Magic embryology (Introduction)

by David Turell @, Tuesday, June 04, 2013, 15:22 (3354 days ago)

The two insides of the body, right and left are not the same and can be found to be flipped backwards (situs inversus). Darwin does not explain the complexity of embryology:-http://www.nytimes.com/2013/06/04/science/growing-left-growing-right-how-a-body-breaks-symmetry.html?pagewanted=1&_r=0&nl=todaysheadlines&emc=edit_th_20130604

Magic embryology:extensive programming on display

by David Turell @, Wednesday, December 13, 2017, 18:28 (1701 days ago) @ David Turell

Take a look at this graphic to see an amazing layer of programming in the early embryo., which of course continues throughout development of the fetus:

https://www.the-scientist.com/?articles.view/articleNo/51010/title/Infographic--How-Emb...

In the first hours after fertilization, maternal factors residing in the oocyte cytoplasm dictate early development. But soon, the zygote’s genes start to take over. This maternal-to-zygotic transition involves massive epigenetic reprogramming, from the overall structure of the chromatin to the complete resetting of methylation on the genome. (Note: Most of the information depicted below is based on studies of mouse embryos; there are some differences in the timing of these events in human embryos.)

In sperm, chromatin is very compact; the overall accessibility of the chromatin in the oocyte, which is still undergoing meiosis, is unclear. Shortly after fertilization, chromatin in both pronuclei undergoes major restructuring, taking on an open configuration before reestablishing local and global organizational features.

Following fertilization, the vast majority of methyl marks?on the genome are removed. The paternal genome undergoes rapid, active demethylation, while the maternal genome loses its methylation passively over the first couple of cell divisions. Simultaneously, the embryonic genome begins to acquire tissue-specific DNA methyl marks as the cells start to differentiate.

Messenger RNAs packaged in the oocyte are gradually depleted over the first week of development. Meanwhile, the zygotic genome undergoes multiple rounds of activation, with the genes expressed early on playing key roles in embryonic organization and cell-fate determination.

By the four-cell stage, some cells begin to express genes that drive them to become the embryonic lineage that will form the fetus, while other cells begin to express genes associated with the extraembryonic lineage that becomes the placenta.

After fertilization, the genomes donated by the sperm and the egg lose many of the organizational features of their chromatin, which must be reestablished in the early embryo. One recent study showed that the paternal pronucleus of the single-cell zygote contained global features known as compartments, in which more-active regions of the genome associate with other active regions, while less-active regions associate more closely with one another. The maternal pronucleus, however, largely lacked compartments. In this study, both pronuclei had local features known as topologically associated domains (TADs), though other studies have failed to identify these organizational characteristics until later in the first week of development.

There are likely many mechanisms governing the global demethylation of the zygotic genome following fertilization. One mechanism at play in the paternal pronucleus involves the excision of the methylated DNA by breaking and repairing the double helix. As those breaks are repaired, nonmethylated cytosines are inserted where methyl marks used to reside. One recent study showed that if these breaks are not repaired, the embryo delays the first cell division.

Recent research has shown that cell-fate bias stems from methylation of arginine 26 on histone 3 (H3R26), which lengthens the time certain transcription factors remain on the DNA. Longer binding promotes expression of genes such as Sox21 that drive cells to become the embryonic lineage (blue) that will form the fetus, while cells with shorter binding form the extraembryonic lineage (green) that becomes the placenta.

Comment: This is an example of precise cellular (zygote) programming. DNA plays a major role but other factors and layers are in play. It is obvious all of klife may b e programmed in this way. Darwin does not explain any of this by his chance process theory.

Magic embryology:extensive programming on display

by David Turell @, Sunday, January 21, 2018, 21:32 (1662 days ago) @ David Turell

I've posted this two times without comment from anyone. When a species advances to a new form there must be enormous changes in the embryology mechanism. Imagine a new Volkswagen that changes from the beetle form. Think of all the machinery that has to be changed before the new model can appear. This article points out the problems for Darwin theory evolution:

http://darwins-god.blogspot.com/2018/01/how-embryonic-development-bears-on.html

"In order for evolution to have occurred, the intricate embryonic development stages of species must have evolved. Indeed, the developmental pathways of the species would be crucial in such a process. If we are to believe the evolutionary claim that the species spontaneously arose, then untold embryonic development pathways must have somehow undergone massive change. But while evolutionists expected the study of such evolution of development to yield great insight into the evolutionary process and history, it has underwhelmed. (my bold)

"This shortcoming is well known, as exemplified in this 2015 paper:

"First, traditional comparative approaches to the evolution of development—whether focused on the morphological or on the molecular/genetic level—are reaching their limits in terms of explanatory power.

"Except that this is an overstatement. To say that comparative approaches “are reaching their limits in terms of explanatory power” is to suggest that there was, at one time, some significant level of explanatory power provided. That would be a very optimistic interpretation of the data.

"The paper continues:

"The more we learn about the evolution of pattern-forming gene networks, or the ontogeny of complex morphological traits, the more it becomes clear that it is less than straightforward to conclude anything about evolutionary origins or dynamics based on such comparisons alone.

“'Less than straightforward”? Let’s be clear—a more accurate descriptor would be “impossible.” In fact, the evidence does not reveal an evolutionary history, but rather is supported by the theory. Evolutionary theory does not follow the data, as Huxley prescribed, but rather the data follow the theory.

"The paper continues:

"On the one hand, homoplasy or convergent evolution abounds at all levels of investigation. One of the most lauded major insights of EvoDevo is that a common toolkit of genes and signaling pathways is reused over and over again to create a large diversity of different body plans, shapes, and organs.

"Most lauded major insights? That would be the mother of all euphemisms. Evolutionists are always rationalizing devastating contradictions as teachable moments, and here we have yet another example. To cast the nonsensical finding of a “common toolkit” as a “major insight” is laughable.

"This becomes clear as the paper continues:

"Because of this, similarities in gene expression patterns or morphological structure often do not necessarily imply common ancestry, since they may as well reflect the frequent reuse of the same regulatory or morphogenetic modules. (my bold)

"Profound similarities “do not necessarily imply common ancestry.” We have now entered a Lewis Carroll world, as Sober would put it. The whole point of evolution was that such similarities revealed and mandated common descent. But now, we have the exact opposite, as similarities cannot be due to common descent, but must have arisen independently. And this is an “insight”? A fundamental prediction is demolished and evolutionists do not skip a beat. This is not science.

"But it gets worse:

"On the other hand, developmental system drift allows conserved networks to change considerably in terms of their component genes and regulatory interactions without changing the phenotypic outcomes such systems produce. This means that even functionally conserved regulatory networks can become unrecognizably divergent at the molecular and genetic level, especially across large evolutionary time spans.

"We have now reached the height of absurdity. First, profound developmental similarities were found which could not be ascribed to common descent. Now we find that those developmental pathways which can (theoretically) be ascribed to common descent are profoundly different."

Comment: Hunter does not believe in common descent, but points raised by the original article are from Darwin scientists. Embryology is one of the black holes of Darwin theory. The original paper is a complex discussion:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357653/

Magic embryology:extensive programming on display

by dhw, Monday, January 22, 2018, 14:30 (1661 days ago) @ David Turell

DAVID: I've posted this two times without comment from anyone. When a species advances to a new form there must be enormous changes in the embryology mechanism. Imagine a new Volkswagen that changes from the beetle form. Think of all the machinery that has to be changed before the new model can appear. This article points out the problems for Darwin theory evolution:
http://darwins-god.blogspot.com/2018/01/how-embryonic-development-bears-on.html

I don’t recall seeing it, but since I am the only person commenting on your posts, I can only plead that I can’t comment on everything! But I do my best, and I’m sorry to have let you down.

Since you yourself believe in common descent, I presume that what you endorse is the argument that the enormous changes cannot be the result of chance. I agree. You know my hypothesis (not dogma and not even belief, but an alternative to hypotheses such as Darwin’s random mutations and your own divine 3.8 billion-year-old computer programme or dabbling). However, since you want me to comment, I can only repeat it: ALL evolutionary changes can be explained by the inventive intelligence of cells and cell communities, which work together to produce new forms out of old (common descent, which you accept). Convergent evolution is responsible for similar solutions to similar problems (i.e. intelligent beings will think in similar ways). It may well be that a God designed this inventive intelligence in the first place. I cannot see any problem in the article that would not be resolved by my hypothesis. I can’t find the author’s own explanation, but perhaps you have not reproduced that. If so, does he mention your computer programme or the dabbling?

Magic embryology:extensive programming on display

by David Turell @, Monday, January 22, 2018, 15:00 (1661 days ago) @ dhw

DAVID: I've posted this two times without comment from anyone. When a species advances to a new form there must be enormous changes in the embryology mechanism. Imagine a new Volkswagen that changes from the beetle form. Think of all the machinery that has to be changed before the new model can appear. This article points out the problems for Darwin theory evolution:
http://darwins-god.blogspot.com/2018/01/how-embryonic-development-bears-on.html

dhw:I don’t recall seeing it, but since I am the only person commenting on your posts, I can only plead that I can’t comment on everything! But I do my best, and I’m sorry to have let you down.

Since you yourself believe in common descent, I presume that what you endorse is the argument that the enormous changes cannot be the result of chance. I agree. You know my hypothesis (not dogma and not even belief, but an alternative to hypotheses such as Darwin’s random mutations and your own divine 3.8 billion-year-old computer programme or dabbling). However, since you want me to comment, I can only repeat it: ALL evolutionary changes can be explained by the inventive intelligence of cells and cell communities, which work together to produce new forms out of old (common descent, which you accept). Convergent evolution is responsible for similar solutions to similar problems (i.e. intelligent beings will think in similar ways). It may well be that a God designed this inventive intelligence in the first place. I cannot see any problem in the article that would not be resolved by my hypothesis. I can’t find the author’s own explanation, but perhaps you have not reproduced that. If so, does he mention your computer programme or the dabbling?

Hunter is a confirmed anti-Darwinist. He doesn't believe in common descent. He and I disagree. But what I find fascinating about him is the fallacies he uncovers in Darwin scientist thinking as in this article, as they twist theories about the latest findings to conform to the underlying principles develop from Darwin theory.

But the other point of his article is how does evolution invent the new factory proceses to manufacture the latest phenotype in a series of new species. Looking at how humans do it, one designer presents a shape of the new Volkswagen, someone else designs the machines to stamp out the sheet steel or plastic. Another set of engineers design the advanced motor, and another group design the machines to make some of the new parts. In nature changes in DNA and other layers produce the new forms. You suggest cell committees contain the intellect to do this. I have never understood this wishful thinking. A designer is required, obviously.

Magic embryology:extensive programming on display

by dhw, Tuesday, January 23, 2018, 12:52 (1660 days ago) @ David Turell

Dhw: Since you yourself believe in common descent, I presume that what you endorse is the argument that the enormous changes cannot be the result of chance. I agree. You know my hypothesis (not dogma and not even belief, but an alternative to hypotheses such as Darwin’s random mutations and your own divine 3.8 billion-year-old computer programme or dabbling).

DAVID: But the other point of his article is how does evolution invent the new factory proceses to manufacture the latest phenotype in a series of new species. Looking at how humans do it, one designer presents a shape of the new Volkswagen, someone else designs the machines to stamp out the sheet steel or plastic. Another set of engineers design the advanced motor, and another group design the machines to make some of the new parts. In nature changes in DNA and other layers produce the new forms. You suggest cell committees contain the intellect to do this. I have never understood this wishful thinking. A designer is required, obviously.

I like the VW analogy. Any major change in an organism will require exactly the same cooperation between the different cell communities, whether your God preprogrammed/dabbled it, or they worked it out for themselves (with the intelligence that God may have given them). I don’t mind your little joke of always substituting “committees” for communities in order to conjure up an unlikely human image, but I will not let you get away with “wishful thinking”. I have nothing to gain from this hypothesis, which at all times allows for the existence of your God. I am simply looking for an explanation of how evolution works, and I find your own hypothesis as illogical as you do (since your ultimate argument seems to be that God’s logic must be different from ours). I am equally unconvinced by Darwin’s hypothesis of random mutations. The intelligent cell is not “wishful thinking” – my hypothesis grew from the findings of some eminent scientists, but I have always acknowledged that there is no evidence that cell communities are capable of the major changes required for speciation. There is no evidence for your divine preprogramming/dabbling hypothesis either. Nobody knows the truth, which is why we continue to look for it. Anyone who firmly believes in his/her hypothesis and rejects alternatives is, I think, far more open to the charge of “wishful thinking” than someone who offers his own as an alternative, and not as dogma or belief. But perhaps you didn’t read the lines at the head of this post.

Magic embryology:extensive programming on display

by David Turell @, Tuesday, January 23, 2018, 14:50 (1660 days ago) @ dhw


DAVID: But the other point of his article is how does evolution invent the new factory proceses to manufacture the latest phenotype in a series of new species. Looking at how humans do it, one designer presents a shape of the new Volkswagen, someone else designs the machines to stamp out the sheet steel or plastic. Another set of engineers design the advanced motor, and another group design the machines to make some of the new parts. In nature changes in DNA and other layers produce the new forms. You suggest cell committees contain the intellect to do this. I have never understood this wishful thinking. A designer is required, obviously.

dhw: I like the VW analogy. Any major change in an organism will require exactly the same cooperation between the different cell communities, whether your God preprogrammed/dabbled it, or they worked it out for themselves (with the intelligence that God may have given them). I don’t mind your little joke of always substituting “committees” for communities in order to conjure up an unlikely human image, but I will not let you get away with “wishful thinking”. I have nothing to gain from this hypothesis, which at all times allows for the existence of your God. I am simply looking for an explanation of how evolution works, and I find your own hypothesis as illogical as you do (since your ultimate argument seems to be that God’s logic must be different from ours). I am equally unconvinced by Darwin’s hypothesis of random mutations. The intelligent cell is not “wishful thinking” – my hypothesis grew from the findings of some eminent scientists, but I have always acknowledged that there is no evidence that cell communities are capable of the major changes required for speciation. There is no evidence for your divine preprogramming/dabbling hypothesis either. Nobody knows the truth, which is why we continue to look for it. Anyone who firmly believes in his/her hypothesis and rejects alternatives is, I think, far more open to the charge of “wishful thinking” than someone who offers his own as an alternative, and not as dogma or belief. But perhaps you didn’t read the lines at the head of this post.

