few small changes here and there, some of them still elusive, are able to make an embryo generate “simple” new objects like a liver cell, or T and B lymphocytes, or “simple” structure like the kidney and the brain.

    After all, what’s all the fuss about? Neo-darwinian evolution can do almost-miracles like OOL, why should it be afraid to try cell, tissue, organ and body plan development?

    The important point is not to connect too much new information to that, because those tricky creationists, camouflaged as IDists, are proud enough of the functional information they already see in known proteins, and we certainly don’t want to give them further ammunition! 🙂

  30. 30
    gpuccio says:

    rvb8:

    The Wikipedia article you point to is a very good example of the ideological bias I have described in post #29.

    We learn that:

    Among the more surprising and, perhaps, counterintuitive (from a neo-Darwinian viewpoint) results of recent research in evolutionary developmental biology is that the diversity of body plans and morphology in organisms across many phyla are not necessarily reflected in diversity at the level of the sequences of genes, including those of the developmental genetic toolkit and other genes involved in development. Indeed, as Gerhart and Kirschner have noted, there is an apparent paradox: “where we most expect to find variation, we find conservation, a lack of change”.[43] So, if the observed morphological novelty between different clades does not come from changes in gene sequences (such as by mutation), where does it come from? Novelty may arise by mutation-driven changes in gene regulation.

    OK. But my OP here:

    http://www.uncommondescent.com.....-analysis/

    is about the huge modfications that have to occur in the proteome too, so that gene regulation may be different. That is an important point, often underestimated in current biological thinking.

    And:

    The protein products of the regulatory toolkit are reused not by duplication and modification, but by a complex mosaic of pleiotropy, being applied unchanged in many independent developmental processes, giving pattern to many dissimilar body structures.[36] The loci of these pleiotropic toolkit genes have large, complicated and modular cis-regulatory elements. For example, while a non-pleiotropic rhodopsin gene in the fruit fly has a cis-regulatory element just a few hundred base pairs long, the pleiotropic eyeless cis-regulatory region contains 6 cis-regulatory elements in over 7000 base pairs.[36] The regulatory networks involved are often very large. Each regulatory protein controls “scores to hundreds” of cis-regulatory elements. For instance, 67 fruit fly transcription factors controlled on average 124 target genes each.[36] All this complexity enables genes involved in the development of the embryo to be switched on and off at exactly the right times and in exactly the right places. Some of these genes are structural, directly forming enzymes, tissues and organs of the embryo. But many others are themselves regulatory genes, so what is switched on is often a precisely-timed cascade of switching, involving turning on one developmental process after another in the developing embryo.[36]

    Emphasis mine.

    OK, That seems a fine passage. Merely descriptive again, but at least it admits the complexity of the whole.

    But then, just a few vague words about “The origin of novelty”, and in particular this jewel:

    Given that small changes in toolbox genes can cause significant changes in body structures, they have often enabled the same function convergently or in parallel.

    Emphasis mine.

    ???????

    Wait a moment, what does that mean?

    All that talk about “all this complexity”, and “large, complicated and modular cis-regulatory elements”, and all they can say is that:

    small changes in toolbox genes can cause significant changes in body structures”?

    So, the idea is simple and elegant:

    I just change a couple of aminoacids in a transcription factor and look:

    Before: it interacted with 1000 other modular components so that it generated the eye in drosophila.

    After. it interacts with some other 1000 modular components, so that it generate the eye in the mouse.

    Perfect! Everybody can see how a very small change (no real complex functional information implied) has implement an apparently complex result. That procedure is so simple, that it has certainly “often enabled the same function convergently or in parallel”.

    Where’s the problem?

    Well, for myself, I definitely feel fooled. Like in the old three-card trick. A simple and elegant trick, but a trick just the same.

    Anybody else feels fooled, like me? 🙂

  31. 31
    Dionisio says:

    gpuccio,

    Excellent explanation!

    Are you saying that at this point scientists can describe many processes right as they are observed, but that doesn’t tell us much about how exactly all those biological shows are managed and where are the scripts for all the actors and the choreographies kept stored, so that they are easily accessible when needed?

    Could it be compared to someone going to a theatre and seeing a beautiful ballet performance, then later being able to describe the whole show in many details, but not knowing how exactly that show was managed or directed and not having any idea where the documents containing the choreographies are stored?

    Note that in the case of how the actual management processes occur they may have some clues or hints, though perhaps many times vague or blurred. But much less is known about the location where the procedures are stored and the format they are stored in.

    Did I understand this right?

    Thanks.

    PS. I still want to read your comment mere carefully. It’s possible will have more questions.

  32. 32
    Dionisio says:

    KF,

    I think GP is cooking a delicious meal for thoughts.

    Despite some noise in the environment, caused by jellyfish that got trapped in the net. 🙂

    Let’s stay tuned. GP’s comments are keeping me at the edge of the seat.

    🙂

  33. 33
    gpuccio says:

    Dionisio:

    “Did I understand this right?”

    Yes!

    “I think GP is cooking a delicious meal for thoughts.”

    Thank you. That’s probably the only kind of thing I can cook! 🙂

    “Despite some noise in the environment, caused by jellyfish that got trapped in the net.”

    Maybe a jellyfish is better than nothing! 🙂

  34. 34
    gpuccio says:

    mike1962:

    Thank you for the very kind words.

    “Write a book”

    Maybe, maybe…

  35. 35
    kairosfocus says:

    GP, it is often a feature of communication-based and cybernetic systems that they contain switches, short/ small, seemingly simple components that redirect complex processes down alternative paths. I think of the not function in logic, or of mode bits in assembly languages, or of comparators [or subtractors or differencing amplifiers) in control loops, or even of word shifts like “moral” vs “amoral” vs again something like “non-moral.” But to focus on the switch misses the key: for the alternative pathways to exist, they have to each be present, nodes that trigger modified pathways do not remove the need for valid pathways to be present. If a similar switch element triggers compound vs mammalian eye development, that does not change the differing and astonishingly precise information and process requisites for both. Optical systems often require surfaces set up correctly to order a fraction of the wavelength of light; and here there are significant architectural differences and even strategies. The issue of Hox genes pops up just as a term. When an eye is to be built into an organism, too, it does not stand on its own: skeletal structure, nerve paths and brain structures to process the notoriously wide bandwidth information involved with video come into play. There have to be wider issues on what to do with visual info, as in: that’s a cat there, run. Pattern recognition in real time and appropriate rapid responsiveness, etc. The wings of various animals come to mind also: a wing is already a complex aerodynamic entity, and it needs muscles, power flows, control, etc to work. And much more. KF

  36. 36
    rvb8 says:

    gpuccio, Dionisio,

    I can’t answer your in depth reply.

    As said, take these brilliant insights to a wider audience at say Pandas, WEIT, or the more friendly TSZ.

    Let them be eviscerated there.

  37. 37
    gpuccio says:

    KF:

    Wonderful point about switches.

    Switches are, definitely, the best tool for the old three-card trick.

    Just an example:

    We know well that overexpression of just 4 TFs, Oct4, Sox2, Klf4 and c-Myc, can induce pluripotent stem cells from differentiated fibroblasts. Indeed, even simpler cocktails can do that.

    A miracle? Does that mean that we understand how pluripotent stem cells work? Does that mean that we understand the process of differentiation or de-differentiation?

    No and no. Not at all.

    Those are switches. Wonderful, powerful, elegant switches.

    In a sense, a switch that lights a lamp can be the same as a switch that turns on a computer.

    Same complexity in the switch, but some small difference in the circuit! 🙂

  38. 38
    gpuccio says:

    rvb8:

    “I can’t answer your in depth reply.”

    Well, that’s a honest admission, at least. Thank you.

    “take these brilliant insights to a wider audience ”

    I think they are public enough here. However, thank you for the kind suggestion. 🙂

  39. 39
    gpuccio says:

    Dionisio:

    Maybe the jellyfish has escaped… 🙂

  40. 40
    Dionisio says:

    gpuccio @29:

    Please, note that I have said:
    “Nobody knows how morphogenesis is controlled and guided.”

    Not:
    Nobody knows how morphogenesis is implemented.

    C’mon doctor, I can see you’re ‘picky’ about the contextual meaning of different words. 🙂

    That seems old fashioned. These days many people don’t pay that kind of careful attention to words and meanings.

    🙂

  41. 41
    gpuccio says:

    Dionisio:

    Ah, words! I love them. 🙂

    By the way, did you notice that the Wikipedia article says:

    “at exactly the right times and in exactly the right places”

    using “exactly” not once but twice, without even bolding it?

    Tricky article that it is! 🙂

  42. 42
    gpuccio says:

    Dionisio:

    “That seems old fashioned.”

    Well, I am not exactly (!) a teenager.

  43. 43
    Dionisio says:

    gpuccio:

    Ah, it’s fun to argue with “l’italiano vero”!

    🙂

    BTW, I’m not a teenager either.

    This modern lack of attention to details and word meaning is annoying.

    But perhaps you’re right when you said that words should be bolder in the questions.

    🙂

  44. 44
    Dionisio says:

    gpuccio @41:

    By the way, did you notice that the Wikipedia article says:
    “at exactly the right times and in exactly the right places”
    using “exactly” not once but twice, without even bolding it?
    Tricky article that it is!

    Tricky?

    That’s how we call it, but the distinguished Canadian biochemistry professor would call it dishonest article! 🙂
    According to his criteria, the referenced article proves that Wikipedia doesn’t have honest articles!

  45. 45
    Bob O'H says:

    gpuccio @ 29 – the questions you raise are important ones, and are central to developmental genetics. So, I’m curious to know – have you read much about that area? I found Endless Forms Most Beautiful helpful in explaining how cell differentiation is controlled. It’s not a simple process, I’m afraid, but we actually do have a lot of knowledge about it (“we”, BTW, means scientists and humanity, not including me specifically).

    Your argument in the OP is largely from ignorance. I can’t comment on what Larry Moran meant (partly because I’m too lazy to try to find the original quote), but what is (mostly*) encoded in our genes is the process to produce a body plan, not the plan itself.

    * ‘mostly’ because there are also maternal factors in play too, i.e. the mother provides some of the information for development to occur correctly. As with most of biology, it’s more complicated than we’d wish.

  46. 46
    Dionisio says:

    gpuccio:

    Your example on the use and meaning of the words ‘controlled’ and ‘guided’ vs. the word ‘implemented’ is an excellent illustration I may refer to in future discussions.

  47. 47
    gpuccio says:

    KF, Dionisio:

    In my post #54 at the other thread:

    http://www.uncommondescent.com.....ent-627591

    I wrote:

    “Transcription factors are a good example: the DNA binding domain is usually the most conserved part of the molecule. But TFs do not simply interact with DNA: they interact with one another, often in complex cumulative structures, and with other molecules and biochemical pathways.

    That part, the “regulatory” part, that in the end determines what the TF bound to DNA will do, is much less understood, and often less conserved, probably because it is functionally tweaked to different final functions.”