You sure try hard and drag God in when it looks good to do so. And drag in prejudiced Darwinist scientists to stress your points. I'll stick with my own comment: logically a designer is required.

Magic embryology:extensive programming on display

by dhw, Wednesday, January 24, 2018, 13:57 (1659 days ago) @ David Turell

dhw: The intelligent cell is not “wishful thinking” – my hypothesis grew from the findings of some eminent scientists, but I have always acknowledged that there is no evidence that cell communities are capable of the major changes required for speciation. There is no evidence for your divine preprogramming/dabbling hypothesis either. Nobody knows the truth, which is why we continue to look for it. Anyone who firmly believes in his/her hypothesis and rejects alternatives is, I think, far more open to the charge of “wishful thinking” than someone who offers his own as an alternative, and not as dogma or belief.

DAVID: You sure try hard and drag God in when it looks good to do so. And drag in prejudiced Darwinist scientists to stress your points. I'll stick with my own comment: logically a designer is required.

I am an agnostic. Any hypothesis I come up with must make allowances for the existence of God. I have no quarrel with your belief in a designer. I challenge your interpretation of his possible motives and methods, which on several occasions you have admitted is illogical (hence the claim that God’s logic must be different from human logic). As for “prejudiced” scientists, you have agreed that there is a 50/50 chance that they are right, since nobody can tell from the outside whether intelligent behaviour stems from intelligence or from preprogramming. If you think these dedicated scientists, who have spent a lifetime studying cell behaviour, are prejudiced because they opt for the 50% you don’t like, I’m afraid your espousal of the other 50% makes you just as prejudiced.

Magic embryology:extensive programming on display

by David Turell @, Wednesday, January 24, 2018, 15:17 (1659 days ago) @ dhw


dhw: I am an agnostic. Any hypothesis I come up with must make allowances for the existence of God. I have no quarrel with your belief in a designer. I challenge your interpretation of his possible motives and methods, which on several occasions you have admitted is illogical (hence the claim that God’s logic must be different from human logic). As for “prejudiced” scientists, you have agreed that there is a 50/50 chance that they are right, since nobody can tell from the outside whether intelligent behaviour stems from intelligence or from preprogramming. If you think these dedicated scientists, who have spent a lifetime studying cell behaviour, are prejudiced because they opt for the 50% you don’t like, I’m afraid your espousal of the other 50% makes you just as prejudiced.

My background in biochemistry allows me to disagree with your scientists on the basis of more than prejudice. You cannot deny their Darwin bias. My ID science folks agree with me.

Magic embryology:extensive programming on display

by dhw, Friday, January 26, 2018, 13:31 (1657 days ago) @ David Turell

dhw: As for “prejudiced” scientists, you have agreed that there is a 50/50 chance that they are right, since nobody can tell from the outside whether intelligent behaviour stems from intelligence or from preprogramming. If you think these dedicated scientists, who have spent a lifetime studying cell behaviour, are prejudiced because they opt for the 50% you don’t like, I’m afraid your espousal of the other 50% makes you just as prejudiced.

DAVID: My background in biochemistry allows me to disagree with your scientists on the basis of more than prejudice. You cannot deny their Darwin bias. My ID science folks agree with me.

Cellular intelligence plays no part in Darwin’s theory, and I do not believe for one second that “my” scientists’ conclusions have been influenced by a belief in common descent – a belief you share with them. The concept actually provides a potentially devastating blow to Darwin’s hypothesis of random mutations. And I cannot see why you think experts with both background and foreground in cytogenetics, biochemistry, biology, bacterial genetics, cell biology etc., who share your belief in common descent, are prejudiced, whereas you, with your background in biochemistry and your firm belief in divine preprogramming and/or dabbling, are not.

Magic embryology:extensive programming on display

by David Turell @, Saturday, January 27, 2018, 00:22 (1657 days ago) @ dhw

dhw: As for “prejudiced” scientists, you have agreed that there is a 50/50 chance that they are right, since nobody can tell from the outside whether intelligent behaviour stems from intelligence or from preprogramming. If you think these dedicated scientists, who have spent a lifetime studying cell behaviour, are prejudiced because they opt for the 50% you don’t like, I’m afraid your espousal of the other 50% makes you just as prejudiced.

DAVID: My background in biochemistry allows me to disagree with your scientists on the basis of more than prejudice. You cannot deny their Darwin bias. My ID science folks agree with me.

dhw: Cellular intelligence plays no part in Darwin’s theory, and I do not believe for one second that “my” scientists’ conclusions have been influenced by a belief in common descent – a belief you share with them. The concept actually provides a potentially devastating blow to Darwin’s hypothesis of random mutations. And I cannot see why you think experts with both background and foreground in cytogenetics, biochemistry, biology, bacterial genetics, cell biology etc., who share your belief in common descent, are prejudiced, whereas you, with your background in biochemistry and your firm belief in divine preprogramming and/or dabbling, are not.

We are left with our same disagreement. Common descent is not the issue. It is the total Neo-Darwin synthesis from the 1950's, about which I have presented many articles on the current discussions and disagreements, because the newer science doesn't fit the earlier suppositions. Your folks come from that era. Much of this has been revealed by Susan Mazur's reporting:

http://www.suzanmazur.com/

Magic embryology:extensive programming on display

by dhw, Saturday, January 27, 2018, 13:22 (1656 days ago) @ David Turell

dhw: Cellular intelligence plays no part in Darwin’s theory, and I do not believe for one second that “my” scientists’ conclusions have been influenced by a belief in common descent – a belief you share with them. The concept actually provides a potentially devastating blow to Darwin’s hypothesis of random mutations. And I cannot see why you think experts with both background and foreground in cytogenetics, biochemistry, biology, bacterial genetics, cell biology etc., who share your belief in common descent, are prejudiced, whereas you, with your background in biochemistry and your firm belief in divine preprogramming and/or dabbling, are not.

DAVID: We are left with our same disagreement. Common descent is not the issue. It is the total Neo-Darwin synthesis from the 1950's, about which I have presented many articles on the current discussions and disagreements, because the newer science doesn't fit the earlier suppositions. Your folks come from that era. Much of this has been revealed by Susan Mazur's reporting:

Red herring. “My” scientists say cells are intelligent. You accuse them of prejudice because you say they believe(d) in the Neo-Darwin synthesis of the 1950s, the essence of which is that the whole of evolution can be explained by random mutations and natural selection; this has nothing whatsoever to do with cellular intelligence. You say cells are not intelligent, because you believe God preprogrammed or dabbled everything that cells have done and still do. All of you believe that science supports you. If their belief in Neo-Darwinism makes them prejudiced (which I do not believe for one instant), then by the same token your belief in divine preprogramming makes you prejudiced. Please don’t answer with a reading list.

Magic embryology:extensive programming on display

by David Turell @, Saturday, January 27, 2018, 14:55 (1656 days ago) @ dhw


DAVID: We are left with our same disagreement. Common descent is not the issue. It is the total Neo-Darwin synthesis from the 1950's, about which I have presented many articles on the current discussions and disagreements, because the newer science doesn't fit the earlier suppositions. Your folks come from that era. Much of this has been revealed by Susan Mazur's reporting:

dhw: Red herring. “My” scientists say cells are intelligent. You accuse them of prejudice because you say they believe(d) in the Neo-Darwin synthesis of the 1950s, the essence of which is that the whole of evolution can be explained by random mutations and natural selection; this has nothing whatsoever to do with cellular intelligence. You say cells are not intelligent, because you believe God preprogrammed or dabbled everything that cells have done and still do. All of you believe that science supports you. If their belief in Neo-Darwinism makes them prejudiced (which I do not believe for one instant), then by the same token your belief in divine preprogramming makes you prejudiced. Please don’t answer with a reading list.

No point in continuing. We should agree to disagree and move on.

Magic embryology: forming fetus totally unexplained

by David Turell @, Saturday, January 27, 2018, 21:33 (1656 days ago) @ David Turell

Scientists currently have no explanation for the development of animal form:

https://www.sciencedaily.com/releases/2016/08/160831085527.htm

Abstract: " We present a plausible account of the origin of the archetypal vertebrate bauplan. We offer a theoretical reconstruction of the geometrically regular structure of the blastula resulting from the sequential subdivision of the egg, followed by mechanical deformations of the blastula in subsequent stages of gastrulation. We suggest that the formation of the vertebrate bauplan during development, as well as fixation of its variants over the course of evolution, have been constrained and guided by global mechanical biases. Arguably, the role of such biases in directing morphology—though all but neglected in previous accounts of both development and macroevolution—is critical to any substantive explanation for the origin of the archetypal vertebrate bauplan. We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis—currently an elusive goal—will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences." (my bold)

Another review of it:

https://www.sciencedaily.com/releases/2016/08/160831085527.htm

"Embryo geometry, developed by a team from the University of San Diego, Mount Holyoke College, Evergreen State College, and Chem-Tainer Industries, Inc.. in the USA, looks at animal complexity generally and the vertebrate body in particular as more the products of mechanical forces and the laws of geometry than solely the outcome of random genetic mutation.

"'At the suggestion of evolutionary biologist Stephen Jay Gould, preliminary attempts at a solution to this problem were undertaken over many years. But these -- as well as other, similar efforts -- were met with strong opposition by supporters of the Neo-Darwinian interpretation of natural selection," commented senior author Stuart Pivar. "We hope that the theory of embryo geometry will stimulate further investigation by biologists of all stripes across a variety of fields."

"Anatomists have long postulated that animal complexity arises during development of the embryo -- called embryogenesis -- but despite detailed descriptions of the embryonic stages of all major types of animal, the evolution of organismal complexity and its expression during individual development have remained mysterious processes -- until now.

"The researchers behind embryo geometry have shown that the vertebrate embryo could conceivably arise from mechanical deformation of the blastula, a ball of cells formed when the fertilized egg divides. As these cells proliferate, the ball increases in volume and surface area, altering its geometry. The theory posits that the blastula retains the geometry of the original eight cells produced by the first three divisions of the egg, which themselves determine the three axes of the vertebrate body.

***

"These illustrations explain how the vertebrate body might plausibly arise from a single cell, both over evolutionary time, and during individual embryogenesis."

Comment: Daarwinism has no explanation for embryogenesis. No genes are found to controlthe formation of animals or plants, thus the result to proposing mechanical factors which somehow create a completely organized living individual. This is the black box of Darwin theory as Cornelius Hunter observed. Perhaps through a mechanism at a quatnum level designed by God.

Magic embryology: forming fetus totally unexplained

by David Turell @, Monday, April 16, 2018, 00:50 (1578 days ago) @ David Turell

The original paper is here:

https://www.sciencedirect.com/science/article/pii/S0079610716300542?via%3Dihub

"Abstract
We present a plausible account of the origin of the archetypal vertebrate bauplan. We offer a theoretical reconstruction of the geometrically regular structure of the blastula resulting from the sequential subdivision of the egg, followed by mechanical deformations of the blastula in subsequent stages of gastrulation. We suggest that the formation of the vertebrate bauplan during development, as well as fixation of its variants over the course of evolution, have been constrained and guided by global mechanical biases. Arguably, the role of such biases in directing morphology—though all but neglected in previous accounts of both development and macroevolution—is critical to any substantive explanation for the origin of the archetypal vertebrate bauplan. We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis—currently an elusive goal—will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences."

***

"From conclusion:

The causal account that the model provides for the development of complex vertebrate morphology is necessarily presented by a speculative series of schematic images representing sequences of key mechanical events during embryogenesis, akin to a series of blueprints. The vast—and largely non-pictorial—literature on this subject does not offer a global mechanism to explain the rise of diverse forms of animal phyla. Though highly speculative, the model offered here may suggest just such a mechanism. The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry. Accordingly, the choices available to natural selection may be limited to the possible variations in proportions of the body parts of otherwise relatively conservative and invariant phyletic forms, rather than simply provided by random genetic mutations resulting from errors in transcription. Animal form may thus be seen as the product of physical forces—or biases—acting upon cells and populations of cells with very specific and constrained geometric properties, rather than arising solely from the vagaries of chance."(my bold)

Comment: Note the bold. Not Darwin. As can be seen embryogesnesis is not explained. The authors' initial point about their theory:

"Though neither rigorous nor exhaustive in an empirical sense, our model offers an intuitive and plausible description of the emergence of form via simple geometrical and mechanical forces and constraints. The model provides a template, or roadmap, for further investigation, subject to confirmation (or refutation) by interested researchers."

Magic embryology: forming a blastocyst envelope:

by David Turell @, Wednesday, August 01, 2018, 23:01 (1470 days ago) @ David Turell

Shortly after fertilization of the egg a hollow sphere of cells appear which need an envelope:

https://www.the-scientist.com/the-literature/these-molecules-zipper-embryos-closed-6454...

"Not long after egg meets sperm, the resulting mulberry-like mass of cells morphs into a hollow sphere called a blastocyst, sealing itself off from the external environment before implantation. If such sealing doesn’t happen, pregnancy can fail, but “the precise mechanisms that give rise to embryo sealing prior to blastocyst formation remained incompletely understood,” says cell biologist Maté Biro of the University of New South Wales.

"Biro and his colleagues used advanced imaging techniques to study live, fully intact mouse embryos as they developed in a Petri dish and found that rings of the protein actin form across the ball of cells and help to zipper the embryo closed in a multistep process. First, microtubules at the outward-facing poles of the cells pull actin proteins into rings that expand across each cell. Then, when one ring touches another ring, motor proteins called myosins accumulate along the regions where the rings touch. There they continue to build up, pushing the edges of the rings together, zippering them shut and sealing the outside of the ball of cells from its external environment, Biro and colleagues report in Cell.

“'Following the observation of the expanding actin rings, we realized just how beautiful and intricate the coordination between all the outer cells of the embryo is,” Biro tells The Scientist. “Such consistency and coordination does not happen simply by chance.”

"It’s now clear that filamentous actin and the plasma membrane are “the rails of the zipper,” notes study coauthor Nicolas Plachta of the Agency for Science, Technology and Research in Singapore, while myosin motors “drive the advancement of the zipper and allow for the recruitment of [additional myosin and other components] that then tightly seal the junction.”

"The phenomenon is the opposite of another mechanism by which cells generate mechanical force: the formation of purse string–like actin rings, according to Gabriel Galea, who studies cellular mechanobiology at University College London and was not involved in the study. Those rings typically form through “collaboration” between neighboring cells, with each cell forming a small proportion of the overall structure, which can ultimately help the cells contract and then divide. In the new study, the actin rings instead form in individual cells and expand to coalesce as they join the cell’s neighboring rings. “Not only does this reveal the ‘birth’ of cytoskeleton-bound cell-cell junctions in the early embryo, but also identifies cellular processes likely to be unique to these early stages of development which could cause infertility or early embryo loss if defective,” Galea writes in an email to The Scientist."

Comment: This occurs with no relation to being exposed to nature, so there is no way for natural selection to act on it. Only design can be considered.

Magic embryology: seed to plant needs complex steps

by David Turell @, Thursday, August 02, 2018, 22:12 (1469 days ago) @ David Turell

A seed is tough and doesn't want to become a weak seedling unless the right conditions are present. A rapid process occurs controlled by chemical signals:

https://phys.org/news/2018-08-seed-hours-survive.html

"During germination, the embryo within a seed must develop into a young seedling capable of photosynthesis in less than 48 hours. During this time, it relies solely on its internal reserves, which are quickly consumed. It must therefore rapidly create functional chloroplasts, cellular organelles that will enable it to produce sugars to ensure its survival. Such a mechanism ensures a rapid transition to autonomous growth, as soon as the seed decides to germinate.

"The surprising propagation and diversification of flowering plants in terrestrial environments are mainly due to the appearance of seeds during evolution. The embryo, which is dormant, is encapsulated and protected in a very resistant structure, which facilitates its dispersion. At this stage, it cannot perform photosynthesis and, during germination, it will thus consume the nutritive reserves stored in the seed. This process induces the transformation of a strong embryo into a fragile seedling. "This is a critical stage in the life of a plant, which is closely regulated, notably by the growth hormone gibberellic acid (GA). The production of this hormone is repressed when external conditions are unfavorable," explains Luis Lopez-Molina, Professor at the Department of Botany and Plant Biology of the UNIGE Faculty of Science.

"The awakening of the embryo causes the differentiation of its proplastids into chloroplasts, biological factories capable of producing sugar thanks to photosynthesis. "Thousands of different proteins must be imported into the developing chloroplasts, and this process can only take place in the presence of a protein called TOC159. If it is lacking, the plant will be depleted in chloroplasts and will remain albino," explains Felix Kessler, director of the Plant Physiology Lab and vice-rector of the UniNE.

"How does the seed decide whether to keep the embryo in a protected state or, on the contrary, to take a chance and let it germinate? "We have discovered that, as long as GA is suppressed, a mechanism is set up, which ensures that TOC159 proteins are transported to the cellular waste bin in order to be degraded," explains Venkatasalam Shanmugabalaji, researcher within the Neuchâtel group and first author of the study. In addition, other proteins
needed for photosynthesis, of which TOC159 facilitates importation, suffer the same fate.

"When external conditions become favorable for germination, the GA concentration increases in the seed. The biologists discovered that high concentrations of this hormone indirectly block the degradation of TOC159 proteins. The latter can therefore be inserted into the membrane of the proplastids and enable the import of photosynthetic proteins cargoes, which also escape the cellular waste bin.

"The genesis of the first functional chloroplasts, implemented in less than 48 hours, therefore ensures a rapid transition from a growth depending on the embryo's reserves to an autonomous development. This high-performance mechanism contributes to the survival of the seedling in an inhospitable environment, in which it will have to face many challenges."

Comment: How did seeded plants evolve if such complex controls are required to ensure a speedy reaction in a short time if the conditions are right. The series of engries I've presented today support my claim that all forms of life are too complex for chance evolution to work.

Magic embryology: egg sends protein signal to guide sperm

by David Turell @, Saturday, August 04, 2018, 23:07 (1467 days ago) @ David Turell

That signal has finally been found:

https://phys.org/news/2018-08-scientists-elusive-molecule-sperm-egg.html

"More than 100 years ago, MBL Director F.R. Lillie of the University of Chicago discovered that eggs from marine invertebrates release a chemical factor that attracts sperm, a process called chemotaxis. Sperm, for their part, swim up a chemical gradient to reach the egg, assisted by a pulsatile rise in calcium ion (Ca2+) concentration in the sperm tail that controls its beating.

"In past years, many of the cellular components that translate chemoattractant stimulation into a Ca2+ response have been revealed, but a crucial ingredient has been missing. A prerequisite for Ca2+ ions from the sperm's environment being able to enter the tail is that the sperm cell's pH becomes more alkaline. The molecule that brings about this change in pH has been elusive.

"In this new report, U. Benjamin Kaupp, a MBL Whitman Center Scientist from the Center of Advanced European Studies (Caesar) in Bonn, Germany, identifies this molecule. Kaupp spent 18 summers at the MBL conducting research in the footsteps of F.R. Lillie's original quest.

***

"The molecule that Kaupp and colleagues identified allows sodium ions to flow into the sperm cell and, in exchange, transports protons out of the cell. Such so-called sodium/proton exchangers have been known for a long time, but this one is special. It is a chimaera that shares structural features with ion channels, called pacemaker channels, which control our heartbeat and electrical activity in the brain.

"This sodium/proton exchange in the sperm cell, like in the pacemaker channels, is activated by a stretch of positively charged amino acids called the voltage sensor. When sperm capture chemoattractant molecules, the voltage becomes more negative, because potassium channels open and potassium ions leave the cell. The voltage-sensor registers this voltage change and the exchanger begins exporting protons from the cell; the cell's interior becomes more alkaline. When this mechanism is disabled, the Ca2+ pulses in the sperm tail are suppressed, and sperm are lost on their voyage to the egg. "

Comment: this article shows the complexity that sexual reproduction requires. How did it happen when early life had the simpler process of splitting single cells, although that process is itself very complex? This supports the concept that evolution contains a complexification mechanism as a driving force.

Magic embryology: physical forces form organs

by David Turell @, Wednesday, September 05, 2018, 21:04 (1435 days ago) @ David Turell

Out of an original jumble of cells organs take shape and form guided by physical shapes and forces:

https://phys.org/news/2018-09-uncover-tissues-sculpted-embryogenesis.html

"'In a nutshell, we discovered a fundamental physical mechanism that cells use to mold embryonic tissues into their functional 3-D shapes," said Campàs, a professor of mechanical engineering in UCSB's College of Engineering who holds the Duncan & Suzanne Mellichamp Chair in Systems Biology.

***

"Cells coordinate by exchanging biochemical signals, but they also hold to and push on each other to build the body structures we need to live, such as the eyes, lungs and heart. And, as it turns out, sculpting the embryo is not far from glass molding or 3-D printing. In their new work,"A fluid-to-solid jamming transition underlies vertebrate body axis elongation," published in the journal Nature, Campàs and colleagues reveal that cell collectives switch from fluid to solid states in a controlled manner to build the vertebrate embryo, in a way similar to how we mold glass into vases or 3-D print our favorite items. Or, if you like, we 3-D print ourselves, from the inside.

"Most objects begin as fluids. From metallic structures to gelatin desserts, their shape is made by pouring the molten original materials into molds, then cooling them to get the solid objects we use. As in a Chihuly glass sculpture, made by carefully melting portions of glass to slowly reshape it into life, cells in certain regions of the embryo are more active and 'melt' the tissue into a fluid state that can be restructured. Once done, cells 'cool down' to settle the tissue shape, Campàs explained.

"'The transition from fluid to solid tissue states that we observed is known in physics as 'jamming'," Campàs said. "Jamming transitions are a very general phenomena that happens when particles in disordered systems, such as foams, emulsions or glasses, are forced together or cooled down."

***

"Zebrafish, like other vertebrates, start off from a largely shapeless bunch of cells and need to transform the body into an elongated shape, with the head at one end and tail at the other," Campàs said. The physical reorganization of the cells behind this process had always been something of a mystery. Surprisingly, researchers found that the cell collectives making the tissue were physically like a foam (yes, as in beer froth) that jammed during development to 'freeze' the tissue architecture and set its shape.

"These observations confirm a remarkable intuition made by Victorian-era Scottish mathematician D'Arcy Thompson 100 years ago in his seminal work "On Growth and Form."
"He was convinced that some of the physical mechanisms that give shapes to inert materials were also at play to shape living organisms. Remarkably, he compared groups of cells to foams and even the shaping of cells and tissues to glassblowing," Campàs said. A century ago, there were no instruments that could directly test the ideas Thompson proposed, Campàs added, though Thompson's work continues to be cited to this day."

Comment: Getting to fertilized egg to whole new organism requires major planned processes which are all coordinated in achieving the new whole one. There is no way a Darwin process could have developed this process. It is totally unexplained from an evolutionary standpoint. It had to be designed from the beginning.

Magic embryology: physical forces form organs

by Balance_Maintained @, U.S.A., Thursday, September 06, 2018, 04:05 (1435 days ago) @ David Turell

Out of an original jumble of cells organs take shape and form guided by physical shapes and forces:

https://phys.org/news/2018-09-uncover-tissues-sculpted-embryogenesis.html

"'In a nutshell, we discovered a fundamental physical mechanism that cells use to mold embryonic tissues into their functional 3-D shapes," said Campàs, a professor of mechanical engineering in UCSB's College of Engineering who holds the Duncan & Suzanne Mellichamp Chair in Systems Biology.

***

"Cells coordinate by exchanging biochemical signals, but they also hold to and push on each other to build the body structures we need to live, such as the eyes, lungs and heart. And, as it turns out, sculpting the embryo is not far from glass molding or 3-D printing. In their new work,"A fluid-to-solid jamming transition underlies vertebrate body axis elongation," published in the journal Nature, Campàs and colleagues reveal that cell collectives switch from fluid to solid states in a controlled manner to build the vertebrate embryo, in a way similar to how we mold glass into vases or 3-D print our favorite items. Or, if you like, we 3-D print ourselves, from the inside.

"Most objects begin as fluids. From metallic structures to gelatin desserts, their shape is made by pouring the molten original materials into molds, then cooling them to get the solid objects we use. As in a Chihuly glass sculpture, made by carefully melting portions of glass to slowly reshape it into life, cells in certain regions of the embryo are more active and 'melt' the tissue into a fluid state that can be restructured. Once done, cells 'cool down' to settle the tissue shape, Campàs explained.

"'The transition from fluid to solid tissue states that we observed is known in physics as 'jamming'," Campàs said. "Jamming transitions are a very general phenomena that happens when particles in disordered systems, such as foams, emulsions or glasses, are forced together or cooled down."

***

"Zebrafish, like other vertebrates, start off from a largely shapeless bunch of cells and need to transform the body into an elongated shape, with the head at one end and tail at the other," Campàs said. The physical reorganization of the cells behind this process had always been something of a mystery. Surprisingly, researchers found that the cell collectives making the tissue were physically like a foam (yes, as in beer froth) that jammed during development to 'freeze' the tissue architecture and set its shape.

"These observations confirm a remarkable intuition made by Victorian-era Scottish mathematician D'Arcy Thompson 100 years ago in his seminal work "On Growth and Form."
"He was convinced that some of the physical mechanisms that give shapes to inert materials were also at play to shape living organisms. Remarkably, he compared groups of cells to foams and even the shaping of cells and tissues to glassblowing," Campàs said. A century ago, there were no instruments that could directly test the ideas Thompson proposed, Campàs added, though Thompson's work continues to be cited to this day."

Comment: Getting to fertilized egg to whole new organism requires major planned processes which are all coordinated in achieving the new whole one. There is no way a Darwin process could have developed this process. It is totally unexplained from an evolutionary standpoint. It had to be designed from the beginning.

Even at the lowest possible element, we contain at least 4 pieces of information during development space (x,y,z) and time. How can that be explained?

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Magic embryology: physical forces form organs

by David Turell @, Thursday, September 06, 2018, 14:00 (1434 days ago) @ Balance_Maintained

Out of an original jumble of cells organs take shape and form guided by physical shapes and forces:

https://phys.org/news/2018-09-uncover-tissues-sculpted-embryogenesis.html

"'In a nutshell, we discovered a fundamental physical mechanism that cells use to mold embryonic tissues into their functional 3-D shapes," said Campàs, a professor of mechanical engineering in UCSB's College of Engineering who holds the Duncan & Suzanne Mellichamp Chair in Systems Biology.

***

"Cells coordinate by exchanging biochemical signals, but they also hold to and push on each other to build the body structures we need to live, such as the eyes, lungs and heart. And, as it turns out, sculpting the embryo is not far from glass molding or 3-D printing. In their new work,"A fluid-to-solid jamming transition underlies vertebrate body axis elongation," published in the journal Nature, Campàs and colleagues reveal that cell collectives switch from fluid to solid states in a controlled manner to build the vertebrate embryo, in a way similar to how we mold glass into vases or 3-D print our favorite items. Or, if you like, we 3-D print ourselves, from the inside.

"Most objects begin as fluids. From metallic structures to gelatin desserts, their shape is made by pouring the molten original materials into molds, then cooling them to get the solid objects we use. As in a Chihuly glass sculpture, made by carefully melting portions of glass to slowly reshape it into life, cells in certain regions of the embryo are more active and 'melt' the tissue into a fluid state that can be restructured. Once done, cells 'cool down' to settle the tissue shape, Campàs explained.

"'The transition from fluid to solid tissue states that we observed is known in physics as 'jamming'," Campàs said. "Jamming transitions are a very general phenomena that happens when particles in disordered systems, such as foams, emulsions or glasses, are forced together or cooled down."

***

"Zebrafish, like other vertebrates, start off from a largely shapeless bunch of cells and need to transform the body into an elongated shape, with the head at one end and tail at the other," Campàs said. The physical reorganization of the cells behind this process had always been something of a mystery. Surprisingly, researchers found that the cell collectives making the tissue were physically like a foam (yes, as in beer froth) that jammed during development to 'freeze' the tissue architecture and set its shape.