    I think it can be interesting to offer an example of that here, because it can show the point that specific changes in the existing proteome can have great importnace in new body plans, and happen in jumps.

    So, let’s take Pax-6, an important transcription factor active during embryonic development, which is so quoted in the Wikipedia page so kindly linked by rvb8:

    The field is characterised by some key concepts, which took biologists by surprise. One is deep homology, the finding that dissimilar organs such as the eyes of insects, vertebrates and cephalopod molluscs, long thought to have evolved separately, are controlled by similar genes such as pax-6, from the evo-devo gene toolkit. These genes are ancient, being highly conserved among phyla; they generate the patterns in time and space which shape the embryo, and ultimately form the body plan of the organism.

    True. But let’s take a more detailed look to this important TF using the concept of Human Conserved Information (from now on, HCI), developed in my OP.

    The functional density (per aminoacid site) of HCI in PAX-6 is as follows:

    Cnidaria: 0.7393365
    Cephalopoda: 1.21564
    Deuterostomia (not vertebrates): 1.232227
    (jump here)
    Cartilaginous fish: 1.966825
    Bony fish: 2.007109
    Amphibia: 2.035545
    Crocodylia: 2.052133
    Marsupialia: 2.033175
    Afrotheria: 2.061611

    As everybody can see, while the protein has a very good homology with the human form already in protostomia (1.21 baa in Cephalopoda), there is a sudden and important jump in cartilaginous fish, of:

    0.7345972 baa

    That jump is obviosuly linked to the new vertebrate body plan.

    Moreover, the density of HCI in cartilaginous fish reaches almost its maximum value (remember, 2,2 baa is the value for identity), and remains rather constant up to mammals and humans.

    Now, let’s try to understand in detail what happens.

    I have blasted the human protein against Drosophila melanogaster (fruit fly, a Protostome) and Callorhincus milii (a shark, Cartilaginous fish).

    Well, as expected, the homology is:

    Drosophila: 435 bits, 52% identities, 1.030805 baa

    Callorhincus: 830 bits, 95% identities, 1.966824 baa

    Here, again, the jump is conspicuous.

    But the interesting thing is: what changes?

    If we look at the blast, it is i,,ediately obvious that the homology found in Drosophila (or, say, in all protostomia and non vertebrate dueterostomia) is strictly confined to two well defined regions of the sequence:

    1) The Paired Box domain (AAs 4 – 128)

    2) The Homeobox domain (AAs 211 – 266)

    Both are DNA binding domains. Together, they are responsible for the about 50% identity, slightly more than 400 bits homology, slightly more than 1 baa, that we find between pre-vertebrates and humans.

    IOWs, the basci homology of PAX-6 in pre-vertebrates with the human protein is almost entirely attributable to the two recognizable DNA binding domains, which are both highly conserved.

    But what about the rest of the sequence?

    PAX-6 is 422 AAs long. The two domains, together, are less than 200 AAs. And the rest?

    The rest is essentially made of two parts:

    a) A segment of slightly more than 50 AAs, between the two domains.

    b) The C-terminal part of the molecule, about 150 AAs long.

    Well, the interesting point is:

    These two parts of the molecule (not corresponding to recognizable domains), when compared to the human protein, are almost completely different in Drosophila (and, in general, in pre-vertebrates), while they are almost identical already in Cartilaginous fish, and so they remain, almost unchanged, throughout the following natural evolutionary history (more than 400 million years).

    So, not only a big jump, but a very specific, targeted jump.

    Just as a check, I will paste here again my statement from my other thread, that was the starting point for this post:

    Transcription factors are a good example: the DNA binding domain is usually the most conserved part of the molecule. But TFs do not simply interact with DNA: they interact with one another, often in complex cumulative structures, and with other molecules and biochemical pathways.

    That part, the “regulatory” part, that in the end determines what the TF bound to DNA will do, is much less understood, and often less conserved, probably because it is functionally tweaked to different final functions.

    What do you think? Am I right here?

  48. 48
    gpuccio says:

    Bob O’H:

    Thank you for your very balanced intervention.

    No, I have not read that book, but I read much of what is published in the scientific literature, because I am very interested in this field.

    I don’t agree that “my argument in the OP is largely from ignorance”. I think it is a reasonable way to ask questions about what we observe. However, you are obviously entitled to your opinion.

    You say:

    “what is (mostly*) encoded in our genes is the process to produce a body plan, not the plan itself”

    I can agree. But frankly, I can’t see the difference. A plan is the recording of the procedures to obtain a final result. I can agree that we will not find in the genome something like the “homunculus” we find in the cerebral cortex, but still we have to find there all the detailed and complex information that controls and guides the process to the end. And I don’t thing that it will be all in the protein coding genes, although I have tried to argue here that some relevant part of it is there, and is often underestimated, Please, read my post #47 here for that.

    Of course, there are also maternal (or other) epigenetic components, and personally I think that much is to be found, probably in unsuspected forms, in non coding DNA. But you will probably think differently about that.

    Finally, I would really like to know if you have read my OP from which this OP is derived:

    http://www.uncommondescent.com.....-analysis/

    I would really like to know what you think about that. If you like to tell.

  49. 49
    Bob O'H says:

    GPuccio – I’m not sure how much of the scientific literature you’ve read, but I think you should read it more carefully. You write

    Of course, there are also maternal (or other) epigenetic components, and personally I think that much is to be found, probably in unsuspected forms, in non coding DNA.

    but we already know this – a major theme of Endless Forms Most Beautiful, and indeed the evo-devo revolution, is that a lot of evolution in development is due to changes in the control of gene expression (i.e. epigenetics is involved, in one form or another).

  50. 50
    LocalMinimum says:

    Dionisio @ 28:

    Yeah, RVB8 is far well too documented by now and I’ve spent too much time debating in some of the dumbest places on the internet for me to not know better. A bit foolish of me to try squeezing blood from a turnip. Thanks for the consideration.

    RVB8:

    If you wish to retreat from a challenge for specifics to a vacuous literary polemic, I really feel no need or point to giving chase. Should you ever decide on a proper argument, I would gladly engage you at that point.

  51. 51
    gpuccio says:

    Bob O’H:

    Of course, one can always read more and better.

    However, what I meant, and in the rush did not express well, is that IMO many new regulatory functions will be found in the bulk of non coding DNA, that part that almost all still consider junk. I was giving for granted the parts that we already know of, enhancers, miRNAs, lncRNAs for which funtions have already been described, and so on.

    That said, I am still interested in your opinion about my OP about engineering in the vertebrate proteome, and about my notes here regarding TFs and PAX 6 in particular.

    If you find the time, of course.

  52. 52
    Dionisio says:

    KF and GP:

    Sorry for bringing up this off-topic info, but I thought you would like to see it too:

    Circular RNAs (circRNAs) comprise a family of noncoding RNAs (ncRNAs) that have drawn intense interest in the last few years.

    Although they were first discovered in 1979 by electron microscopy, they were thought to be byproducts of splicing and did not receive much attention due to their low abundance and lack of known functions.

    Emerging roles and context of circular RNAs.
    Panda AC, Grammatikakis I, Munk R, Gorospe M, Abdelmohsen K.
    Wiley Interdiscip Rev RNA. 8(2).
    doi: 10.1002/wrna.1386.

  53. 53
    Dionisio says:

    gpuccio @47:

    While looking at your post, saw this quote from Wikipedia:

    The field is characterised by some key concepts, which took biologists by surprise.

    Still don’t quite understand why they are surprised so often?

    🙂

    Still reading through your insightful comment.
    Thanks.

  54. 54
    Dionisio says:

    gpuccio:

    The term “Human Conserved Information (HCI)” seems key in this and your previous OP that triggered this one.

    Did you coin that term?

  55. 55
    Dionisio says:

    gpuccio @47:

    […] the homology found in Drosophila (or, say, in all protostomia and non vertebrate dueterostomia) is strictly confined to two well defined regions of the sequence:

    1) The Paired Box domain (AAs 4 – 128)

    2) The Homeobox domain (AAs 211 – 266)

    Hmm… Very interesting…

  56. 56
    Dionisio says:

    gpuccio @47:

    These two parts of the molecule (not corresponding to recognizable domains), when compared to the human protein, are almost completely different in Drosophila (and, in general, in pre-vertebrates), while they are almost identical already in Cartilaginous fish, and so they remain, almost unchanged, throughout the following natural evolutionary history (more than 400 million years).

    So, not only a big jump, but a very specific, targeted jump.

    Wow! I see your point. Had you read about this observation somewhere else before? Are you the first to point at this?

  57. 57
    Dionisio says:

    gpuccio @47:

    […] probably because it is functionally tweaked to different final functions.

    This seems to be the “cuore” of this topic, right?

    I think you’ve hit the target right in its center.

    Don’t expect any objection to your clear reasoning on this. By now the politely-dissenting interlocutors are running for the doors. 🙂

  58. 58
    gpuccio says:

    Dionisio:

    “The term “Human Conserved Information (HCI)” seems key in this and your previous OP that triggered this one.

    Did you coin that term?”

    I suppose so. And then, out of mere laziness, the acronym. 🙂

    However, the term derives immediately from the methodology I have used in the analysis.

  59. 59
    gpuccio says:

    Dionisio:

    “Wow! I see your point. Had you read about this observation somewhere else before? Are you the first to point at this?”

    Maybe. As far as I know…

  60. 60
    gpuccio says:

    Dionisio:

    “This seems to be the “cuore” of this topic, right?”

    Yes. It’s an old concept of mine. In the proteome, I believe that a lot of functional information is underestimated, because it is less conserved throughout evolutionary history: but the reason why it is less conserved is that it is “branch specific”, or “organism specific”. IOWs, “taxonomically restricted”. Therefore, very functional.

    I think that there are ways to clearly show that. My reasoning about PAX 6 here is an example. A similar reasoning is applied in this older OP, which was not very popular at the time, probably because it is rather technical:

    http://www.uncommondescent.com.....ted-genes/

    Of course, I do believe that a relevant part of protein sequences that are not conserved are not functional, or at least not essential to the function. Neutral variation does act on protein sequences, and we know that well.

    The problem is that, while for sequences that are always conserved we can easily assume function, for sequences that change two possibilities remain: non relevant function (and therefore neutral variation) or function that changes. There is no immediate way to distinguish the two, but I believe that reasonable comparisons and analyses, such as the ones I have proposed, can really help.

  61. 61
    gpuccio says:

    Dionisio:

    By the way, Circular RNAs are really interesting. And fashionable, I believe! 🙂

    Another tier of information that emerges from non coding DNA (I have really stopped counting).

  62. 62
    Dionisio says:

    gpuccio: @61:

    I have not been able to keep up with all this research information avalanche. The whole thing is getting overwhelming with every new discovery.

    I’m told to start wrapping up the research part so I can move on to the next phase of the project, but I’m dragging my feet unable to resist the temptation to look at what is next. It’s like watching those TV serials with adventures for kids and waiting for the next episode.