"These observations confirm a remarkable intuition made by Victorian-era Scottish mathematician D'Arcy Thompson 100 years ago in his seminal work "On Growth and Form."
"He was convinced that some of the physical mechanisms that give shapes to inert materials were also at play to shape living organisms. Remarkably, he compared groups of cells to foams and even the shaping of cells and tissues to glassblowing," Campàs said. A century ago, there were no instruments that could directly test the ideas Thompson proposed, Campàs added, though Thompson's work continues to be cited to this day."

Comment: Getting to fertilized egg to whole new organism requires major planned processes which are all coordinated in achieving the new whole one. There is no way a Darwin process could have developed this process. It is totally unexplained from an evolutionary standpoint. It had to be designed from the beginning.


Tony: Even at the lowest possible element, we contain at least 4 pieces of information during development space (x,y,z) and time. How can that be explained?

Not by chance

Magic embryology: physical forces form organs

by dhw, Monday, September 10, 2018, 09:38 (1431 days ago) @ David Turell

DAVID: Out of an original jumble of cells organs take shape and form guided by physical shapes and forces:
https://phys.org/news/2018-09-uncover-tissues-sculpted-embryogenesis.html

QUOTES: "'In a nutshell, we discovered a fundamental physical mechanism that cells use to mold embryonic tissues into their functional 3-D shapes."
"Cells coordinate by exchanging biochemical signals, but they also hold to and push on each other to build the body structures we need to live, such as the eyes, lungs and heart. And, as it turns out, sculpting the embryo is not far from glass molding or 3-D printing.

DAVID: Getting to fertilized egg to whole new organism requires major planned processes which are all coordinated in achieving the new whole one. There is no way a Darwin process could have developed this process. It is totally unexplained from an evolutionary standpoint. It had to be designed from the beginning.

Cells coordinate or cooperate in using an amazingly flexible mechanism to create new structures as well as to repeat existing ones. This discovery suggests that from the very beginning cells had the "fundamental physical mechanism" to produce all the varieties of life in evolution’s history, and they also had the means of cooperating in order to use that mechanism. You claim that every twist and turn in the history of cellular cooperation was divinely preprogrammed or dabbled, but as it is impossible to tell the difference between automatic and autonomous behaviour, this cooperation could just as well be brought about by interaction between intelligent organisms (cells) - allowing, as always, for both mechanism and intelligence to be the work of your designer God. This ties in with the entry under "Immunity" (and thank you for both articles):

QUOTES: Macrophages are cells critical to the immune system – and new imaging reveals how they actively monitor their surroundings, searching for invaders.

The cells are highly specialised. They are the body’s frontline troops when it comes to detecting, combatting and destroying invading bacteria and other unwanted microbes.

“'This is discovery science at the cutting edge of microscopy and reveals how much we still have to learn about how cells function.'

I am struck by the parallel with ant communities – different types of ant/cell perform different functions within the colony/body, and it is the task of certain ants/cells to be the frontline troops in detecting, combating and destroying any invaders. It would be interesting to know how many people believe ants to be automatons, and if they opt for ant intelligence, to ask how they differentiate between ant and cellular behaviour.

Magic embryology: physical forces form organs

by Balance_Maintained @, U.S.A., Monday, September 10, 2018, 17:15 (1430 days ago) @ dhw

DAVID: Out of an original jumble of cells organs take shape and form guided by physical shapes and forces:
https://phys.org/news/2018-09-uncover-tissues-sculpted-embryogenesis.html

QUOTES: "'In a nutshell, we discovered a fundamental physical mechanism that cells use to mold embryonic tissues into their functional 3-D shapes."
"Cells coordinate by exchanging biochemical signals, but they also hold to and push on each other to build the body structures we need to live, such as the eyes, lungs and heart. And, as it turns out, sculpting the embryo is not far from glass molding or 3-D printing.

DAVID: Getting to fertilized egg to whole new organism requires major planned processes which are all coordinated in achieving the new whole one. There is no way a Darwin process could have developed this process. It is totally unexplained from an evolutionary standpoint. It had to be designed from the beginning.

Cells coordinate or cooperate in using an amazingly flexible mechanism to create new structures as well as to repeat existing ones. This discovery suggests that from the very beginning cells had the "fundamental physical mechanism" to produce all the varieties of life in evolution’s history, and they also had the means of cooperating in order to use that mechanism. You claim that every twist and turn in the history of cellular cooperation was divinely preprogrammed or dabbled, but as it is impossible to tell the difference between automatic and autonomous behaviour, this cooperation could just as well be brought about by interaction between intelligent organisms (cells) - allowing, as always, for both mechanism and intelligence to be the work of your designer God. This ties in with the entry under "Immunity" (and thank you for both articles):

QUOTES: Macrophages are cells critical to the immune system – and new imaging reveals how they actively monitor their surroundings, searching for invaders.

The cells are highly specialised. They are the body’s frontline troops when it comes to detecting, combatting and destroying invading bacteria and other unwanted microbes.

“'This is discovery science at the cutting edge of microscopy and reveals how much we still have to learn about how cells function.'

DHW I am struck by the parallel with ant communities – different types of ant/cell perform different functions within the colony/body, and it is the task of certain ants/cells to be the frontline troops in detecting, combating and destroying any invaders. It would be interesting to know how many people believe ants to be automatons, and if they opt for ant intelligence, to ask how they differentiate between ant and cellular behaviour.

Yes, but their function is set, it is static.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Magic embryology: physical forces form organs

by David Turell @, Monday, September 10, 2018, 21:41 (1430 days ago) @ Balance_Maintained

DAVID: Out of an original jumble of cells organs take shape and form guided by physical shapes and forces:
https://phys.org/news/2018-09-uncover-tissues-sculpted-embryogenesis.html

QUOTES: "'In a nutshell, we discovered a fundamental physical mechanism that cells use to mold embryonic tissues into their functional 3-D shapes."
"Cells coordinate by exchanging biochemical signals, but they also hold to and push on each other to build the body structures we need to live, such as the eyes, lungs and heart. And, as it turns out, sculpting the embryo is not far from glass molding or 3-D printing.

DAVID: Getting to fertilized egg to whole new organism requires major planned processes which are all coordinated in achieving the new whole one. There is no way a Darwin process could have developed this process. It is totally unexplained from an evolutionary standpoint. It had to be designed from the beginning.

Cells coordinate or cooperate in using an amazingly flexible mechanism to create new structures as well as to repeat existing ones. This discovery suggests that from the very beginning cells had the "fundamental physical mechanism" to produce all the varieties of life in evolution’s history, and they also had the means of cooperating in order to use that mechanism. You claim that every twist and turn in the history of cellular cooperation was divinely preprogrammed or dabbled, but as it is impossible to tell the difference between automatic and autonomous behaviour, this cooperation could just as well be brought about by interaction between intelligent organisms (cells) - allowing, as always, for both mechanism and intelligence to be the work of your designer God. This ties in with the entry under "Immunity" (and thank you for both articles):

QUOTES: Macrophages are cells critical to the immune system – and new imaging reveals how they actively monitor their surroundings, searching for invaders.

The cells are highly specialised. They are the body’s frontline troops when it comes to detecting, combatting and destroying invading bacteria and other unwanted microbes.

“'This is discovery science at the cutting edge of microscopy and reveals how much we still have to learn about how cells function.'

DHW I am struck by the parallel with ant communities – different types of ant/cell perform different functions within the colony/body, and it is the task of certain ants/cells to be the frontline troops in detecting, combating and destroying any invaders. It would be interesting to know how many people believe ants to be automatons, and if they opt for ant intelligence, to ask how they differentiate between ant and cellular behaviour.


Tony: Yes, but their function is set, it is static.

Agree. In studies their reaction is always the same and automatic.

Magic embryology: physical forces form organs

by David Turell @, Monday, September 10, 2018, 21:33 (1430 days ago) @ dhw

DAVID: Out of an original jumble of cells organs take shape and form guided by physical shapes and forces:
https://phys.org/news/2018-09-uncover-tissues-sculpted-embryogenesis.html

QUOTES: "'In a nutshell, we discovered a fundamental physical mechanism that cells use to mold embryonic tissues into their functional 3-D shapes."
"Cells coordinate by exchanging biochemical signals, but they also hold to and push on each other to build the body structures we need to live, such as the eyes, lungs and heart. And, as it turns out, sculpting the embryo is not far from glass molding or 3-D printing.

DAVID: Getting to fertilized egg to whole new organism requires major planned processes which are all coordinated in achieving the new whole one. There is no way a Darwin process could have developed this process. It is totally unexplained from an evolutionary standpoint. It had to be designed from the beginning.

dhw: Cells coordinate or cooperate in using an amazingly flexible mechanism to create new structures as well as to repeat existing ones. This discovery suggests that from the very beginning cells had the "fundamental physical mechanism" to produce all the varieties of life in evolution’s history, and they also had the means of cooperating in order to use that mechanism.

And who or what gave those early cells such amazing ability? Did they teach themselves? It is more logical they were designed that way.

dhw: You claim that every twist and turn in the history of cellular cooperation was divinely preprogrammed or dabbled, but as it is impossible to tell the difference between automatic and autonomous behaviour, this cooperation could just as well be brought about by interaction between intelligent organisms (cells) - allowing, as always, for both mechanism and intelligence to be the work of your designer God.

It didn't come without a designer.

dhw: This ties in with the entry under "Immunity" (and thank you for both articles):

dhw: QUOTES: Macrophages are cells critical to the immune system – and new imaging reveals how they actively monitor their surroundings, searching for invaders.

The cells are highly specialised. They are the body’s frontline troops when it comes to detecting, combatting and destroying invading bacteria and other unwanted microbes.

“'This is discovery science at the cutting edge of microscopy and reveals how much we still have to learn about how cells function.'

I am struck by the parallel with ant communities – different types of ant/cell perform different functions within the colony/body, and it is the task of certain ants/cells to be the frontline troops in detecting, combating and destroying any invaders. It would be interesting to know how many people believe ants to be automatons, and if they opt for ant intelligence, to ask how they differentiate between ant and cellular behaviour.

It is easy to see that automatic programmed action can be the answer. In ants automatic individual action has been shown in studies I have presented.

Magic embryology: physical forces form organs

by dhw, Tuesday, September 11, 2018, 13:15 (1429 days ago) @ David Turell

dhw: Cells coordinate or cooperate in using an amazingly flexible mechanism to create new structures as well as to repeat existing ones. This discovery suggests that from the very beginning cells had the "fundamental physical mechanism" to produce all the varieties of life in evolution’s history, and they also had the means of cooperating in order to use that mechanism.

DAVID: And who or what gave those early cells such amazing ability? Did they teach themselves? It is more logical they were designed that way.

Why do you ask this question, when you quote one possible answer below? We are not discussing the origin of life, but the mechanism of evolution.

dhw: You claim that every twist and turn in the history of cellular cooperation was divinely preprogrammed or dabbled, but as it is impossible to tell the difference between automatic and autonomous behaviour, this cooperation could just as well be brought about by interaction between intelligent organisms (cells) - allowing, as always, for both mechanism and intelligence to be the work of your designer God.

DAVID: It didn't come without a designer.

Belief in a single, unknown, unknowable, sourceless, eternal designer is a matter of faith, as is belief in chance.

dhw: This ties in with the entry under "Immunity" (and thank you for both articles):

dhw: QUOTES: Macrophages are cells critical to the immune system – and new imaging reveals how they actively monitor their surroundings, searching for invaders.
The cells are highly specialised. They are the body’s frontline troops when it comes to detecting, combatting and destroying invading bacteria and other unwanted microbes.
“'This is discovery science at the cutting edge of microscopy and reveals how much we still have to learn about how cells function.
'”

dhw: I am struck by the parallel with ant communities – different types of ant/cell perform different functions within the colony/body, and it is the task of certain ants/cells to be the frontline troops in detecting, combating and destroying any invaders. It would be interesting to know how many people believe ants to be automatons, and if they opt for ant intelligence, to ask how they differentiate between ant and cellular behaviour.

TONY: Yes, but their function is set, it is static.

DAVID: Agree. In studies their reaction is always the same and automatic.

You are talking of functions that are already established. Firstly, that does not explain how those functions originated, and secondly, the fulfilment even of those functions requires the ability to deal with new threats.

DAVID: It is easy to see that automatic programmed action can be the answer. In ants automatic individual action has been shown in studies I have presented.

The studies you have presented show no such thing. They show the automatic use of chemicals as ants and cells put their highly sophisticated strategies into practice, just as humans use chemicals to implement their thoughts. And the studies certainly do not prove that the highly sophisticated strategies used to cope with ever changing conditions were preprogrammed by your God 3.8 billion years ago.

Magic embryology: physical forces form organs

by David Turell @, Tuesday, September 11, 2018, 14:02 (1429 days ago) @ dhw

TONY: Yes, but their function is set, it is static.

DAVID: Agree. In studies their reaction is always the same and automatic.

dhw: You are talking of functions that are already established. Firstly, that does not explain how those functions originated, and secondly, the fulfilment even of those functions requires the ability to deal with new threats.

DAVID: It is easy to see that automatic programmed action can be the answer. In ants automatic individual action has been shown in studies I have presented.

dhw: The studies you have presented show no such thing. They show the automatic use of chemicals as ants and cells put their highly sophisticated strategies into practice, just as humans use chemicals to implement their thoughts. And the studies certainly do not prove that the highly sophisticated strategies used to cope with ever changing conditions were preprogrammed by your God 3.8 billion years ago.

You have forgotten. The study on ants travelling quotes the authors as saying the individual ants acted automatically in their roles.

Magic embryology: physical forces form organs

by dhw, Wednesday, September 12, 2018, 09:00 (1429 days ago) @ David Turell

DAVID: It is easy to see that automatic programmed action can be the answer. In ants automatic individual action has been shown in studies I have presented.

dhw: The studies you have presented show no such thing. They show the automatic use of chemicals as ants and cells put their highly sophisticated strategies into practice, just as humans use chemicals to implement their thoughts. And the studies certainly do not prove that the highly sophisticated strategies used to cope with ever changing conditions were preprogrammed by your God 3.8 billion years ago.

DAVID: You have forgotten. The study on ants travelling quotes the authors as saying the individual ants acted automatically in their roles.

There have been dozens of studies of ants, and you and I always reach opposite conclusions from them! In any case, since when did you accept the verdict of authors? Shapiro has studied bacteria and says they are intelligent, but do you take his word for it?

Magic embryology: physical forces form organs

by David Turell @, Wednesday, September 12, 2018, 14:48 (1428 days ago) @ dhw

DAVID: It is easy to see that automatic programmed action can be the answer. In ants automatic individual action has been shown in studies I have presented.

dhw: The studies you have presented show no such thing. They show the automatic use of chemicals as ants and cells put their highly sophisticated strategies into practice, just as humans use chemicals to implement their thoughts. And the studies certainly do not prove that the highly sophisticated strategies used to cope with ever changing conditions were preprogrammed by your God 3.8 billion years ago.

DAVID: You have forgotten. The study on ants travelling quotes the authors as saying the individual ants acted automatically in their roles.

dhw: There have been dozens of studies of ants, and you and I always reach opposite conclusions from them! In any case, since when did you accept the verdict of authors? Shapiro has studied bacteria and says they are intelligent, but do you take his word for it?

I analyze results and reach my own conclusions when I have a proper background of training. I accept Shapiro's findings, not his interpretation. As for ants, all I can do is quote the author's conclusions, as you do with Shapiro.

Magic embryology: placenta maintains symmetry

by David Turell @, Monday, September 17, 2018, 21:14 (1423 days ago) @ David Turell

How does the embryo maintain symmetry in growth is shown:

https://www.scientificamerican.com/article/how-mammals-maintain-symmetry-during-develop...

"Species with symmetrical body plans have been roaming the earth for about 400 million years. Human beings have long shown an intense interest in this property in our own species—

***

"Now scientists have gone a step further. Alberto Roselló-Díez, a developmental biologist currently at the Australian Regenerative Medicine Institute at Monash University, led a study of how a mouse fetus maintains symmetry as it develops. By making one of the fetus’s limbs grow more slowly than the other, the team observed how cells communicate to ultimately correct the asymmetry. No study had successfully examined this phenomenon until now.

"After a year of failed attempts, Roselló-Díez and his team created a model in mice. Borrowing a technique previously developed for modifying cells in a laboratory dish, the researchers injected into the mouse fetus’s left hind leg a type of cell that restricted the leg’s growth. They found that the cells surrounding the suppressed tissue communicated with the placenta, which then signaled the rest of the organism’s tissues—including the other hind leg—to slow their growth until the hindered limb caught up. Then, uniform growth resumed.

"Think of this process as a “three-legged race,” says Kim Cooper, a cell and developmental biologist at the University of California, San Diego, who was not involved in the study. “If one person is going faster, it’s harder to stay in sync. This placenta mechanism makes it possible for the slower one to catch up,” Cooper says.


"The study offers insight into limb development and so-called catch-up growth. But the research also raises new questions: for example, once the limb has reached the same level of growth, how does the other limb know to start growing again? “We kind of expect symmetry in our limbs,” says Adrian Halme, a cell biologist at the University of Virginia, who was also not involved with the study. “But how they achieve that symmetry is really striking.'”

Comment: In placental embryology the control systems have to be designed, when one recognizes that there is no competition for survival of the fittest as Darwin proposes. The fetus is in as safe place for its development and that development must have feedback loop controls. From my standpoint embryology is a complete refutation of Darwin style chance evolution.

Magic embryology: placenta maintains symmetry

by Balance_Maintained @, U.S.A., Tuesday, September 18, 2018, 00:42 (1423 days ago) @ David Turell

How does the embryo maintain symmetry in growth is shown:

https://www.scientificamerican.com/article/how-mammals-maintain-symmetry-during-develop...

"Species with symmetrical body plans have been roaming the earth for about 400 million years. Human beings have long shown an intense interest in this property in our own species—

***

"Now scientists have gone a step further. Alberto Roselló-Díez, a developmental biologist currently at the Australian Regenerative Medicine Institute at Monash University, led a study of how a mouse fetus maintains symmetry as it develops. By making one of the fetus’s limbs grow more slowly than the other, the team observed how cells communicate to ultimately correct the asymmetry. No study had successfully examined this phenomenon until now.

"After a year of failed attempts, Roselló-Díez and his team created a model in mice. Borrowing a technique previously developed for modifying cells in a laboratory dish, the researchers injected into the mouse fetus’s left hind leg a type of cell that restricted the leg’s growth. They found that the cells surrounding the suppressed tissue communicated with the placenta, which then signaled the rest of the organism’s tissues—including the other hind leg—to slow their growth until the hindered limb caught up. Then, uniform growth resumed.

"Think of this process as a “three-legged race,” says Kim Cooper, a cell and developmental biologist at the University of California, San Diego, who was not involved in the study. “If one person is going faster, it’s harder to stay in sync. This placenta mechanism makes it possible for the slower one to catch up,” Cooper says.


"The study offers insight into limb development and so-called catch-up growth. But the research also raises new questions: for example, once the limb has reached the same level of growth, how does the other limb know to start growing again? “We kind of expect symmetry in our limbs,” says Adrian Halme, a cell biologist at the University of Virginia, who was also not involved with the study. “But how they achieve that symmetry is really striking.'”

David Comment: In placental embryology the control systems have to be designed, when one recognizes that there is no competition for survival of the fittest as Darwin proposes. The fetus is in as safe place for its development and that development must have feedback loop controls. From my standpoint embryology is a complete refutation of Darwin style chance evolution.

And there is no other way to explain that mechanism than design. Fascinating.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Magic embryology: placenta maintains symmetry

by dhw, Tuesday, September 18, 2018, 13:33 (1422 days ago) @ Balance_Maintained

David’s comment: In placental embryology the control systems have to be designed, when one recognizes that there is no competition for survival of the fittest as Darwin proposes. The fetus is in as safe place for its development and that development must have feedback loop controls. From my standpoint embryology is a complete refutation of Darwin style chance evolution.

TONY: And there is no other way to explain that mechanism than design. Fascinating.

DAVID: (Under "plant immunity") Immunity processes are necessary from the appearance of any organism, or infections will run roughshod over then and they will not survive. Only design can do this.

Thank you for these extremely illuminating articles. I have complete sympathy with the comments you both make about design, but how would you both feel if every time you mentioned design as opposed to chance, I redressed the balance by repeating the following exchange (taken from “pointy eggs”)?

Dhw: The choice is between your magically intelligent God and magically intelligent matter, either innately intelligent – panpsychism – or having originated by chance, though in both cases evolving. “Logically I strongly doubt” any form of magic, which is why I am an agnostic, but as I keep admitting, I am wrong one way or the other.

DAVID: Granted, and logical.

DAVID: (under "Junk DNA”): There is very little junk DNA, to the disappointment of Darwinists.

Another of your mantras repeated ad nauseam, so let me repeat ad nauseam that the less junk DNA there is, the more evidence we have of natural selection at work, whereby what is useful survives, which would be to the delight of Darwinists who realized it.

Magic embryology: placenta maintains symmetry

by David Turell @, Tuesday, September 18, 2018, 15:28 (1422 days ago) @ dhw

David’s comment: In placental embryology the control systems have to be designed, when one recognizes that there is no competition for survival of the fittest as Darwin proposes. The fetus is in as safe place for its development and that development must have feedback loop controls. From my standpoint embryology is a complete refutation of Darwin style chance evolution.

TONY: And there is no other way to explain that mechanism than design. Fascinating.

DAVID: (Under "plant immunity") Immunity processes are necessary from the appearance of any organism, or infections will run roughshod over then and they will not survive. Only design can do this.

Thank you for these extremely illuminating articles. I have complete sympathy with the comments you both make about design, but how would you both feel if every time you mentioned design as opposed to chance, I redressed the balance by repeating the following exchange (taken from “pointy eggs”)?

Dhw: The choice is between your magically intelligent God and magically intelligent matter, either innately intelligent – panpsychism – or having originated by chance, though in both cases evolving. “Logically I strongly doubt” any form of magic, which is why I am an agnostic, but as I keep admitting, I am wrong one way or the other.

DAVID: Granted, and logical.

DAVID: (under "Junk DNA”): There is very little junk DNA, to the disappointment of Darwinists.

dhw: Another of your mantras repeated ad nauseam, so let me repeat ad nauseam that the less junk DNA there is, the more evidence we have of natural selection at work, whereby what is useful survives, which would be to the delight of Darwinists who realized it.

And I have repeatedly told you, that devote Darwinists have said if DNA is not junk Darwinism is dead. Their point is chance is proven by the appearance of junk which is discarded DNA due to changes as a result of natural selection. Junk, in their view, shows helter-skelter development. Perhaps they will come to accept your logic, which is not theirs. And finally do you really believe in evolution thru natural selection by competition and survival of the fittest?

Magic embryology: more junk has function

by David Turell @, Tuesday, September 18, 2018, 18:09 (1422 days ago) @ David Turell

Darwinists consider transposons as junk. It isn't:

https://phys.org/news/2018-09-genes-deletion-genome.html

"Transposons are pieces of DNA that move around in the genome, transported by enzymes called transposases that bind to them. As transposons jump around during evolution, host organisms can acquire the genes they carry and use them to gain new functions in a process known as domestication.

"Transposases from a family called PiggyBac have repeatedly been domesticated in various organisms. Although their function is poorly understood, they are known to play an essential role in the reproduction of ciliates, such as Paramecium.

***

"'We knew that PiggyMac, a domesticated transposase in the PiggyBac family, was responsible for cleaving the DNA, but what we didn't know is exactly how the removal machinery is accurately positioned at the ends of this DNA," explains lead author Julien Bischerour, researcher at the Institute for Integrative Biology of the Cell, CNRS, University of Paris-Saclay, France.

"In this study, the team identified five further groups of the PiggyBac family of transposases that work together with PiggyMac to accurately delete specific pieces of DNA in the Paramecium genome. By silencing the different domesticated PiggyBac transposases, they found that each group plays an architectural role and is essential for the movement of PiggyMac to the cell nucleus during reproduction and subsequent gene removal.

"Moreover, blocking the activity of the PiggyBac transposases caused a number of errors in the removal process. This showed that some family members retained activity, but the process became less efficient and accurate. It also revealed insights into the preferred lengths of DNA cleaved by these molecules. The fact that some sequences were mechanistically difficult to remove shed new light on potential constraints on gene deletion in Paramecium during evolution.

"'Our discovery of novel PiggyMac partners, coded by five groups of duplicated genes in the Paramecium genome, brings new insight into the removal mechanism of these non-coding sequences by transposases and deeper understanding of the machinery involved," explains senior author Mireille Bétermier, researcher at the Institute for Integrative Biology of the Cell, CNRS, University of Paris-Saclay. "Based on our work, future investigations into human domesticated transposases should take into consideration the possibility that these molecules may be involved together in the same cellular function.'"

Comment: More function found for transposions which have been considered part of non-coding 'junk' DNA by Darwinists.

Magic embryology: placenta maintains symmetry

by dhw, Wednesday, September 19, 2018, 10:09 (1422 days ago) @ David Turell

DAVID: (under "Junk DNA”): There is very little junk DNA, to the disappointment of Darwinists.

dhw: Another of your mantras repeated ad nauseam, so let me repeat ad nauseam that the less junk DNA there is, the more evidence we have of natural selection at work, whereby what is useful survives, which would be to the delight of Darwinists who realized it.

DAVID: And I have repeatedly told you, that devote Darwinists have said if DNA is not junk Darwinism is dead. Their point is chance is proven by the appearance of junk which is discarded DNA due to changes as a result of natural selection. Junk, in their view, shows helter-skelter development. Perhaps they will come to accept your logic, which is not theirs.

I know what they say. I do wish you would respond to my logic and not to theirs.

DAVID: And finally do you really believe in evolution thru natural selection by competition and survival of the fittest?

And through cooperation, and through intelligent innovation by means of a mechanism possibly designed by your God, with the possibility that if your God exists, he may occasionally have dabbled. I’m surprised you don’t know this already. I know you believe in evolution by way of a divine 3.8-billion-year-old computer programme for every non-dabbled innovation, lifestyle and natural wonder in the whole history of life, and somehow every one was geared to the production of the brain of Homo sapiens. We have spent years discussing both versions.

TONY: We would of course point to the fact that the complexity is irreducible, unless of course you can show an evolutionary pathway that could conceivably lead to that mechanism, which I can not see. Not to say it doesn't exist, but the complexity in terms of timing and chemical messaging necessary is staggering.

The complexity is indeed staggering, as is that of the single cell, but the argument that it is irreducible is not a fact. It is a theory. Behe believes it, and lots of other scientists do not. I personally am not in any position to trace an evolutionary pathway from the single cell (which you agree was the first form of material life) to all the complexities of us humans. Nor, I suspect, are you in a position to trace a pathway from pure energy to conscious energy to the spawning of its spirit son to the spawning of more spirits to the spawning of material cells to the spawning of every innovation in the history of material life. However, I can imagine that over the course of 3.8 billion years, cells used their possibly God-given intelligence to cooperate in forming increasingly complex organs and organisms.

Magic embryology: placenta maintains symmetry

by David Turell @, Wednesday, September 19, 2018, 15:00 (1421 days ago) @ dhw

DAVID: (under "Junk DNA”): There is very little junk DNA, to the disappointment of Darwinists.

dhw: Another of your mantras repeated ad nauseam, so let me repeat ad nauseam that the less junk DNA there is, the more evidence we have of natural selection at work, whereby what is useful survives, which would be to the delight of Darwinists who realized it.

DAVID: And I have repeatedly told you, that devote Darwinists have said if DNA is not junk Darwinism is dead. Their point is chance is proven by the appearance of junk which is discarded DNA due to changes as a result of natural selection. Junk, in their view, shows helter-skelter development. Perhaps they will come to accept your logic, which is not theirs.

dhw: I know what they say. I do wish you would respond to my logic and not to theirs.

Your logic implies natural selection has power which I think does not exist. Junk implies chance evolution very directly, a point they must defend. If chance disappears, what is left? If you read their papers you would understand.


DAVID: And finally do you really believe in evolution thru natural selection by competition and survival of the fittest?

dhw: And through cooperation, and through intelligent innovation by means of a mechanism possibly designed by your God, with the possibility that if your God exists, he may occasionally have dabbled. I’m surprised you don’t know this already. I know you believe in evolution by way of a divine 3.8-billion-year-old computer programme for every non-dabbled innovation, lifestyle and natural wonder in the whole history of life, and somehow every one was geared to the production of the brain of Homo sapiens. We have spent years discussing both versions.