  63. 63
    Dionisio says:

    gpuccio:

    Does pax-6 work alone or in conjunction with another protein? Did the other protein also experience any jump around the same timeframe?
    Are there other cases of proteins that could be analyzed in conjunction?

  64. 64
    Dionisio says:

    gpuccio:

    I officially add myself to the folks that have encouraged you to gather all this research work you have done and compile it into a book. I would like to ask you for an autograph on my copy before other buyers start lining up for the book signing session at the bookstore! That would give me another valid excuse to travel to Italy! Can the eBooks be autographed by the authors? 🙂

  65. 65
    Origenes says:

    Bob O’H: … a major theme of Endless Forms Most Beautiful, and indeed the evo-devo revolution, is that a lot of evolution in development is due to changes in the control of gene expression (i.e. epigenetics is involved, in one form or another).

    Yes, it’s undeniable, and the ‘beyond genes’ aspect of epigenetics constitutes a tremendous problem for neo-darwinism and/or neutral theory. Of course Larry Moran wants none of it:

    Moran: We’re only going to cover epigenetics for a few minutes in today’s class because there aren’t any serious arguments in favor of changing our view of evolution because of epigenetics.

    However, we are going to spend a lot more time learning that evo-devo is just as stupid because there are some seriously misled developmental biologists who think that discoveries in their field change how we should view evolution. 🙂

    – – – – – – //

    Bob O’H: I can’t comment on what Larry Moran meant (partly because I’m too lazy to try to find the original quote) …

    Here you can find the original quote.

  66. 66
    gpuccio says:

    Dionisio:

    PAX 6 is a Master Regulator, specially involved in the embrional development of the eye and the brain. Here is a recent paper about its role:

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4706819/

    It interacts with lots of proteins. I have rapidly checked just a few: some are strongly engineered in the vertebrate transition, other not specially.

    Just anecdotically, I mention here one that is particularly extreme:

    DNA-binding protein SATB2 (Q9UPW6)

    From UNIPROT:

    “Binds to DNA, at nuclear matrix- or scaffold-associated regions. Thought to recognize the sugar-phosphate structure of double-stranded DNA. Transcription factor controlling nuclear gene expression, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin-loop remodeling. Acts as a docking site for several chromatin remodeling enzymes and also by recruiting corepressors (HDACs) or coactivators (HATs) directly to promoters and enhancers. Required for the initiation of the upper-layer neurons (UL1) specific genetic program and for the inactivation of deep-layer neurons (DL) and UL2 specific genes, probably by modulating BCL11B expression. Repressor of Ctip2 and regulatory determinant of corticocortical connections in the developing cerebral cortex. May play an important role in palate formation. Acts as a molecular node in a transcriptional network regulating skeletal development and osteoblast differentiation.”

    Length: 733 AAs

    This protein practically “appears” in cartilaginous fish:

    Cnidaria: 0.0893588
    Cephalopoda: 0.1251023
    Deuterostomia (not vertebrates): 0.1705321
    (jump here)
    Cartilaginous fish: 1.568895
    Bony fish: 1.450205
    Amphibia: 1.754434
    Crocodylia: 1.869031
    Marsupialia: 2.024557
    Afrotheria: 2.050477

    Jump in cartilaginous fish:

    1.398363 baa

    However, the behaviour of specific groups of proteins will be the theme of a next OP. 🙂

  67. 67
    Eric Anderson says:

    Origenes @6:

    Thanks for reminding us about that laughable assertion that 340 mutations could turn an ape-like creature into a human being.

    —–

    And anyone who thinks an organism will self-assemble once the various DNA gene products are produced (because they influence each other and so forth) is both unaware of the chemistry involved and incredibly naive about systems engineering.

  68. 68
    Eric Anderson says:

    rvb8 @22 and @27:

    Great literature bluff.

    Coupled with this kind of attitude:

    No! If you can’t, or won’t read it I can’t and won’t make you. But these two parts are full of links you can and, no doubt with the curiosity inherrant in ID folk, will ignore.

    C’mon, rvb8, we’ve asked over and over again. Just a paragraph or two, in your own words, describing the key points. You are the one claiming you have found an explanation. Well, let’s hear it.

    Otherwise, don’t bother throwing at the wall the results of your quick Google/Wikipedia search to find something to that kinda, sorta, has a title that might, perhaps, be relevant to the fundamental questions on the table.

  69. 69
    Eric Anderson says:

    Bob O’H @45:

    Bob, can you comment on this further:

    . . . the mother provides some of the information for development to occur correctly.

    When you say the mother provides “information” are you talking about information in the autosomal DNA, information in the X chromosome, information in the mitochondrial DNA, or information located elsewhere in the egg cell?

    I presume you mean the latter, but just wanted to confirm.

    Thanks,

    —–

    As with most of biology, it’s more complicated than we’d wish.

    Yes, it is absolutely more complicated than the fanciful stories about mutations resulting in this or that outcome, or claims of “plasticity” or general assertions of “change over time,” or naive ideas that once gene products exist in the cell they just come together in the right way by virtue of chemistry and physics. This is why scientists with simplistic notions keep getting surprised.

    On the other hand, if we approach biology from an engineering standpoint, we can anticipate a lot of the complexity. To be sure, we are noobs at this type of engineering and will still be surprised at the complexity, but there is a great deal of coordinated complexity and engineering that can be foreseen if we are willing to look for it.

  70. 70
    bill cole says:

    Origenes
    Here is Dr Morans answer.

    Which do you think is more likely?

    Here’s a hint. The pufferfish genome is only about 12% of the size of our genome but pufferfish have bodies and brains. Clearly, they don’t need a lot of extra DNA to make their bodies.

    Humans don’t need it either.

    Human body plans appear to be more complex than pufferfish. The difference appears to be TE”s. Are TE’s critical to the mammal lineage? If so, then Larry’s argument is incorrect. Thoughts?

  71. 71
    gpuccio says:

    Eric Anderson:

    “I presume you mean the latter, but just wanted to confirm”

    I presume too, probably mainly epigenetic states transmitted through the egg’s cytoplasm (and, of course, also the epigenetic state of the egg’s nucleus).

  72. 72
    gpuccio says:

    bill cole:

    At present, we don’t understand how body plans are really controlled. Until we do, reasonings like Moran’s are really arbitrary and pointless.

    I do believe TEs have an important role in information development (I have many times expressed the idea that transposons are optimal tools for design), and probably in cell development. But we really don’t know, yet.

    I believe that the growth of non coding DNA (especially TEs) in mammals and humans has a meaning. I don’t believe that it is only a passive effect of the accumulation of “errors”.

    But the field is still open. Let’s see what happens.

  73. 73
    bill cole says:

    GP

    I believe that the growth of non coding DNA (especially TEs) in mammals and humans has a meaning. I don’t believe that it is only a passive effect of the accumulation of “errors”.

    I agree, this is a very likely prediction 🙂 If we have an ancestor shared with the puffer fish millions of years ago why would our lineage start to accumulate useless junk in our genome?

    Could knowledge of the function of TE’s be the end of evolutionary theory as we know it?

  74. 74
    Origenes says:

    Bob O’H,

    Stephen Meyer on the ideas of evo-devo advocates such as Sean B. Carroll (the author of ‘Endless Forms Most Beautiful’, 2006) and Jeffrey Schwartz:

    Despite the enthusiasm surrounding the field, evo-devo fails, and for an obvious reason: its main proposal, that early-acting developmental mutations can cause stably heritable, large-scale changes in animal body plans, contradicts the results of one hundred years of mutagenesis experiments.13 As we saw in Chapter 13, the experiments of scientists such as Nüsslein-Volhard and Wieschaus have shown definitively that early-acting body-plan mutations invariably generate embryonic lethals—dead animals incapable of further evolution. The results of these experiments have generated the dilemma for evolutionary biologists that geneticist John McDonald aptly described as the “great Darwinian paradox.” Recall that McDonald noted that early-acting regulatory mutations do not produce viable alterations in form that will persist in populations, as evolution absolutely requires. Instead, these mutations are eliminated immediately by natural selection because of their invariably destructive consequences. On the other hand, later-acting mutations can generate viable changes in the features of animals, but these changes do not affect global animal architectures. This generates a dilemma: major changes are not viable; viable changes are not major. In neither case do the kinds of mutation that actually occur produce viable major changes of the kind necessary to build new body plans.
    [Stephen Meyer, ‘Darwin’s Doubt’, Ch. 16]

  75. 75
    Eric Anderson says:

    Origines @74:

    Meyer:

    This generates a dilemma: major changes are not viable; viable changes are not major.

    Welcome to real-world engineering. This is always true for complex functional systems.

    Only in fantasy-world Darwinian thought does the evolutionary paradigm stand a chance.

  76. 76
    Dionisio says:

    gpuccio @66:

    Can the informational jumps for PAX-6 and SATB2 be considered combined as a requirement for the transition that you described? Are there more protein information jumps that could be considered in combination with PAX-6 and SATB2?

  77. 77

    The Origin of the Body Plans is a very interesting Challenge for materialists/naturalists and for ID skeptics.

    The topic Extremely Difficult Engineering Problems are Brilliantly Solved in Living Organisms presented on 25 February 2017 at AM-NAT BIOLOGY CONFERENCE – and soon to be available on youtube – touched this problem as a tangible, undeniable super-function of organisms: sexual reproduction, problem that cannot be resolved but only through exceptionally engineered elements: information, processes and procedures, i.e. through Super, Exceptional, Transcendental Intelligent Design.

    Below are two slides from that AM-NAT presentation that seem related to the topic of this blog.

    Problem: Construct a Body through cellular divisions

    Here are the empirical assumptions for this problem that is solved brilliantly by all organisms that replicate through sexual reproduction:

    * The body construction is driven and controlled by information
    * The information that controls the body development and construction is supplied in the fecundated female egg that develops in female body (placenta) until the baby is delivered

    Here are questions and challenges that are raised when considering how this body develops from the single fecundated female egg – one single cell:

    * What is the estimated amount of information needed to drive body construction through cellular division?
    * What is the nature and format of this information; how is this information coded and physically represented in the original cell and in the descendent cells?

    Is the body development process centrally controlled (let’s say from the original cell) or is a distributed process: i.e. are there many, control centers that develop during body growth through cellular division?

    * How is the information copied and distributed (if it happens) from the original cells to all or some of the descended cells?
    * We are going to consider and analyze each of the above question separately on the next slides

    Q: What is the estimated amount of information needed to drive body construction through cellular division??

    We are going to consider this question for the human species. Here are some primary facts on which will base the computation for our estimate.

    * There is an estimate of 37*10^12 (10^12 means 10 power 12) cells in an adult human body
    * We are assuming that a human baby at the moment of delivery will have 37 times fewer cells, i.e. a count of 10^12 cells.
    * We calculated x = number of cellular divisions to reach from the single fecundated ovum cell to a count of 10^12 cells in the delivered baby by solving the equation below logarithmically:

    2^x = 10^12

    and found out that Number of Divisions ND is about:

    ND = x = 42

    * The number of distinct cell types in the human body is estimated to be 200

    …………..
    We do not show the Slides with computation of Information Estimate. We may add them later.

    But we show below the amount of Estimated Information in the Conclusion Slide for this computation:
    …………..

    Estimated amount of information -Conclusions

    We concluded that a conservative estrimate for the baby construction plan is an unimaginable huge number:

    INFO’ = 10 ^661,971,970,618

    i.e. a 1 followed by over 600 billion zeroes.

    The literature estimate for the number of atoms in a cell is 10^14 atoms. Let’s assume that the actual number for a fecundated female ovum is one million times larger than that, i.e. 10^20

    Still we cannot comprehend that the unimaginable large information for body construction plan quantified in INFO’ above can be contained, codified in the 10^20 atoms of the originating cell.

  78. 78
    gpuccio says:

    bill cole:

    “Could knowledge of the function of TE’s be the end of evolutionary theory as we know it?”

    That would be a very safe bet.

    But I am rather sure that neo darwinists will do their best to imagine new “solutions”, “theories”, fairy tales and so on… 🙂

  79. 79
    gpuccio says:

    InVivoVeritas:

    Well, that’s a rather big number! And I was so proud of my 1.7 million bits for the vertebrate proteome… 🙂

  80. 80
    LocalMinimum says:

    Origenes @ 74 / Eric Anderson @ 75:

    I’ve spent some time rewriting/expanding interdependent code. In my experience it usually requires you to build parallel structures that simply imitate the original, which involves writing the code you want, then writing even more code to make it act exactly like what you have; then, once you have covered the whole of what you want to change, you can start removing the code that makes it act like what you had, locally, though you have to make sure to keep the neighboring adaptation code compatible with each local removal.

    Basically, a multi-staged, neutrally at best (though surely negatively with any practical expectation) selected process that requires complete, top-down knowledge of the code structure and function, with complexity growth being something more than linear.

    Of course, chasing after a modification that produces some desirable result is always a terrible idea that practically always leads to a circular route, most often of small radius but perhaps even more often as a singular point phenomenon. This is what Darwin thought ultimately built everything from germs to super computers, as well as any program ever written. I never tried such a process from the onset; but landing close to the solution after your careful plans prove insufficient, you sometimes flail and thrash about; and even then it doesn’t ever get you there, and more often than not will carry you away and you can actually ruin your code if you don’t get back to the drawing board.

    Start overs from backups aren’t an option for critters whose ancestors aren’t maintaining a benevolent stasis.

  81. 81
    J-Mac says:

    The only logical explanation for the origins of body plans is that the body plans had existed before the organism came to be-the so called top to bottom origins of organisms.

    The bottom to top origins of body plans-an evolutionary one-just doesn’t cut it because too much foresight and experimentation is required. The natural, random processes just don’t have that… as simple as that…

    The ID/God must have had a lot of fun and satisfaction in designing and perfecting some of the creatures…

    In Job 39:26 He asks Job about some features of his creation:

    26″Is it by your understanding that the hawk soars, Stretching his wings toward the south? 27″Is it at your command that the eagle mounts up And makes his nest on high?…”

    No human can even make a change to what one of those birds was designed to do…Job couldn’t do it and the scientists today can’t do it either…

    All they can do is complain about the so called “bad designs” they couldn’t do themselves and can’t do anything about the improving designs and making them better…

    So, all they have left is to worship the natural processes for their superior intelligence and dumb luck for being smarter than them that drives it…

    Why don’t we ever have Nobel Prizes awarded to dumb luck? I guess there would be no-one to pick them up and there would be some pissed off communities of those who spent most of their life trying to figure out how the dumb luck did it and not being awarded for it… taking the credit for what the dumb luck did , as if they had created it themselves, is the way to go…

    Can anybody see how cleverly this deception was designed?

    It was designed in such a way that people who promote this nonsense would eventually believe it…

    “If you repeat a lie often enough, people will believe it, and you will even come to believe it yourself.”

  82. 82
    gpuccio says:

    Dionisio:

    PAX 6 is implied in a huge number of events and networks, many of them not really well understood.

    “Are there other cases of proteins that could be analyzed in conjunction?”

    Yes, a lot of them.

    But let’s do one thing at a time. 🙂

  83. 83
    Eric Anderson says:

    bill cole @70, quoting Moran:

    Which do you think is more likely?

    Here’s a hint. The pufferfish genome is only about 12% of the size of our genome but pufferfish have bodies and brains. Clearly, they don’t need a lot of extra DNA to make their bodies.

    Humans don’t need it either.

    Seriously? This is his argument? Talk about an argument from ignorance. Not to mention failed analogy.

  84. 84
    rvb8 says:

    Let us ask some sensible questions about body plans, ones scientists use to explain us, and flys etc.

    Why do we move forwards, and not backwards? Why is our head, where it is? Why are we largely symmetrical?

    Well, sponges aren’t ‘designed’ this way, and they are complex multi-cellular animals. So what is it about symmetricity, front/back movement, and heads being where they are that is beneficial to the symetrical, head on top, move forward not backward, animal?

    Once you understand this question, selection, and mutation are th best answer. Design, is a weak one!

    Once again, feel free to bring your astoundingly poor reasoning, to other sites.

    I am a poor interlocuter for the self imposed genius that roams these halls. You can indeed tear me down. However, I also know that the contributors to at least four science sites that I know of, would make short shrift of your Bible based arguments.

  85. 85
    Mung says:

    gpuccio,

    I can’t answer your in depth reply.

    So take your brilliant insights to a wider audience and let them be eviscerated there.

    Given that someone, somewhere else, can answer you.

    I can safely dismiss your in depth reply as spurious nonsense.

  86. 86
    kairosfocus says:

    RVB8:

    Instantly, you are setting up and knocking over strawmen. GP’s argument is not about “Bible-based arguments.” You are just showing what you wished you were dealing with.

    Some years ago now, to give another perspective, this is how I looked at one facet of the body plan origin challenge:

    Meyer observed [in his 2004 paper]:

    One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information. Molecular biologists have recently estimated that a minimally complex single-celled organism would require between 318 and 562 kilobase pairs of DNA to produce the proteins necessary to maintain life (Koonin 2000). More complex single cells might require upward of a million base pairs. Yet to build the proteins necessary to sustain a complex arthropod such as a trilobite would require orders of magnitude more coding instructions. The genome size of a modern arthropod, the fruitfly Drosophila melanogaster, is approximately 180 million base pairs (Gerhart & Kirschner 1997:121, Adams et al. 2000). Transitions from a single cell to colonies of cells to complex animals represent significant (and, in principle, measurable) increases in CSI . . . .

    Thus, the sort of novel body plans observed in the Cambrian fossil life revolution reasonably required 10 – 100+ millions of functional four-state DNA bases. This is more than 100,000 times the 500 – 1,000 bit threshold at which the undirected search resources of the observed cosmos would be inadequate to carry out a credible search of the relevant configuration spaces.

    Some would doubt such a range, so let us do a fresh calculation: 50 new tissue types to make up the organs for a new body plan would easily take up probably 10 – 100 proteins [[including enzymes etc] per type, i.e we are looking at 500 – 5,000 proteins as a reasonable/ conservative estimate — VERY conservative at the low end. 500 * 300 = 1.5 *10^5 codons, or 4.5 *10^5 bases, plus regulatory, let’s say about 10% more, 1/2 mn bases.At the upper end, we would arrive at 4.5 *10^6 bases.

    But this estimate is too low:

    Arabidopsis thaliana [[a flowering plant] 115,409,949 DNA bases

    Anopheles gambiae [[a mosquito] 278,244,063 bases

    Sea urchin 8.14 x 10^8 bases

    Amphibians 10^9–10^11

    Tetraodon nigroviridis (a pufferfish) 3.42 x 10^8

    In short, 10 – 100 million bases for a novel body plan is reasonable, even generous. And in any case the config space of 500 k bases is: 9.9 *10^301,029 possibilities.

    Let us recall too, that say an insect routinely emerges from a single cell (the egg) and develops into an adult organism by a replication, specialisation and integrated body plan development process. In the case of complete metamorphosis, there is first one body plan the larva, then there is an intermediate pupal “soup” stage that refashions itself into a completely new plan, the adult.

    For the explanation that this has come about by chance variation and natural selection, step by step, from a “simple” unicellular ancestor to be well-warranted, we need to see a good account with observational evidence, of how this can happen. That account has to explain how the embryological development algorithm that transforms a single cell into a complex organism based on specialised cell types, organised into tissues, organs and integrated coherent systems comprising a viable life form, came to be.

    On the face of it, the bare concept that such a complex algorithm could have come about by accidental duplications and chance variations that hit on new function, then were incorporated somehow into the regulatory processes of the organism and just happening to give us a fully integrated functioning organism that unfolds from the single cell to the organism on a body plan is not plausible absent specific empirical evidence that this is what can happen and did happen. That, within the resources of our solar system over the course of the sort of window of at most several hundred millions of years to a few billion years. if the usual timelines for the Cambrian life revolution are reasonable, we may be talking about a window of maybe 2 or 3 – 10 MY, 540 or so MYA.

    In fact, there is no such body of undeniable observations.

    GP has been doing a much more sophisticated analysis and is even more generous to the Darwinist narrative.

    No practical difference.

    And, we have yet to address the most pivotal of all, the first, cell-based life body plan.

    KF

  87. 87
    rvb8 says:

    Kairos,

    I know the odds. It is ID’s only argument! It is the, ‘This is simply beyond my ken’; ‘I simply don’t believe this is possible’; ‘Look at the numbers..’ etc etc ad infinitum.

    However, endless incredulity makes your argument look unsupported by any actual science or evidence; like, fossils, DNA, Lenski studies, Nobel Prize winners etc.

    Long meaningless posts, supported by ‘hangers on’, does not good science, or science arguments make.

    Honestly, bring yours, and your fellow travellers arguments to a wider audience. Don’t lock away this ground breaking genius, that the world has been ignoring, in a small largely ignored stage. Give it to the ignorent world.

    FSCO/I, must be shared, do not hog this insight that nobody knows about. Recieve your reward, and I don’t mean in the, ‘here after’.

  88. 88
    groovamos says:

    rvb: The article on, ‘Evollutionary (sic) development biology’,in Wikipedia would be a convenient non-threatening place for you ostriches to start with. Again, you won’t like it. It’s full of clear evidence based theories, with elegant hypotheses explaining likely routes, and even predictive possible futures

    Oh great more promissory “science”.

    So you know what I did? After realizing that I don’t normally encounter “threaten(ed)” people on this board other than ones who fling pejorative and name-calling I went to the page to which you refer and I did a search on ‘information’. And there were actually 6 instances and every one of them were paired with ‘further’ as in “further information”. So I decided that to spend time reading would be a waste, because really you Darwin worshipers seem to be threatened by the quantification of information in the genome and elsewhere, speaking of “threatening”.