I have my beliefs and you yours.


TONY: We would of course point to the fact that the complexity is irreducible, unless of course you can show an evolutionary pathway that could conceivably lead to that mechanism, which I can not see. Not to say it doesn't exist, but the complexity in terms of timing and chemical messaging necessary is staggering.

dhw: The complexity is indeed staggering, as is that of the single cell, but the argument that it is irreducible is not a fact. It is a theory. Behe believes it, and lots of other scientists do not. I personally am not in any position to trace an evolutionary pathway from the single cell (which you agree was the first form of material life) to all the complexities of us humans. Nor, I suspect, are you in a position to trace a pathway from pure energy to conscious energy to the spawning of its spirit son to the spawning of more spirits to the spawning of material cells to the spawning of every innovation in the history of material life. However, I can imagine that over the course of 3.8 billion years, cells used their possibly God-given intelligence to cooperate in forming increasingly complex organs and organisms.

Yes, imagine what is not logical. It is too complex as Tony describes.

Magic embryology: placenta maintains symmetry

by dhw, Thursday, September 20, 2018, 12:12 (1420 days ago) @ David Turell

DAVID: I have repeatedly told you, that devote Darwinists have said if DNA is not junk Darwinism is dead. Their point is chance is proven by the appearance of junk which is discarded DNA due to changes as a result of natural selection. Junk, in their view, shows helter-skelter development. Perhaps they will come to accept your logic, which is not theirs.

dhw: I know what they say. I do wish you would respond to my logic and not to theirs.

DAVID: Your logic implies natural selection has power which I think does not exist. Junk implies chance evolution very directly, a point they must defend. If chance disappears, what is left? If you read their papers you would understand.

My argument does not attribute any power whatsoever to natural selection. Natural selection simply means that it is natural for useful things to survive and useless things not to survive. Therefore if there is no junk, this clearly means that whatever has survived is useful and what is useless has not survived. It’s self-evident, and it presents no problem to Darwinism.

TONY: We would of course point to the fact that the complexity is irreducible, unless of course you can show an evolutionary pathway that could conceivably lead to that mechanism, which I can not see. Not to say it doesn't exist, but the complexity in terms of timing and chemical messaging necessary is staggering.

dhw: The complexity is indeed staggering, as is that of the single cell, but the argument that it is irreducible is not a fact. It is a theory. Behe believes it, and lots of other scientists do not. I personally am not in any position to trace an evolutionary pathway from the single cell (which you agree was the first form of material life) to all the complexities of us humans. Nor, I suspect, are you in a position to trace a pathway from pure energy to conscious energy to the spawning of its spirit son to the spawning of more spirits to the spawning of material cells to the spawning of every innovation in the history of material life. However, I can imagine that over the course of 3.8 billion years, cells used their possibly God-given intelligence to cooperate in forming increasingly complex organs and organisms.

DAVID: Yes, imagine what is not logical. It is too complex as Tony describes.

Firstly, I was correcting Tony: irreducible complexity is a theory not a fact. Nobody knows how all these complexities arose, and the argument that we cannot “show” an evolutionary pathway from one organ or organism to another can be applied to any theory: e.g. you cannot “show” an unknown sourceless power designing every single complexity. We ONLY have theories. May I ask if you find Tony’s “spawning” theory logical?

Magic embryology: placenta maintains symmetry

by David Turell @, Thursday, September 20, 2018, 18:01 (1420 days ago) @ dhw

DAVID: Your logic implies natural selection has power which I think does not exist. Junk implies chance evolution very directly, a point they must defend. If chance disappears, what is left? If you read their papers you would understand.

dhw: My argument does not attribute any power whatsoever to natural selection. Natural selection simply means that it is natural for useful things to survive and useless things not to survive. Therefore if there is no junk, this clearly means that whatever has survived is useful and what is useless has not survived. It’s self-evident, and it presents no problem to Darwinism.

Atheistic Darwinism relies on the truth of chance mutation causing an advance in fitness. In their view chance mutations that are good are rare, but they attach to the DNA and therefore an enormous amount of useless DNA proves their point! It is all mindless chance. And they have stated, without junk, Darwin is dead!


TONY: We would of course point to the fact that the complexity is irreducible, unless of course you can show an evolutionary pathway that could conceivably lead to that mechanism, which I can not see. Not to say it doesn't exist, but the complexity in terms of timing and chemical messaging necessary is staggering.

dhw: The complexity is indeed staggering, as is that of the single cell, but the argument that it is irreducible is not a fact. It is a theory. Behe believes it, and lots of other scientists do not. I personally am not in any position to trace an evolutionary pathway from the single cell (which you agree was the first form of material life) to all the complexities of us humans. Nor, I suspect, are you in a position to trace a pathway from pure energy to conscious energy to the spawning of its spirit son to the spawning of more spirits to the spawning of material cells to the spawning of every innovation in the history of material life. However, I can imagine that over the course of 3.8 billion years, cells used their possibly God-given intelligence to cooperate in forming increasingly complex organs and organisms.

DAVID: Yes, imagine what is not logical. It is too complex as Tony describes.

dhw: Firstly, I was correcting Tony: irreducible complexity is a theory not a fact. Nobody knows how all these complexities arose, and the argument that we cannot “show” an evolutionary pathway from one organ or organism to another can be applied to any theory: e.g. you cannot “show” an unknown sourceless power designing every single complexity. We ONLY have theories. May I ask if you find Tony’s “spawning” theory logical?

Tony and I use different reference sources, obviously, Bible vs. pure science. we generally agree on a designer, and I can't fault his theories from his sources as illogical.

Magic embryology: placenta maintains symmetry

by dhw, Friday, September 21, 2018, 15:31 (1419 days ago) @ David Turell

DAVID: Atheistic Darwinism relies on the truth of chance mutation causing an advance in fitness. In their view chance mutations that are good are rare, but they attach to the DNA and therefore an enormous amount of useless DNA proves their point! It is all mindless chance. And they have stated, without junk, Darwin is dead!

You are behind the times. Here is Dawkins’ volte face:

Egnorance: Richard Dawkins on junk DNA in 2009. …
http://www.egnorance.blogspot.com/2013/02/richard-dawkins-on-junk-dna-in-2009...

Dawkins in 2009:
"It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene -- a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something -- unless he was deliberately setting out to fool us...
Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.
"

The 2009 iteration of Richard Dawkins asserts confidently that most of the genome is junk, just as Darwinism predicts! What an embarrassment to Darwin doubters!

Dawkins in 2012:
"I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that's awkward for Darwinism. Quite the contrary it's exactly what a Darwinist would hope for, to find usefulness in the living world.... (dhw's bold)

Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something. What it's doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals -- mice and men have the same number, roughly speaking, of protein-coding genes and that's always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that's calling them into action is the rest [of the genome] which had previously been written off as junk."


TONY: The options for DHW's question always seem to devolve to:
Is it more plausible that:
• A) The laws of govern all energy, matter, and information, spontaneously spring into existence followed by, or perhaps part and parcel with, all matter becoming simultaneously intelligent and then said intelligent matter communicated and designed, all life, with its vastly more complex systems, and so on.
• B) A single intellect emerged once out of eternal form of energy, taking time beyond measure to become capable of bringing another single entity into existence, both of which were energy and information only (non-material). The two intelligences over time, worked together to develop/birth/spawn more similar to themselves (non-material), eventually learning to manifest energy and information into the material universe we know.
• C) Flip a coin...there was no intelligence, guidance, planning, or outside influence at all. Stuff just happened.

A is inaccurate. My hypothesis is that energy and matter are the eternal first cause, constantly giving rise to endless combinations. Intelligence “somehow” evolved through these changes, just as your first cause God energy “somehow” simply has his intelligence. If you want to pin me down, I actually find it impossible to believe that all matter is intelligent, but I do not find the idea that some matter evolved intelligence any more or any less plausible than that first cause energy already had intelligence. From the moment when matter intelligently coalesced to form the first living organisms, your account is correct.

I do not accept C. I believe that stuff happened because of intelligence, but I do not know whether that intelligence was there from the beginning (your God) or evolved out of impersonal energy and materials eternally entering into new combinations.

dhw: (under "pointy eggs") First cause unconsciousness somehow evolving consciousness is just as logical or illogical or believable or unbelievable as first cause consciousness somehow just being there, but they are both first causes.

DAVID: Agreed, and you can't pick one.

You’ve got it.

Xxxxxx

Magic embryology: placenta maintains symmetry

by Balance_Maintained @, U.S.A., Friday, September 21, 2018, 20:18 (1419 days ago) @ dhw

DAVID: Atheistic Darwinism relies on the truth of chance mutation causing an advance in fitness. In their view chance mutations that are good are rare, but they attach to the DNA and therefore an enormous amount of useless DNA proves their point! It is all mindless chance. And they have stated, without junk, Darwin is dead!

You are behind the times. Here is Dawkins’ volte face:

Egnorance: Richard Dawkins on junk DNA in 2009. …
http://www.egnorance.blogspot.com/2013/02/richard-dawkins-on-junk-dna-in-2009...

Dawkins in 2009:
"It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene -- a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something -- unless he was deliberately setting out to fool us...
Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.
"

The 2009 iteration of Richard Dawkins asserts confidently that most of the genome is junk, just as Darwinism predicts! What an embarrassment to Darwin doubters!

Dawkins in 2012:
"I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that's awkward for Darwinism. Quite the contrary it's exactly what a Darwinist would hope for, to find usefulness in the living world.... (dhw's bold)

Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something. What it's doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals -- mice and men have the same number, roughly speaking, of protein-coding genes and that's always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that's calling them into action is the rest [of the genome] which had previously been written off as junk."


TONY: The options for DHW's question always seem to devolve to:
Is it more plausible that:
• A) The laws of govern all energy, matter, and information, spontaneously spring into existence followed by, or perhaps part and parcel with, all matter becoming simultaneously intelligent and then said intelligent matter communicated and designed, all life, with its vastly more complex systems, and so on.
• B) A single intellect emerged once out of eternal form of energy, taking time beyond measure to become capable of bringing another single entity into existence, both of which were energy and information only (non-material). The two intelligences over time, worked together to develop/birth/spawn more similar to themselves (non-material), eventually learning to manifest energy and information into the material universe we know.
• C) Flip a coin...there was no intelligence, guidance, planning, or outside influence at all. Stuff just happened.

DHW: A is inaccurate. My hypothesis is that energy and matter are the eternal first cause, constantly giving rise to endless combinations. Intelligence “somehow” evolved through these changes, just as your first cause God energy “somehow” simply has his intelligence. If you want to pin me down, I actually find it impossible to believe that all matter is intelligent, but I do not find the idea that some matter evolved intelligence any more or any less plausible than that first cause energy already had intelligence. From the moment when matter intelligently coalesced to form the first living organisms, your account is correct.

I do not accept C. I believe that stuff happened because of intelligence, but I do not know whether that intelligence was there from the beginning (your God) or evolved out of impersonal energy and materials eternally entering into new combinations.

I think energy always existed. I think the entity referred to as God, is comprised of that energy. However, I do not assert that his intelligence has always existed. The energy itself is eternal, and in that sense, God is eternal, having neither a beginning nor an end. However, I am perfectly ok with the concept that the information that comprises his intellect developed slowly over unimaginably long periods of time.

dhw: (under "pointy eggs") First cause unconsciousness somehow evolving consciousness is just as logical or illogical or believable or unbelievable as first cause consciousness somehow just being there, but they are both first causes.

DAVID: Agreed, and you can't pick one.

You’ve got it.

Xxxxxx

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Magic embryology: placenta maintains symmetry

by David Turell @, Friday, September 21, 2018, 21:00 (1419 days ago) @ Balance_Maintained

DHW: A is inaccurate. My hypothesis is that energy and matter are the eternal first cause, constantly giving rise to endless combinations. Intelligence “somehow” evolved through these changes, just as your first cause God energy “somehow” simply has his intelligence. If you want to pin me down, I actually find it impossible to believe that all matter is intelligent, but I do not find the idea that some matter evolved intelligence any more or any less plausible than that first cause energy already had intelligence. From the moment when matter intelligently coalesced to form the first living organisms, your account is correct.

I do not accept C. I believe that stuff happened because of intelligence, but I do not know whether that intelligence was there from the beginning (your God) or evolved out of impersonal energy and materials eternally entering into new combinations.


Tony: I think energy always existed. I think the entity referred to as God, is comprised of that energy. However, I do not assert that his intelligence has always existed. The energy itself is eternal, and in that sense, God is eternal, having neither a beginning nor an end. However, I am perfectly ok with the concept that the information that comprises his intellect developed slowly over unimaginably long periods of time.

I'm of the opinion that God is eternal energy and always had His knowledge and there have been more than this universe in the past, in that universes stretch back to a previous eternity. We are in the current iteration.

Magic embryology: placenta maintains symmetry

by Balance_Maintained @, U.S.A., Saturday, September 22, 2018, 00:21 (1419 days ago) @ David Turell

DHW: A is inaccurate. My hypothesis is that energy and matter are the eternal first cause, constantly giving rise to endless combinations. Intelligence “somehow” evolved through these changes, just as your first cause God energy “somehow” simply has his intelligence. If you want to pin me down, I actually find it impossible to believe that all matter is intelligent, but I do not find the idea that some matter evolved intelligence any more or any less plausible than that first cause energy already had intelligence. From the moment when matter intelligently coalesced to form the first living organisms, your account is correct.

I do not accept C. I believe that stuff happened because of intelligence, but I do not know whether that intelligence was there from the beginning (your God) or evolved out of impersonal energy and materials eternally entering into new combinations.


Tony: I think energy always existed. I think the entity referred to as God, is comprised of that energy. However, I do not assert that his intelligence has always existed. The energy itself is eternal, and in that sense, God is eternal, having neither a beginning nor an end. However, I am perfectly ok with the concept that the information that comprises his intellect developed slowly over unimaginably long periods of time.


David: I'm of the opinion that God is eternal energy and always had His knowledge and there have been more than this universe in the past, in that universes stretch back to a previous eternity. We are in the current iteration.