    Let me put it to you this way rvb. How many bits of information does it take to build your facial appearance? I’ll even make it easy for you: ignore skin tone and hair distribution How many bits dude, and where exactly does this information reside that determines your facial features so that all of your associates recognize you?

    We all experience facial recognition every day, proving also that there is an informatic template of which our associates are possessed, correlated to information which built your face, otherwise facial recognition would not exist. You could not ask for better proof of information context of your face morphology.

    That’s it: (a) how many bits and (b) what and where is the storage medium – for the specification of your facial appearance?

  89. 89
    Eric Anderson says:

    rvb8 @87:

    However, endless incredulity makes your argument look unsupported by any actual science or evidence . . .

    Incredulity, let us remember, about the wild, unfounded, laughable claims of the materialist creation story.

    Yes, I will gladly stick to incredulity.

    As opposed to the credulity that evidently allows some here to believe just about any wild story that supports the materialistic narrative, no matter how preposterous.

  90. 90
    rvb8 says:

    Not convincing groovamos,

    however, I believe you should have the freedom to explain your ideas, and the Kairos invented concept of FSCO/I, as well.Science is all about new ideas, confronting those new ideas with experimentation, and reaching solid conclusions, based on those empirical approaches.

    I am simply saying that after almost 20 years since Dembski fortold the doom of Evolutionary Biology in ‘The Wedge’, we have as yet nothing approaching good science from ID.

    Science being science, it would not do to shout down a brilliant insight such as, ‘wow that looks complex, must have been outside help.’

    So naturalists such a myself will continue to say that the ingredients, and necessary energy (gravity, the sun, earth molten core, water etc) for life, are in front of us and easily understood.

    The ‘unnaturalists’, such as yourself and the other Christians will continue to say, ‘No! Jesus had a hand in IT!’

    One of these approaches is testable, the other relies on faith, something beyond the bounds of science. I’ll leave you to figure out which is which.

  91. 91
    gpuccio says:

    rvb8:

    Just a curiosity:

    Why do you come to this “largely ignored stage”, at all?

    Why do you waste your time with us?

    Do you think you have some kind of mission?

    But you admit, yourself, that you are “a poor interlocuter”. Maybe if you stick to your “wider audience”, to your “four sites” supported by brilliant scientists, you could in time learn something, and become a better discussant! 🙂

    Let’s go to your “argument” (the only thing that seems to have the form of an argument, at least).

    You say:

    Let us ask some sensible questions about body plans, ones scientists use to explain us, and flys etc.

    Why do we move forwards, and not backwards? Why is our head, where it is? Why are we largely symmetrical?

    Well, sponges aren’t ‘designed’ this way, and they are complex multi-cellular animals. So what is it about symmetricity, front/back movement, and heads being where they are that is beneficial to the symetrical, head on top, move forward not backward, animal?

    Once you understand this question, selection, and mutation are th best answer. Design, is a weak one!

    Well, I am not sure I understand the question. After all, I am only a fellow traveller of the deluded crowd of self imposed geniuses that roam these halls.

    But, wait a moment:

    An airplane moves in the air, can host people inside, and even keep the pressure right at high altitudes.

    A table clock does not move, just stays where we put it, cannot host anything.

    Moreover, the two objects have clearly very different form and simmetry.

    Once you understand this example, it’s obvious to anybody that selection, and mutation are the best answer, and design, is a weak one!

    Well, I hope you will forgive this blatantly Bible based argument. It’s the best I can do… 🙂

  92. 92
    gpuccio says:

    Mung:

    Nice to see you! 🙂

    I really missed your brilliant arguments!

    Where did you pick the “eviscerated” idea? Brilliant, brilliant… 🙂

  93. 93
    Dionisio says:

    J-Mac @81:

    Thanks for your commentary.

  94. 94
    Dionisio says:

    gpuccio @92:

    The comment posted @85 seems somehow related to the nonsense posted @36. However, this could be just an illusion. 🙂

  95. 95

    I am trying below to render the way I estimated the Amount of Information needed to Construct a human baby Body by assemblage of cells of different types. Copied from Slides in the Presentation specified below. Using a huge simplification to arrive empirically to a defensible number.

    The topic Extremely Difficult Engineering Problems are Brilliantly Solved in Living Organisms presented on 25 February 2017 at AM-NAT BIOLOGY CONFERENCE – and soon to be available on youtube – touched this problem as a tangible, undeniable super-function of organisms: sexual reproduction, problem that cannot be resolved but only through exceptionally engineered elements: information, processes and procedures, i.e. through Super, Exceptional, Transcendental Intelligent Design.

    Below x^y is a notation for x power y and x^y^z is a notation for x power y power z.

    SLIDE 1. Q: What is the estimated amount of information needed to drive body construction through cellular division?

    We are going to consider this question for the human species. Here are some primary facts on which will base the computation for our estimate.

    * There is an estimate of 37*10^12 cells in an adult human body
    We are assuming that a human baby at the moment of delivery will have 37 times fewer cells, i.e. a count of 10^12 cells.

    * We calculated x = number of cellular divisions to reach from the single fecundated ovum cell to a count of 10^12 cells in the delivered baby by solving the equation below logarithmically:

    2^x = 10^12

    and found out that Number of Divisions ND is about:

    ND = x = 42

    The number of distinct cell types in the human body is estimated to be 200

    SLIDE 2. Estimated amount of information -continued

    The estimation is based on the following:

    When a cell divides there are the following options available:

    * The place where the daughter cell will “link” to the “mother” cell after division. We considered that there are 8 placement options – one for each of the 8 corners of the mother cell considered a cube – as illustrated below (8 = 2^3).

    (( Below was a picture (not included) of a Cube: At Each of the 8 corners of the cube there was a small cube – to illustrate 8 possible placements of a daughter cell Relative to the Mother cell))

    * The type of cell for the daughter cell. Let’s assume that there are only 32 type of cells in human body (32 = 2^5). So, each cell division may produce any of the 32 type of cells. For a conservative estimate of information we considered 32 cell types instead of 200.

    Thus after each cellular division for EACH daughter cell there are a total of 8 * 32 = 256 = 2^8 options – as ‘body construction options’

    SLIDE 3. Estimated amount of information -continued

    Estimation procedure for body construction options for 1st Round of cellular division: D1

    * We have one cell to divide (the original cell)
    * We have 2^8 = 256 independent outcomes for each resulting daughter cell

    * So the combined number of construction options for round D1 of division is: 1 * 2^8 = 256

    Estimation procedure for body construction options for 2nd Round of cellular division:D2

    * We have two cells to divide (total cells after round D1)
    * We have 2^8 independent outcomes for each resulting daughter cell

    * So the combined number of construction options for round D2 of division is: 256 * 256 = 256^2

    The table on next page shows the above results and extends results for all 42 Division Rounds. Please note that we use products of (multiplication between) individual cell construction options since these are independent options between the constructed daughter cells.

    SLIDE 4. Estimated amount of information -continued

    Column 1: Division Round

    Column 2: Number of cells that divide in this Round

    Column 3: Number of Options for Each Daughter Cell Construction

    Column 4: Combined number of Construction Options for All Daughter Cells Being Constructed in This Division Round

    1 ; 2^0 = 1 ; 256 ; CO1 = 256

    2 ; 2^1 = 2 ; 256 ; CO2 = 256^2

    3 ; 2^2 = 4 ; 256 ; CO3 = 256^4

    4 ; 2^3 = 8 ; 256 ; CO4 = 256^8

    5 ; 2^4 = 16 ; 256 ; CO5 = 256^16

    .. ; …. ; …. ; ….

    41 ; 2^(41-1) = 2^40 ; 256 ; CO41 = 256 ^2 ^40

    42 ; 2^(42-1) = 2^41 ; 256 ; CO42 = 256 ^2^ 41= 256^ 2,199,023,255,552

    SLIDE 5. Estimated amount of information -continued

    The combined number of construction options for all daughter cells in division round 42 is:

    CO42 = 256^ 2,199,023,255,552 = 10^ 5,295,775,764,950

    The overall number of body plan construction options across all 42 division rounds is the product:

    COtotal = CO1 * CO2 * CO3 * CO4 * …. CO41 * CO42

    However since the CO42 is such a huge number: larger than a 1 followed by over 5 trillion zeroes, it is sufficient to consider it as an estimate of the information for the baby’s body construction plan: INFO:

    INFO = 10^ 5,295,775,764,950

    Note that if we consider that for the construction of each daughter cell through cell division we have only 2 options instead of 256 the calculation of CO42 changes into:

    CO’42 = 2^ 2^ 41= 2^ 2,199,023,255,552 = (approx) = 10 ^661,971,970,618

    which is still a HUGE number: INFO’ = 10^ 661,971,970,618

    SLIDE 6. Estimated amount of information -Conclusions

    We concluded that a conservative estrimate for the baby construction plan is unimaginable huge number:

    INFO’ = 10^ 661,971,970,618

    The literature estimate for the number of atoms in a cell is 10^14 atoms. Let’s assume that the actual number for a fecundated female ovum is one million times larger than that, i.e. 10^20

    Still we cannot comprehend that the unimaginable large information for body construction plan quantified in INFO’ above can be contained, codified in the 10^20 atoms of the originating cell.

  96. 96
    Dionisio says:

    gpuccio @82:

    PAX 6 is implied in a huge number of events and networks, many of them not really well understood.

    “Are there other cases of proteins that could be analyzed in conjunction?”

    Yes, a lot of them.

    But let’s do one thing at a time.

    Agree. No rush on this.

    As you have shown in your OPs and follow-up comments, it takes quite an effort to analyze just one protein.

    Your PAX-6 example raises fundamental questions about the observed information jump at one point.

    However, as you just stated in the above quoted comment, Pac-6 may have pleiotropic functionality and also it is not the only player in the game. You’ve clearly indicated that there are more proteins involved in the developmental processes. For some of them you’ve seen information jumps too. All that taken together compounds the magnitude of the problem and the coverage of the posed questions.
    Did I understand this right? Please, correct anything I write that is wrong or inaccurate. Thanks.

  97. 97

    gpucio

    It seems that the way I estimated the Body Construction Plan Information in post #95 above aligns nicely with the “body development model” you sketched in your entry #29 that I quote below:

    What kind of information is necessary in a cell so that it can differentiate along some pathway or some other pathway in different conditions?

    I will try to be even more clear with a generic example.

    Let’s say that we have a simple multicellular organism A where a cell “a” generates 30 cells that are all similar:

    aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa.

    That’s all, in the development of that organism.

    Now, let’s say that from that organism derives a more complex, but still rather simple, multicellular organism B where an original cell “b” generates three different layers of cells, each with very different features and functionalities, and specific spatial arrangements:

    ccccccccccddddddddddeeeeeeeeee

  98. 98
    Dionisio says:

    InVivoVeritas @95:

    Still we cannot comprehend that the unimaginable large information for body construction plan quantified in INFO’ above can be contained, codified in the 10^20 atoms of the originating cell.