I could even go with the first part of that, though the answer is likely moot, even if we did have it. I don't think the time scales are fathomable really by humans in any significant way.

However, the latter part I have a harder time with. I see evidence of a designer everywhere. What evidence is there for prior universes?

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Magic embryology: placenta maintains symmetry

by David Turell @, Saturday, September 22, 2018, 15:51 (1418 days ago) @ Balance_Maintained

DHW: A is inaccurate. My hypothesis is that energy and matter are the eternal first cause, constantly giving rise to endless combinations. Intelligence “somehow” evolved through these changes, just as your first cause God energy “somehow” simply has his intelligence. If you want to pin me down, I actually find it impossible to believe that all matter is intelligent, but I do not find the idea that some matter evolved intelligence any more or any less plausible than that first cause energy already had intelligence. From the moment when matter intelligently coalesced to form the first living organisms, your account is correct.

I do not accept C. I believe that stuff happened because of intelligence, but I do not know whether that intelligence was there from the beginning (your God) or evolved out of impersonal energy and materials eternally entering into new combinations.


Tony: I think energy always existed. I think the entity referred to as God, is comprised of that energy. However, I do not assert that his intelligence has always existed. The energy itself is eternal, and in that sense, God is eternal, having neither a beginning nor an end. However, I am perfectly ok with the concept that the information that comprises his intellect developed slowly over unimaginably long periods of time.


David: I'm of the opinion that God is eternal energy and always had His knowledge and there have been more than this universe in the past, in that universes stretch back to a previous eternity. We are in the current iteration.


Tony: I could even go with the first part of that, though the answer is likely moot, even if we did have it. I don't think the time scales are fathomable really by humans in any significant way.

However, the latter part I have a harder time with. I see evidence of a designer everywhere. What evidence is there for prior universes?

My statement is based on First Cause as a concept. Nothingness cannot become somethingness. Therefore a creating God is eternal. As for evidence of a previous universe, that is not possible since we are fully contained in this one. So only God contains the evidence, and I don't see that He will impart it to us.

Magic embryology: placenta invades Mother

by David Turell @, Tuesday, December 04, 2018, 15:18 (1345 days ago) @ David Turell

The entire process is magical. the Mother's uterus is attacked but not harmed and as mentioned before the placenta has effects on the growing fetus:

https://www.nytimes.com/2018/12/03/health/placenta-pregnancy-health.html?emc=edit_th_18...

"The placenta may be dismissed as “afterbirth,” deemed an afterthought in discussions about pregnancy and even relegated, literally, to the trash bin. But at long last it is beginning to get its due.

"In the past three weeks, scientists have published three significant studies of this ephemeral organ. One gave a detailed analysis of all the genes expressed, or converted into functioning proteins, in the placenta; another experimented with a way to silence that expression when it causes trouble. In the third, researchers created mini-placentas, three-dimensional clusters of cells, or organoids, that mimic the real thing in the lab, and can be used as models for studying it.

***

“'The missing link between complications during pregnancy and development of the fetal brain has been hiding in plain sight for a long time,” said Dr. Daniel R. Weinberger, director of the Lieber Institute for Brain Development in Baltimore, Md. “It’s the placenta.”

"During the course of human pregnancy, the placenta grows from a few cells into an organ weighing more than a pound. It often is compared to an aggressive cancer. But a more apt metaphor might be a military invasion, as 90 percent of the placenta is made up of cells not from the mother but from the fetus.

"Early in gestation, the fertilized egg implants itself in the mother’s uterine lining and sends out a few cells to breach it. These foot soldiers produce proteins that disarm the mother’s defenses, destroy the smooth muscles that line her blood vessels and dilate and redirect the vessels to feed the embryo. As the placental beachhead grows, its cells specialize to do the work of heart, lungs, liver and kidneys until the fetus can fend for itself. Groups of cells exchange oxygen for carbon dioxide; provide nutrients and hormones; protect the fetus from harmful stress, germs and chemicals; and remove waste.

"This incursion fails as often as 20 percent of the time, and when it does, it can cause severe complications for the fetus, at birth and afterward. It may also forecast trouble for the mother’s health later in life: pre-eclampsia can portend heart disease and stroke, and gestational diabetes can signal later obesity and metabolic disease."

Comment: This has to be designed. A foreign system, 90% fetal, invades the Mother like a cancer, and yet they cooperate. This is an arrangement that cannot ever be stepwise, but must be carefully designed. God at work.

Magic embryology: placental role in diet and oxygen

by David Turell @, Saturday, January 19, 2019, 20:03 (1299 days ago) @ David Turell

If diet is poor and oxygen is low, the placenta makes adjustments:

https://medicalxpress.com/news/2019-01-placentas-mothers-poor-diets-oxygen.html

"The placenta develops during pregnancy and connects the developing baby to the mother. It serves as the lungs, kidneys, gut and liver for growing babies and carries oxygen and nutrients to the fetus whilst secreting hormones and discarding waste. (my bold)

***

"Dr. Sferruzzi-Perri said: "The study analysed how mitochondria in the placenta may alter their function to support both the needs of the placenta and the rapidly growing fetus during a healthy pregnancy, and when the mother is challenged by a less desirable environment.

"'We found that in the placenta, mitochondria have a remarkable ability to adapt and compensate for environmental impacts such as when women are living in low oxygen areas at high altitude and not eating enough of a healthy diet during pregnancy."

"Changing lifestyles in society which see women consuming nutritionally deficient diets during pregnancy can cause pregnancy complications and living at high altitudes above 2500m in places such as Bolivia, Peru, Tibet and Ethiopia restricts oxygen levels. It is estimated that around two per cent of the human population—140 million people—live in areas with low oxygen.

***

"The team of scientists introduced challenges—known as hypoxic conditions—in the laboratory. They used the mouse as a model, as its placenta develops and functions in a similar way to humans, looking at how the placenta and their mitochondria reacted and what impact this had on the growth of the fetus.

"Dr. Sferruzzi-Perri explained: "Mitochondria in the placenta work out how to use oxygen and nutrients in the most efficient way so there is still sufficient for transfer to the fetus even in challenged pregnancies. When the placenta cannot compensate for the challenges then this can lead complications such as fetal growth restriction."

"'We know that there is a lasting impact on the health of babies born with fetal growth restriction because organs and tissues like the heart, pancreas, muscles, and liver, are very sensitive when they are developing in the womb. If those organs don't grow properly they are more likely to malfunction in later life."

"The aim of the study—the first of its kind—was to understand what is required for a healthy placenta to perform its vital functions during pregnancy.

"Dr. Sferruzzi-Perri added: "Our findings show mitochondria are really important determinants of placental function and support of fetal growth. The next step would be to target mitochondria in the placenta to alter their function and improve pregnancy success in women where we know the outcome might be poor."

"When babies are born with fetal growth restriction, the team had previously found the buffering mechanism of the placenta was insufficient during pregnancy."

Comment: The evolution of uterine/placental birth was a tremendous advance in reproduction and I know of no research explaining how it might have evolved. Note my bold. The placenta has multiple functions to ensure proper survival of the developing fetus. It had to appear designed for all its functions when uterine pregnancy appeared. Only a designer can create this type of evolutionary advance.

Magic embryology: placental role in diet and oxygen

by dhw, Sunday, January 20, 2019, 12:30 (1298 days ago) @ David Turell

QUOTES: "Dr. Sferruzzi-Perri said: "The study analysed how mitochondria in the placenta may alter their function to support both the needs of the placenta and the rapidly growing fetus during a healthy pregnancy, and when the mother is challenged by a less desirable environment. (dhw’s bold)

"'We found that in the placenta, mitochondria have a remarkable ability to adapt and compensate for environmental impacts such as when women are living in low oxygen areas at high altitude and not eating enough of a healthy diet during pregnancy." (dhw’s bold)

"Dr. Sferruzzi-Perri explained: "Mitochondria in the placenta work out how to use oxygen and nutrients in the most efficient way so there is still sufficient for transfer to the fetus even in challenged pregnancies.." (dhw’s bold)

DAVID: The evolution of uterine/placental birth was a tremendous advance in reproduction and I know of no research explaining how it might have evolved. [The placenta] had to appear designed for all its functions when uterine pregnancy appeared. Only a designer can create this type of evolutionary advance.

We need to be clear about the subject of design. Do you mean that your God included placenta changes in the complete set of instructions given to the first cells but not included in the passive code of DNA, or that he personally dabbled each variation? Or could it be that he gave all cells/cell communities the autonomous ability to work out their own variations?
Xxxx

DAVID’s comment (under plant root branching controls:) Life' s processes always require specifically design protein molecules. I have previously entered research on root receptors that guide where to grow for water and nutrients. Always a series of protein molecules reacting automatically in a standardized progression.

But since DNA is a passive code, and you agree that the organism uses DNA to make the proteins it requires, do you not think it possible that your God gave plant cells the autonomous ability to make the proteins they require – or were these preprogrammed or divinely dabbled. (Please bear in mind that were are talking about how all these processes arose in the first place: once a successful system has been established, of course it will be repeated automatically until things go wrong and there are new problems to solve.)

Under Hermit crab penises

QUOTE: He hypothesized that larger penises may have evolved in this species, which uses extensively remodeled shells and for which sex is particularly dangerous, to minimize the distance they need to come out of their shells in order to mate.

So what do you reckon? Your God, in order to be able to design Homo sapiens, 1) preprogrammed the crab’s large penis 3.8 billion years ago (but not in the DNA, which is simply a passive code); 2) did a dabble?;or 3) do you think it’s possible that he gave the cell communities of the crab the autonomous ability to enlarge its penis in order to improve its chances of survival?

Magic embryology: information and instructions

by David Turell @, Monday, January 28, 2019, 23:07 (1290 days ago) @ dhw

A new study on how the fertilized egg gets itself started:

https://medicalxpress.com/news/2019-01-kick-starting-genome-early.html

"After the fertilisation of an egg cell, two become one; two sets of genetic information combine to form a genome. We can think of the egg and sperm as information capsules with stored instructions for starting a new life, but post fertilisation, what kick starts the interpretation of these instructions? (my bold)

***

"Poetically, waking up the genome occurs through events called the minor wave and major wave. Researchers knew that a transcription factor (a protein that binds DNA to promote expression) called Dux activated a range of genes in the second major wave but not what initiated Dux or the genome activation in the first place.

"'Genome activation is the first things that the embryo has to do," says Dr. Melanie Eckersley-Maslin, a postdoctoral researcher at the Babraham Institute. "Despite it being crucial to the formation of the embryo, we know surprisingly little about it. The 2C-like system provides an experimental approximation of those very early embryo cells and allows us to use the full arsenal of research techniques available to tease apart what is happening."

The researchers started by screening for factors that increased the number of the rare 2C-like cells in a population of mouse embryonic stem cells—indicating positive factors that were able to promote genome activation. The researchers identified two proteins called Development Pluripotency Associated 2 (Dppa2) and 4 (Dppa4).

"Looking at what we have discovered about Dppa2 and Dppa4 they fit the profile of being responsible for kick-starting the expression of the new genome," explains Dr. Eckersley-Maslin. "The proteins are already present in the egg, so already there before the new embryo is formed, and if we delete the Dppa2 and 4 genes from the genome, we see a loss of 2C-like cells and the loss of the Dux-initiated wave of genome expression."

The model proposed by the research connects genome activation with epigenetic reprogramming of the cells that eventually form the sperm and eggs, forming a connected chain of events that secures Dppa2 and 4 expression in egg cells ready to initiate genome activation when the time is right. (my bold)


Comment: It is all set to start making a fetus as these proteins act automatically as noted by the bolds above. Information and instructions ready to go.

Magic embryology: growing mouse kidney in rats

by David Turell @, Tuesday, February 05, 2019, 18:03 (1282 days ago) @ David Turell

Using mouse stem cells and some lab tricks:

https://medicalxpress.com/news/2019-02-closer-made-to-order-human-kidneys.html

"But researchers have been working on ways to grow healthy organs outside the human body. One such method, called blastocyst complementation, has already produced promising results. Researchers take blastocysts, the clusters of cells formed several days after egg fertilization, from mutant animals missing specific organs and inject them with stem cells from a normal donor, not necessarily of the same species. The stem cells then differentiate to form the entire missing organ in the resulting animal. The new organ retains the characteristics of the original stem cell donor, and can thus potentially be used in transplantation therapy.

***

"After implantation into pseudo-pregnant rats, the complemented blastocysts matured into normal fetuses. Remarkably, more than two thirds of the resulting rat neonates contained a pair of kidneys derived from the mouse stem cells. Further screening showed that all of the kidneys were structurally intact, and at least half could potentially produce urine.

"'Our findings confirm that interspecific blastocyst complementation is a viable method for kidney generation," says study corresponding author Masumi Hirabayashi. "In the future, this approach could be used to generate human stem cell-derived organs in livestock, potentially extending the lifespan and improving the quality of life of millions of people worldwide."

"In summary, he chronic global shortage of donor kidneys leaves many end-stage renal disease patients reliant on continued dialysis treatment. To address the donor kidney shortage, a team led by researchers at the National Institute for Physiological Sciences in Japan attempted to grow mouse kidneys inside rats using transplanted stem cells. The resulting kidneys appeared to be functional, providing proof-of-concept validation that this approach could be used to generate human kidneys inside livestock. "

Comment: The stem cells (blastocyst cells) must follow exact directions in their genomes to make perfectly functioning kidneys. This is the expectation of the authors of this study. True automaticity of cells following instructions to make perfectly functional kidneys. These cells cannot decide to anything different, but if there is an abnormal stress they must ignore it or, if they adapt in some way, they may produce an anomaly that is not functional.

All the processes of life must follow instructions or result in an aberration that is not viable. This is the theory behind my position on automaticity.

Magic embryology: special macrophages thin heart valves

by David Turell @, Sunday, February 24, 2019, 01:47 (1264 days ago) @ David Turell

How heart valves are made so thin is discovered. It shows how complex embryological processes are:

https://www.sciencedaily.com/releases/2019/02/190221130250.htm

"UCLA researchers have identified for the first time the origin of an immune cell that plays a critical role in the formation of healthy heart valves.