    That’s because we just don’t understand evolution. 🙂

    We should consult the experts, like the Canadian biochemistry professor who publicly affirmed knowing exactly how morphogen gradients form, or his academic colleagues, who together know exactly how morphogen gradients are interpreted. Or ask one politely dissenting interlocutor in this thread who has demonstrated having exclusive unrestricted access to Wikipedia!

    However, let’s make sure we ask only honest (i.e. not tricky) questions. Always remember that potentially tricky words (example: exactly) should be written in bold characters, so that the experts see them before answering the questions.
    Ok?

    🙂

  99. 99
    Dionisio says:

    gpuccio @66:

    Very interesting paper you referenced @66:

    “Transcriptional and epigenetic mechanisms of early cortical development – an examination of how Pax6 coordinates cortical development”

    Thanks.

  100. 100
    gpuccio says:

    Dionisio:

    “The comment posted @85 seems somehow related to the nonsense posted @36. However, this could be just an illusion.”

    No! Mung would never do such a thing! 🙂

  101. 101
    gpuccio says:

    Dionisio:

    Just an anticipation you could be interested in:

    From my data, that I am still developing and that will be presented in a future OP, Transcription Factors as a whole are not the category that is more strikingly engineered at the vertebrate transition: they are, but not much more than the average protein. In that sense, PAX-6 is more an exception than the rule.

    Other groups of regulatory proteins, instead, are amazingly engineered.

  102. 102
    Dionisio says:

    gpuccio:

    Thank you for the sneak preview of your future OP.
    I look forward to reading it.
    The regulatory proteins seem like a fascinating field of modern biology.

  103. 103
    Dionisio says:

    gpuccio:

    Apparently -as you have clearly demonstrated here and in other threads- in the case of radical changes of biological systems, major information addition might be required from engineering perspective.

    However, can a protein have pleiotropic functionality in its current form and shape, without getting another information boost?

  104. 104

    About embryo and body development problem

    The information in the Embryo: Much beyond the Information for Body Development.

    The Estimate of the Amount of Information needed for a human baby development to birth seems a huge over estimation.

    But let’s ponder this issue by considering a problem somewhat similar (but radically different) – however good enough to help us validate, confirm or infirm the Information Estimate under discussion.

    Now taking a strong materialist, empiricist position on embryo development (the things might not be as they appear). It should be assumed that most information that give shape, form and human behavior and intelligence to a human organism (except some acquired “items”) is somewhat present in the embryo: the female ovum fecundated by a male spermatozoid.

    Let’s contemplate a little bit what this means: what is the scope and extent of this information:

    * is information needed to develop the baby to delivery time in his/her mother’s womb
    * is information that make baby alive and progressing in manifesting biological and neurological functions as the baby grows
    the baby and later the infant, toddler, child, adolescent and adult is a “soft-body growing machine”
    * We humans know how to design mostly hard-body machines. The design and growth of soft-body machines seems to be a “know-how” probably associated with exotic, “out-of-this-world” engineering techniques.
    * The embryo must carry information not only characterizing the human organism , construction, development and mechanical capabilities and behavior, but information that somehow capture all human organisms functions and capabilities: perception of environment, muscular control, thinking, reason, intelligence, problem solving, etc. All this must be present – at a minimum in its “core format” in the embryo (original cell with 2^14 atoms)

    Now let’s imagine a parallel – but much simplified case (hypothetical scenario).

    Let’s assume (a thought experiment) that there exist a MacBook (or Windows laptop) “seed” or embryo. I.e. primordial (uni-cell) element/entity that contains sufficient information for:

    * it is sufficient to produce (construct) a real MacBook laptop
    * it is sufficient to know how to take some feeding substance from the “laptop mother womb” and to use internally those row materials, to convert them appropriately into parts and pieces of the growing laptop
    its sufficient to carry not only how to build the laptop, piece-by-piece, transistor-by-transistor, metal plate by metal plate, LCD cell by LCD cell, printed circuit boards, semiconductors, microprocessor, RAM memory, hard drives or solid state drives. etc, but also:
    * it is sufficient to carry all laptop software hierarchy – from kernel, drivers, operating systems, application software, graphics software.
    * it is sufficient to know how to “install”, “test” and “start” the software into the developing laptop.

    Now, the human embryo, human new-born, human child and adult are entities that diferes Radically from the hypothetical Laptop seed growing into an Adult laptop. And at least with respect to:

    * Human embryo, new-born, adults are REAL while the laptop embryo is just an imagined scenario
    * Everything imagined for the embryo laptop really happens for the human embryo/organism
    * while we engineers will have a real hard time to imagine how the laptop embryo growth may become a material reality, there is absolutely no doubt that an infinitely more challenging “technical proposition” has a routine reality and materialization in our lives.
    * everything in terms of information needed for the growth of human embryo into a child then adult seems to be present in that original biological cell.
    * So what do we have then inside the Embryo assuming that there is no information coming from outside (from the mother, or from who-knows-from-where) during development?

    * we have a organism construction factory design information
    * we have a parts (cells) construction factory
    * we have a sophisticated assemblage factory
    * we have sophisticated design plans, organizations, blueprints, scheduling and coordination plans.
    * we have organism body model, development model, brain development model, “start gradually organism engines” model,
    * we have plans on how to assemble and put together an intelligent being (machine) with amazing thinking, problem solving, reasoning capabilities and conscientiousness.
    * We have plans on how to build this human organism of a superior level of autonomy and self-sufficiency
    * We have plans on how to build this human organism capable of self-reproduction.

    All the above point to us that we are facing transcendental engineering solutions for transcendental ideas: life, seed, self-reproduction capability, logos,

    All the above point to us that life, living organisms, humans in particular are transcendental ideas brought to us with transcendental engineering.

    Considering evolution or any other naturalistic fables when we are contemplating the amazing engineering of life is an insult to reason.

  105. 105
    gpuccio says:

    Dionisio:

    I think that a protein like PAX-6 has probably pleiotropic functionality at all steps of its evolutionary history.

    But that functionality becomes different at different steps.

    So, it’s not that the protein was less functional before the vertebrate transitions: it simply acquires the specific functionality needed for the vertebrate body plan at that transition.

    And it is a lot of specific functionality: so much so that it practically does not significantly change any more in that evolutionary branch. That, indeed, is an exception, because most proteins receive a supplementary boost at the transition to mammals.

    Instead, the 830 bits, 95% identities, 1.966824 baa of PAX-6 between Callorhincus milii and humans is really an exception.

    It’s very similar to the 2.0 baa of histones, that are considered among the most conserved sequences in metazoa.

    The amazing difference is that histones are completely engineered just from the beginning: they already have those 2.0 baa of homology with humans in Cnidaria!

  106. 106
    Dionisio says:

    gpuccio:

    That’s interesting. Thanks.

  107. 107
    kairosfocus says:

    RVB8, your remarks, sadly, boil down to:

    a: we have no observational data that directly shows actually observed origin of body-plan level biodiversity through blind chance and/or mechanical necessity.

    b: given, the remote past of origins is beyond observation, and that we have no direct empirical observation of how FSCO/I can be and is caused by said blind forces, we cannot meet Newton’s rule on causal inference on traces of the unobserved being explained on forces seen to cause the like traces.

    c: by contrast, there is a trillion member observational base on the origin of FSCO/I, it is always seen to come about by intelligently directed configuration.

    d: where, this is backed by search-challenge in sufficiently large configuration spaces.

    e: cell based life is full of FSCO/I. most obviously in D/RNA and proteins, also in the functional organisation, the biochemical rxn network etc.

    f: there is a school of thought that connects these dots by inductive inference on reliable sign backed up by search challenge analysis per inference to best current explanation.
    _________________________________

    g: In absence of an inductively well-warranted account of origin of FSCO/I, across time we objectors have scanted the concept and linked ones. (Never mind, we have had to create cases of FSCO/I that exemplify its origin to make such objections.)

    h: Likewise, we mock the idea of blind search challenge in large config spaces, ignoring evidence of deep isolation of protein fold domains in AA sequence space etc.

    i: Further, we project Biblical Creationist motivations to those who make design inferences.

    j: Moreover, we follow the Lewontin principle and ideologically impose a priori materialism by redefining the nature and methods of science.

    In short, you have made ideologically motivated, fallacy-driven responses to a matter of empirically anchored inductive analysis.

    This error, you and others of like ilk urgently need to correct.

    KF

  108. 108
    kairosfocus says:

    GP, we await the new OP. KF

  109. 109
    kairosfocus says:

    GP et al, interesting onward discussion. I find the way histones seem to get set right then function as a standard component across life forms particularly interesting as a contrast with the jumps in homology in effect when we move into new domains of life for other protein families. The linked info jumps of course are FSCO/I-rich, and the pattern reminds of, don’t re-invent the wheel. I am also being reminded just now on how early, body-plan effecting muts are overwhelmingly lethal, whilst it is the embryologically later, less impact-ful ones, that we see in organisms that survive to be born and grow up (or the equivalent). Blind mutation does not look to be a truly promising explanatory candidate. KF

  110. 110
    Origenes says:

    InVivoVeritas #77, #95, #104
    Your excellent work makes one realize, at least in my opinion, that physically stored information cannot be the complete picture. Surely, besides DNA, there is other storage media — e.g. membrane patterns, ion channels, sugar code, electromagnetic fields — but all of this simply cannot suffice. The fertilized ovum does contain neither a map of the brain nor the instructions of how to build it.
    There must be a non-physical source of information involved.

  111. 111
    gpuccio says:

    Origenes:

    “There must be a non-physical source of information involved.”

    In principle, I could agree. But at present we have not enough data, IMO, to make that strong hypothesis at scientific level. I think some help could come from some unexpected progress in physics.

    We will see…

  112. 112
    gpuccio says:

    KF:

    Very good concepts.

    I believe that, if we look at data from an ID perspective, there is a lot that we can see about the design and its implementation.

    In that sense, ID theory is not at all limited to the demonstration that a designer is needed, but can tell a lot more, if not about the designer, certainly about the design.

    The methodology I am using is just an initial attempt, but IMO it already shows the huge scientific potentialities of ID.

  113. 113
    gpuccio says:

    InVivoVeritas:

    Thank you for your very interesting contributions. I just need a little time to read them in depth. 🙂

  114. 114
    Dr JDD says:

    When we start talking about the number of different cells in the human body, what people should realize is the pathetic attempt to classify this at 200 types. Recent advances in sequencing allows us to sequence cells at the single cell level thus from a tissue you can sequence 1000s of cells that may have been classified the “same” yet you can cluster them into many subdivisions based on their transcriptome profile. Thus take your 200 cell types and add log factors onto that number.

    The problem becomes even harder for the materialist.

    The complexity and awesomeness of the Designer becomes even greater to the theist.

    http://www.nature.com/scitable....._types_one

  115. 115
    gpuccio says:

    Dr JDD:

    Absolutely true.

    I think that, in the ultimate sense, each cell in an organism is different from each other cell, epigenetically, exactly as they are the same at the genome level.

    Of course, we can group them in categories, and how many categories simply depends on our criteria.

    Of course a liver cell is very different from a lymphocyte, but how many classes of lymphocytes can we detect? The number grows constantly.

    And blood cells are those that we can investigate most easily. Tissue cells are more elusive, but I am certain that liver cells are different one from the other, and have different functional states and features.

    The genome-epigenome gestalt is an infinitely complex entity, in continuous dynamic fluctuation, and it can manifest itself in countless different ways, all of them very coordinated and functional, according to the context.

    Considering cells as rather constant objects is the best way not to understand them.

  116. 116
    groovamos says:

    rvb: Not convincing groovamos

    So here we have the crux of the problem with rvb and for him to work out for himself if he is honest. There has been no attempt on this thread by yours truly at argument, so how could there be any “convincing” at stake?

    Instead what we have are two questions directed at rvb regarding the information required to construct his face.

    Very straightforward questions posed @88 to RVB WHO REFUSES TO ATTEMPT TO ANSWER @ 90.

    So this should be proof to all on here that RVB cannot come up with a Darwinian explanation for his own appearance. This would be a huge failing for the theory that RVB worships and lives his days with. Facial recognition is absolutely required for any human culture to survive, you know as Darwinists are always reminding of “survival” in their “theory” er storytelling. But as we all know we are not dealing with theory in the normal sense of the word here.

    Now maybe RVB believes that it requires NO information to construct a human face. Maybe that’s what he meant when he said “not convincing”, maybe in reference to my discussion of facial templates in his people’s memories in order to recognize him.

    Is that what you meant RVB? No information is required for ‘nature’ to construct your face?

    You complain on here we we do not discuss science enough and deviate into philosophy too much. Now is your chance to discuss on a scientific level: where is the information that constructed your face and what is the quantity of information there?

    Do it RVB. Prove you have a theory worth a damn. Prove you’re all about science. We’re discussing science now.

  117. 117
    Origenes says:

    Groovamos, you make an obviously valid point. Rvb8 and kindred spirits seem to hold that some physical domino effect, starting from inception, somehow without information, builds all the fancy stuff in life.

    Concerning constructing faces, allow me to make a not-convincing argument. I’m pretty sure that we have all noticed that with the vast majority of ppl facial features form a coherent whole. A simple example: I’m very glad that my wife doesn’t have my nose and vice versa. A crude example for sure, the coherence we all notice is way more subtle than that. Every person seems to have his/her own uniquely coherent facial design.
    Where does the information come from?

  118. 118
    Eric Anderson says:

    InVivoVeritas @95:

    Interesting thoughts and a fruitful avenue for further investigation, but I’m not sure the math quite holds up.

    —–

    Still we cannot comprehend that the unimaginable large information for body construction plan quantified in INFO’ above can be contained, codified in the 10^20 atoms of the originating cell.

    When you say “we cannot comprehend” do you mean that it is hard for us to figure out how it was done?

    Or are you saying it didn’t happen — meaning, the information is not codified in the atoms of the originating cell?

    And if not codified in the originating cell, then where is the information? Surely it must exist somewhere in the nascent organism?

  119. 119
    Dr JDD says:

    gpuccio @115:

    One of the labs doing this work to map all cell types in the body (good luck!) also produced some interesting results a while ago that shows that something disregarded in the past as an artifact is actually the norm – different individuals replicate their genes at differing rates. Quite fascinating really, but one sentence that stuck out to me in this link:

    http://mccarrolllab.com/dna-re.....ng-humans/

    “We found that there is biological information in genome sequence data,” added McCarroll. “But this was still an accidental biological experiment. Now imagine the results when we and others actually design experiments to study this phenomenon.”

    Biologic information is even in raw sequencing.

    Information.

    Information is not random.

    But hey, I digress – that horse has been flogged a few too many thousand times…

  120. 120
    groovamos says:

    thx Origenes

    I’m going to throw this out and of course the materialist bomb throwers will come on with their fake laughter and all that.

    I was at a presentation by Doug Axe here in Houston. I asked him a question which went something like: “Do you think much about epigenetic information and any possible mechanisms involved?”

    He came back with “That is a profound question.” Not that it was profound in relationship to yours truly – because it is a profound question that millions of people think about.

    He then gave an example to the audience (paraphrase): “No one has proven that the quality and sound of your voice has had the bearing of genetics upon it.”

    OK to add something to my question to him that I left out above, I asked him if he had read the writings of Rupert Sheldrake on the subject, and he indicated the negative.

    Sheldrake postulated back in the ’80’s, mechanisms that are clearly beyond naturalistic science for investigation. He postulated non-physical entities “morphogenetic fields” and “morphic resonances” that are passed on from parent to offspring. These entities would be linked to non-physical intelligence. And he appears open to the possibility of a hierarchy of intelligent forces at work in the generation and maintenance of form and function in biology. Sheldrake I think will be proven correct in his outline, but it may take a couple of hundred years of scientific endeavor not constrained by naturalism.

    Of course Sheldrake has been dismissed as a quack by his colleagues. What else would you expect from materialists, locked in as they are by their life philosophy.

    Doug Axe did not seem to be familiar with that particular line of thinking.

  121. 121

    Some Responses

    gpuccio @ 79

    Well, that’s a rather big number! And I was so proud of my 1.7 million bits for the vertebrate proteome…

    and @113

    Thanks for your feedback, appreciation

    I myself was surprised with the results of my computation. But I tried alternatives ways of thinking to see if logically makes sense to consider such a Huge Info Estimate as realistic.

    Origenes @ 110

    InVivoVeritas #77, #95, #104
    Your excellent work makes one realize, at least in my opinion, that physically stored information cannot be the complete picture. Surely, besides DNA, there is other storage media — e.g. membrane patterns, ion channels, sugar code, electromagnetic fields — but all of this simply cannot suffice. The fertilized ovum does contain neither a map of the brain nor the instructions of how to build it.
    There must be a non-physical source of information involved.

    Definitely the where is the information? for the body plan and organism development is a daunting biological, engineering and philosophical question.

    We can simplify the issue considering a few categories of answers

    A. All information is physically contained in the Embryo: the fecundated ovum (the “original cell”).

    For this type of answer we are still facing bewildering biological, engineering questions:

    * where specifically: in what parts of the embryo, in what cell organelles, in what DNA, in what other cell structures is this information stored?

    * how and what parts of the father and mother were miraculously combined in order to create the information signature for a new being inheriting from both parents?

    * How this INFO is specifically encoded in what material parts of the cell?
    * As you suggested there are multiple known candidates: membrane patterns, ion channels, sugar code, electromagnetic fields, or new candidates to be discovered in the future. Some presentation at AM-NAT suggested that some DNA and stones (?!) form together elements of RAM (Random Access Memory) in the cell.

    * What is the Nature of the Information (at the higher level) that represents Body Shapes, Members Shapes, internal Organs Shapes, Body organization, Interfaces at All Levels between cells, tissues, parts, systems and sub-systems – and this is a kinematic, moving, dynamic process as all body parts are growing in an amazing choreography

    * Is this information Preserved ONLy in the Embryo Cell? Or is Copied, Distributed: a. in Each Daughter Cell – as cell division Happens, OR: b. Copied but Only Retained (Fully or Only Partially) in a SubSet of Daughter Cells – that have subsequently the role of Distributed Control Center for organism development.

    * Is the Body (organism) development a Centrally -Controlled Process (from Embryo – original cell) or is a Distributed-Controlled Process.

    * In Both Types of Control above we still face another daunting question: How Huge amounts of information is send by the Control Center to the Controlled Entity? Since We agree that there is an Humongous Amount of Info, the He Amounts need to be transferred on “communication channels”. Do Biology knows about Such Local/ Remote High Bandwidths communication Channels within the (developing) organism?

    B. (The Most) Important Parts of (Body Development and Organism) Information is Coming from Outside of Embryo/Fetus.

    This type of answer is – as was already remarked – quite speculative. But Considering such a Possibility may have support for a few Reasons:

    * It Seems that the Huge Amount of Necessary Information Cannot be Hosted (can’t physically Fit/Cannot be Encoded) in only 10^14 – 10^20 atoms of the Embryo.

    * When is becoming Clear that we are witnessing Miraculous/Transcendental Engineering all other Living Organisms, why not consider another “Exotic”/Transcendental possibility when trying to understand a biological/engineering/Informational Conundrum?

    In John 14:6
    Jesus answered, “I am the way and the truth and the life. No one comes to the Father except through me.”

    I always wondered when Jesus says that he is “the life” if this has not only a spiritual meaning but also a biological connotation: He is the Omnipresent essence/ingredient for Life in all existential and biological (organismal) form.Not in the sense that He is “part-of” the organism but rather He is involved in guiding somehow (informationally?) these sophisticated biological processes

  122. 122
    Dionisio says:

    InVivoVeritas @121:

    Very interesting analysis. Thanks.

  123. 123
    groovamos says:

    InVivoVeritas:
    As you suggested there are multiple known candidates: membrane patterns, ion channels, sugar code, electromagnetic fields, or new candidates to be discovered in the future. Some presentation at AM-NAT suggested that some DNA and stones (?!) form together elements of RAM (Random Access Memory) in the cell.

    * What is the Nature of the Information (at the higher level) that represents Body Shapes, Members Shapes, internal Organs Shapes, Body organization, Interfaces at All Levels between cells, tissues, parts, systems and sub-systems – and this is a kinematic, moving, dynamic process as all body parts are growing in an amazing choreography

    * Is this information Preserved ONLy in the Embryo Cell? Or is Copied, Distributed: a. in Each Daughter Cell – as cell division Happens, OR: b. Copied but Only Retained (Fully or Only Partially) in a SubSet of Daughter Cells – that have subsequently the role of Distributed Control Center for organism development.

    There is no reason other than a priori naturalism-based assumptions to not consider what was touched upon in the post @120. It seems like there is no progress in the problem of epigenetics for decades, so why hang on to what is clearly not working?

  124. 124
    Eric Anderson says:

    I’m still not quite on board with the idea that there is too much information to be encoded in an embryonic cell and that something outside is required. Perhaps. But I don’t think that has been demonstrated.

    There is still a significant challenge in quantifying the amount of information required.

    That said, I’m certainly in agreement that the information requirement is significant — far beyond what traditional evolutionary theory, or even more thoughtful biological analyses have revealed to date.

    This is part of the reason I am so skeptical of the argument-from-ignorance claim of pervasive amounts of junk DNA. After all, from the materialist side of the argument, all the information for a living organism must be contained in the embryonic cell. Indeed, Neo-Darwinian evolution traditionally taught — and Matzke not long ago confirmed in these pages that this is still his view — that all the information for an organism must ultimately be contained in the DNA (even if there is an intermediate manifestation of it in other cellular processes and systems).

    Now I think it is highly questionable that all the information for an organism is contained in the DNA alone. Be that as it may, I find it incredible — remarkable for its sheer obstinacy, its intellectual paucity, and its engineering naivete — that anyone could look at what is required to build an organism, even a fraction of the information and controlled functional organization required, and not realize that DNA is almost certainly deeply and pervasively embedded with information. Orders of magnitude more than is currently known.

    —–

    Finally, back to the question of whether all the information could fit in an embryonic cell, I would note that there are several avenues of getting information into a particular number of atoms that currently escape our ability.

    It is known, for example, that some genetic sequences can code for hundreds, even over a thousand, different gene products. So with a particular stretch of DNA the cell can produce an astounding array of proteins, by splicing and dicing and concatenating. No-one has a decent clue how this works yet, but it is there as an objective fact, staring us in the face.

    There are other ways to increase information content, such as overlapping sequences, sequences that run in the opposite direction, and so on.

    Then there is the fact that DNA strands are complementary. An ingenious designer could probably make some pretty interesting use of that fact.

    A multi-layered, heavily-spliced, heavily-concatenated, multi-directional database has the potential to be far more information rich and information dense than an initial calculation of molecules in a strand might lead us to believe.

  125. 125
    groovamos says:

    E.A : I’m still not quite on board with the idea that there is too much information to be encoded in an embryonic cell and that something outside is required. Perhaps. But I don’t think that has been demonstrated.

    So you think, contrary to Doug Axe, that there is something in the cell that encodes for the timbre of your voice?

  126. 126

    Eric Anderson @ 124

    I’m still not quite on board with the idea that there is too much information to be encoded in an embryonic cell and that something outside is required. Perhaps. But I don’t think that has been demonstrated.
    ………
    Finally, back to the question of whether all the information could fit in an embryonic cell, I would note that there are several avenues of getting information into a particular number of atoms that currently escape our ability.

    It is known, for example, that some genetic sequences can code for hundreds, even over a thousand, different gene products. So with a particular stretch of DNA the cell can produce an astounding array of proteins, by splicing and dicing and concatenating. No-one has a decent clue how this works yet, but it is there as an objective fact, staring us in the face.

    Yes, there are many encoding ‘layers’ in the DNA. It seems that significant more information is “manifest” in the cell in and around the DNA and it seems that a lot of it results from conjunction between information in the DNA and the interplay with external controlling and modifying factors that trigger methylation, splicing, concatenation, etc.

    They say that sugars have an enormous capacity for encoding information (sugar code) than that manifest in the DNA. So, definitely many more new things about the cell info sources may be revealed in the future.

    On the other hand the presumed information needed to drive in the finer detail the development of the nervous system with its 100 billion neurons and 10^14 synapses (the connectome?), with precise 3 Dimensional placement this development and wiring information is unbelievably large.

    Eric Anderson @118

    InVivoVeritas @95:

    Interesting thoughts and a fruitful avenue for further investigation, but I’m not sure the math quite holds up.

    I would be interested to get the opinion of mathematically and probabilities inclined on this blog if the Info Estimation I made @ 95 make sense or has flaws.

    Eric do you have specific problems with the way I computed the Information Estimate?

    Eric below is the corrected link to the youtube presentation that you requested on another blog

    The Design of the Simplest Self-Replicator youtube presentation

    and this is a link to another youtube presentation
    Methodological Naturalism and Its Creation Story

    that relates somewhat to the topic o this blog.

    and this is a link to another youtube presentation
    Methodological Naturalism and Its Creation Story

    that relates somewhat to the topic o this blog.

  127. 127
    Eric Anderson says:

    groovamos @125:

    Not necessarily.

    One of the interesting areas of research in recent years shows that there are a number of phenotypic characteristics that result from environmental factors and don’t have anything to do with inheritance or genetics or DNA.

    This is extremely common, frankly, to the point that we usually just overlook it. Think of a simple example you’ve seen repeated a hundred times during your life: plant one seed in good soil with the right nutrients and sunlight and water and CO2 level and you end up with a very different plant than if you plant an identical seed in poor soil with poor nutrients and a lack of sunlight and water and CO2. These differences can even be significant enough sometimes to make us think we are dealing with different species, if we don’t know the actual history of the organisms.

    These are the obvious kinds of examples, but more interesting ones also exist, if we look closely:

    Even some of the more touted “evolutionary” phenotypic variations, such as some of the finch beak variations, are, on further inspection, starting to look like they might well arise from a normal organismal response to environmental factors, rather than from an inherited mutation or other genetic changes.

    So, yes, I think there are many phenotypic characteristics that, upon inspection, will turn out to be the result of environmental factors (or, if you prefer, the interplay of the biology in a particular environment).

    But make no mistake. These will be variations on a theme, oscillations around a norm, adaptive responses to the environment, based on the information and instruction sets in the organism. A finch beak might grow slightly larger or smaller or thicker or thinner in response to environmental factors, but the information for the beak in the first place comes from the organism, not its environment.

    —–

    I don’t have any particular horse in the race as to whether timbre of voice is in that category. I tend to think it is significantly genetic, but it can of course be changed somewhat through exercises and training. I don’t yet sound quite like James Earl Jones, but I’m still working on it! 🙂

  128. 128
    Dionisio says:

    KF, considering that this OP + following discussion is quite technical -hence less attractive to the general public than a Hollywood celebrity scandal (welcome to this world!)- it’s encouraging to see the below stats:
    As of now:
    1,125 visits vs. 127 posted comments.
    998 more visits than posted comments (probably including some anonymous onlookers/lurkers).
    Almost 8 times more visits without “footprints” than posted comments.

  129. 129
    Dionisio says:

    Eric Anderson @127:

    I don’t yet sound quite like James Earl Jones, but I’m still working on it!

    That’s funny.

  130. 130
    Dionisio says:

    Dr JDD @114 & @119:

    Interesting comments.

  131. 131
    Dionisio says:

    groovamos, InVivoVeritas, Eric Anderson:

    Very interesting discussion. Thanks.

  132. 132
    kairosfocus says:

    EA, do you spot the amount of smarts it takes to interleave info like that? let’s just say I was glad I had enough reasonable cost RAM [2114’s] and EPROM . . .

    [2716’s and Hitachi RAMs that mimicked for a two-port emulator — I also loved the 74LS245 8-bit tristate isolater and 7476 JKs used in latchup mode so that once they hit they locked to store mode and then had to be separately reset . . . hardware mode bits, also I liked using RS latches to debounce switches and of course Gate based Xtal oscs, in my case pulled with diodes working as voltage controlled caps in PLLs that allowed quasi-synchronisation]

    way back that I did not need to try. KF

  133. 133
    gpuccio says:

    Dionisio at #128:

    You are always good at keeping track of the numbers! 🙂

    OK, I think I can be happy enough: the original OP plus this brilliant follow-up by our friend KF have generated almost 3000 visits in a brief time. Not bad at all, for themes that are certainly “technical”.

    One fact remains amazing, as I have just pointed out in the original thread: not one single specific criticism about the original OP and its content. As far as I can understand, not even at TSZ.

    And I have tried almost everything in the discussion, including renewed criticism of Szostak, which is usually an infallible weapon! 🙂

    Is that some sort of record? 🙂

    Or, to quote Mel Brooks: “Where did we go right?”

  134. 134
    groovamos says:

    E.A. : One of the interesting areas of research in recent years shows that there are a number of phenotypic characteristics that result from environmental factors and don’t have anything to do with inheritance or genetics or DNA.

    OK but that is obviously irrelevant to the facial resemblance to my mother that has been with me all the way back.

    You could say “well you nursed at her breast and lived every day with her at home for the first few years and the facial muscle training came from her which caused a certain morphological unfolding” That would be a real stretch. This is falsified also by identical twins separated at birth who have a lifelong resemblance.

    Additionally now that I’m getting old I notice in the mirror more resemblance to my father (unfortunately ha ha) This could not be because of living with him as I have not since age 18. How could this happen?

    When it comes to this topic I’m convinced that Sheldrake, discussed @120 is the original thinker and a couple of hundred years from now when people consider Darwin an intellectual curiosity, will be seen as a visionary.

    What he has postulated involves morphological forces which are inherently intelligence-based and thus cannot be measured, but possibly detected by careful, ingenious experimentation. By that time the Darwin cult will have fallen. Maybe helped along by extraterrestrials who fail to convert when encountered or contacted by our scientific establishment. (joking here, I’m not a SETI true believer)

  135. 135
    Dionisio says:

    gpuccio:
    I notice this TSZ word every now and then, so I asked Alexa about it, she responded “huh? say what?”
    🙂

  136. 136
    Eric Anderson says:

    gpuccio @133:

    And I have tried almost everything in the discussion, including renewed criticism of Szostak, which is usually an infallible weapon!

    LOL!

    Funny, when I went following InVivoVeritas’ link last night to a YouTube video about self-replication there were a whole bunch of other videos on the YouTube suggested list claiming self-replication of this or that system (all of them nonsense, or at least overblown). Among them was our friend Szostak, with a more serious, but still wildly speculative offering.

    Hey, I respect and appreciate the work he is doing. Maybe someday he will actually acknowledge the implications of the lab work done so far, rather than grasping at speculative straws regarding the origin of life.

  137. 137
    Eric Anderson says:

    groovamos @134:

    Of course. A beak is still a beak, and the reason it is a beak is because of the information that made it a beak.

    —–

    I hope I’m not misunderstood as to the specific point I have been making in the last few comments.

    I have long been one of the primary individuals on this site arguing for vastly more information content in DNA specifically, and in organisms generally, than what is currently known or expected. One of the reasons for that is the incredible amount of information required to define morphological form, of which we have scarcely scratched the surface.

    The point I have been making the last day or so is that certain, limited aspects of form are not necessarily pre-programmed and do not necessarily require information. Not every molecule has to be specified to the precise position — at least not in many gross morphological situations.

    Coupled with that, many morphological variations are clearly the result of environmental factors. This has significant implications, both for our analysis of the information required to produce the form, and for the materialist claims regarding “evolutionary” variations, such as the finch beaks.

    Again, the amount of information in the system has to be vastly greater than what is generally appreciated. No argument there. What I’m focusing on in these last few comments is just making sure that we don’t go a bridge too far with claims that can’t be supported.

  138. 138
    gpuccio says:

    Eric Anderson:

    “Again, the amount of information in the system has to be vastly greater than what is generally appreciated. No argument there. What I’m focusing on in these last few comments is just making sure that we don’t go a bridge too far with claims that can’t be supported.”

    A very wise attitude. I agree with you. 🙂

  139. 139

    Fixing below the broken Link in my post at 126: 

    The presentation: Methodological Naturalism and its Creation Story:

    https://www.youtube.com/watch?v=bBtmOpPSYk0

    Dr JDD 

    Very interesting posts at 114, 119

    Dionisio

    Thanks for your words at 122 and 131

  140. 140

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