"'Ever since we discovered that the heart tube produces some blood progenitor cells, we have been trying to figure out why," Nakano said. "Blood progenitor cells are generated in much greater numbers in other parts of the developing embryo. Having the heart tube produce blood progenitor cells is like having a small, not-very-productive factory just down the street from a larger, more productive factory. If both factories produce the same thing -- in this case blood progenitor cells -- why not just have one big factory?"

***

"Macrophages ("big eaters" in Greek) reside in tissues and travel around the body in the blood, seeking out and consuming harmful, damaged or unnecessary cells. Previous research had shown that macrophages exist in the heart valves, but Nakano's team was the first to discover their role there: eating up excess cells to make the valves paper-thin and hyper-efficient. This process begins in the developing embryo and continues after birth; the macrophages remain in the valves to help keep them in shape throughout the lifecycle.
"Macrophages were known to exist in heart valves, but nobody had nailed down when they arrived there and where they came from until we watched them develop in the heart tube," Nakano said.

"To test just how essential heart-derived macrophages are to valve formation and remodeling, the scientists blocked their production to see if it had any effect. They found that the other macrophages in the body -- those from circulating blood -- traveled to the heart, but they weren't very effective at remodeling the valves. Without the heart-derived macrophages, the heart valves remained thick and unwieldy.

"'This showed us that the macrophages that are generated in the heart tube are particularly adept at eating up excess tissue," Nakano said. "This makes them essential not just to heart valve formation, but to heart valve maintenance throughout life.'"

Comment: Early evolution had fluids moving around body cavities due to organ movements such as muscles. Later as heart tubes developed they contracted to move fluid. Eventually those tubes were twisted and eventually formed chambers to manage a back and forth circulation . Valves had to be added to control flow in one circular direction, with the delicate valves leaflets paper thin to move very quickly because the heart beats are timed by the second. Most human pulses average rest rates that are an average 70 per minute. I can't image all of this complexity happened by chance.

Magic embryology: special chemicals used to signal

by David Turell @, Sunday, March 03, 2019, 01:28 (1257 days ago) @ David Turell

In addition to physical stresses between growing tissues there are chemical signals:

https://phys.org/news/2019-03-embryos-proteins.html

"How cells in developing embryos communicate depends a great deal on context, according to scientists at Rice University.

"They found that a protein signaling pathway known as WNT and its interactions are far more dynamic than once thought as the response of different cell types to the same signals is dramatically different.

"Researchers already knew that WNT, which carries messages across the cell membrane, is central to the early development of organisms and later helps stabilize cells in adults. Now they're gaining a more complete picture of the pathway's function.

"Near the start of life, WNT signals provide key developmental cues from outside the cell, according to Rice bioscientist Aryeh Warmflash and graduate student and lead author Joseph Massey. These extracellular WNT signals help direct cell differentiation by triggering beta-catenin proteins that affect gene expression in the cell's nucleus.

"They found the WNT pathway not only listens for signals from a wider range of triggers than previously known but that while it is influencing the identities of new cell types during embryonic development, those new cell types are themselves beginning to change how they interpret WNT signals.

"'To do that in the right place and at the right time, they have to have some kind of positional timing cues, and share information with each other," he said

***

"'The WNT pathway is different in stem cells and differentiated cells. Cells probably tune the dynamics of the WNT pathway to make it perform different functions in different contexts."

"'We found that the signaling dynamics—how the cells respond to signaling cues—in pluripotent cells is very different from what happens in some of the other cell types we looked at," Massey said. "Not only that, whenever pluripotent cells begin to differentiate to a type of cells called the primitive streak, the response to the signal is also very different."
The primitive streak is a structure that forms early in the development of an embryo, establishes the organism's bilateral symmetry and serves as the focal point of gastrulation, where multiple layers of differentiation begin.

"'Our research highlights for the first time for this signaling pathway that the dynamics, the way the cells interpret these signals, is very much context-dependent," Massey said.

"The researchers investigated some of the causes of these changing dynamics. They found that by altering levels of activin and bone morphogenetic protein (BMP), both members of the TGF beta "superfamily" of growth factor proteins, they were able to change the dynamics of beta-catenin signaling. As TGFb factors are also involved in cellular differentiation, this is a possible cause of the changing dynamics of WNT signaling during development, Warmflash said.
The experiments demonstrated one way that beta-catenin signaling in stem cells adapts to a constantly changing environment.

"'What's interesting is that all of these developmental pathways are, throughout the course of an organism's development, recycled for different roles," Massey said. "At the beginning, the WNT signaling pathway is perhaps specifying different tissues to become the right type of tissue in the right place. Later on, it's maintaining homeostasis or other processes in the adult.


"'What natural pathways do is much more intricate and complex than anything people have been able to build," he said. "If you can understand it, you can use it.'" (my bold)

Comment: Embryo development is highly complex as this study shows. Note my bold. Fetal formation is smarter than we are. Not by chance.

Magic embryology: placental role in pregnancy

by David Turell @, Wednesday, February 05, 2020, 22:40 (917 days ago) @ David Turell

Another view of this complex organ that is the only one ever finally dispensed with:

https://www.mercatornet.com/features/view/together-baby-forever-baby/23266

"The placenta is amazing. Well, for one, it is the only organ made in cooperation by two people. It is made from the growing baby’s tissue and the mother’s tissue together. Therefore, the placenta is known as a ‘feto-maternal’ organ. It is the first time that mother and baby come together to do something in cooperation.

"The placenta, as many of your readers know, is the organ through which the baby and mother interface. This name ‘placenta’ is derived from the Latin word for a type of cake, as it is a flat organ and averages about a pound in weight. It is attached to the wall of the mother’s uterus and is connected to the growing baby by his or her umbilical cord. The placenta is the only purposely transient organ in human beings.

"It also is amazing because it functions as many organs in one. The placenta helps the prenatal child get rid of waste, helps provide nutrition and also produces hormones and protects the baby against infection. The placenta is acting like a lung, kidney, gastrointestinal tract and the endocrine and immune system. Pretty amazing for this one organ to have so many important functions.

***

"‘The placenta is arguably one of the most important organs in the body.’ A healthy placenta is not only crucial for healthy development of the prenatal child, but also affects the health of the child and mother for years to come.

***

"In science, microchimerism refers to the presence of a small population of genetically distinct and separately derived cells within an individual. In pregnancy, small amounts of cells travel across the placenta. Some of these cells are the prenatal child’s cells that travel from the baby into her mother, and some cells also pass from the mother into her child. The cells from the prenatal child into her mother are pluripotent, which means they haven’t yet differentiated into the type of cell specific for one organ or tissue in particular. These cells find their way into mother’s tissue and start acting like the tissue in which they find themselves. This process is known as feto-maternal microchimerism.

Interviewer question: "That is fascinating! In what ways can these fetal cells protect the mother in later life – or put her at risk?

"Their full impact is still being understood, but some of these cells have been hypothesized to help mom in the time after birth and also for years to come. For example, these cells have been found in Caesarean sections incisions helping to make collagen to help mom heal after a surgical delivery. These cells have also been found in the maternal breast and have been hypothesized to help reduce mom’s risk of breast cancer in her later years.

"The ’gift’ of these cells from the baby, entering into mom’s body and helping her heal and protecting her from cancer, is amazing to think of and really challenges our ideas of people as autonomous beings. In reality, many human beings carry remnants of other human beings in their body. These cells may even play a part in how future siblings are spaced.

"What is also interesting, these cells that enter the mother are allowed to survive and are not attacked by the mother’s immune system, even though they are somewhat ‘foreign’. This again speaks to a cooperation, at the cellular level, between mother and child. And it would be one thing if these cells were inert and existed as a gift of sorts, from the child in the mother, but to think of these cells in some ways benefiting the health of the mother really speaks to a radical mutuality at the cellular level between two people that only serves to enhance our understanding of the maternal-child bond."

Comment: A very intricate organ which could not have been invented step by step, as the problems it handles require such complex and delicate processes. This had to be designed all at once or us placental mammals would not be here. I have had one case where the placenta overcame the normal controls and killed the mother. Since the placenta invades the wall of the uterus like a cancer would, tight controls are very necessary. Apparently this patient's controls ere weakened.

Magic embryology: placental forms before embryo

by David Turell @, Thursday, September 24, 2020, 20:39 (685 days ago) @ David Turell

Special cells in the earliest cell divisions are set apart:

https://phys.org/news/2020-09-placental-days-embryo.html


"In a study published today in the journal Nature, researchers looked at the biological pathways active in human embryos during their first few days of development to understand how cells acquire different fates and functions within the early embryo.

"They observed that shortly after fertilization as cells start to divide, some cells start to stick together. This triggers a cascade of molecular events that initiate placental development. A subset of cells change shape, or polarize, and this drives the change into a placental progenitor cell—the precursor to a specialized placenta cell—that can be distinguished by differences in genes and proteins from other cells in the embryo.

***

"The team also examined the same developmental pathways in mouse and cow embryos. They found that while the mechanisms of later stages of development differ between species, the placental progenitor is still the first cell to differentiate.

"'We've shown that one of the earliest cell decisions during development is widespread in mammals, and this will help form the basis of future developmental research...'"

Comment: Such a complex arrangement must be designed. Not by chance!

Magic embryology: placenta maintains symmetry

by David Turell @, Friday, September 21, 2018, 20:36 (1419 days ago) @ dhw

DAVID: Atheistic Darwinism relies on the truth of chance mutation causing an advance in fitness. In their view chance mutations that are good are rare, but they attach to the DNA and therefore an enormous amount of useless DNA proves their point! It is all mindless chance. And they have stated, without junk, Darwin is dead!

dhw: You are behind the times. Here is Dawkins’ volte face:

Egnorance: Richard Dawkins on junk DNA in 2009. …
http://www.egnorance.blogspot.com/2013/02/richard-dawkins-on-junk-dna-in-2009...

Dawkins in 2009:
"It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene -- a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something -- unless he was deliberately setting out to fool us...
Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes.
"

The 2009 iteration of Richard Dawkins asserts confidently that most of the genome is junk, just as Darwinism predicts! What an embarrassment to Darwin doubters!

Dawkins in 2012:
"I have noticed that there are some creationists who are jumping on [the ENCODE results] because they think that's awkward for Darwinism. Quite the contrary it's exactly what a Darwinist would hope for, to find usefulness in the living world.... (dhw's bold)

Whereas we thought that only a minority of the genome was doing something, namely that minority which actually codes for protein, and now we find that actually the majority of it is doing something. What it's doing is calling into action the protein-coding genes. So you can think of the protein-coding genes as being sort of the toolbox of subroutines which is pretty much common to all mammals -- mice and men have the same number, roughly speaking, of protein-coding genes and that's always been a bit of a blow to self-esteem of humanity. But the point is that that was just the subroutines that are called into being; the program that's calling them into action is the rest [of the genome] which had previously been written off as junk."

I've read all Dawkins ' stuff. A quick backtrack from his previous views. Graur and Moran are still active with others claiming the death of junk kills Darwin.

Magic embryology: placenta maintains symmetry

by Balance_Maintained @, U.S.A., Thursday, September 20, 2018, 22:35 (1420 days ago) @ dhw

HW: Firstly, I was correcting Tony: irreducible complexity is a theory not a fact. Nobody knows how all these complexities arose, and the argument that we cannot “show” an evolutionary pathway from one organ or organism to another can be applied to any theory: e.g. you cannot “show” an unknown source-less power designing every single complexity. We ONLY have theories. May I ask if you find Tony’s “spawning” theory logical?

The options for DHW's question always seem to devolve to:

Is it more plausible that:

  • A) The laws of govern all energy, matter, and information, spontaneously spring into existence followed by, or perhaps part and parcel with, all matter becoming simultaneously intelligent and then said intelligent matter communicated and designed, all life, with its vastly more complex systems, and so on.
  • B) A single intellect emerged once out of eternal form of energy, taking time beyond measure to become capable of bringing another single entity into existence, both of which were energy and information only (non-material). The two intelligences over time, worked together to develop/birth/spawn more similar to themselves (non-material), eventually learning to manifest energy and information into the material universe we know.
  • C) Flip a coin...there was no intelligence, guidance, planning, or outside influence at all. Stuff just happened.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Magic embryology: placenta maintains symmetry

by Balance_Maintained @, U.S.A., Wednesday, September 19, 2018, 05:14 (1422 days ago) @ dhw

David’s comment: In placental embryology the control systems have to be designed, when one recognizes that there is no competition for survival of the fittest as Darwin proposes. The fetus is in as safe place for its development and that development must have feedback loop controls. From my standpoint embryology is a complete refutation of Darwin style chance evolution.

TONY: And there is no other way to explain that mechanism than design. Fascinating.

DAVID: (Under "plant immunity") Immunity processes are necessary from the appearance of any organism, or infections will run roughshod over then and they will not survive. Only design can do this.

Thank you for these extremely illuminating articles. I have complete sympathy with the comments you both make about design, but how would you both feel if every time you mentioned design as opposed to chance, I redressed the balance by repeating the following exchange (taken from “pointy eggs”)?

Dhw: The choice is between your magically intelligent God and magically intelligent matter, either innately intelligent – panpsychism – or having originated by chance, though in both cases evolving. “Logically I strongly doubt” any form of magic, which is why I am an agnostic, but as I keep admitting, I am wrong one way or the other.

DAVID: Granted, and logical.

DAVID: (under "Junk DNA”): There is very little junk DNA, to the disappointment of Darwinists.

DHW: Another of your mantras repeated ad nauseam, so let me repeat ad nauseam that the less junk DNA there is, the more evidence we have of natural selection at work, whereby what is useful survives, which would be to the delight of Darwinists who realized it.

We would of course point to the fact that the complexity is irreducible, unless of course you can show an evolutionary pathway that could conceivably lead to that mechanism, which I can not see. Not to say it doesn't exist, but the complexity in terms of timing and chemical messaging necessary is staggering.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Magic embryology: it is all in the timing

by David Turell @, Friday, October 19, 2018, 20:51 (1391 days ago) @ Balance_Maintained

Making a fetus involves the timing of DNA expression and particular protein productions all in 3-D. This is an interview with a scientist studying how embryology works:

https://www.quantamagazine.org/stem-cell-researcher-renee-reijo-pera-studies-embryonic-...

Q: But developmental timing is important not just for the immediate survival of the embryo, but for health and disease further down the line, right?

"Yes, that’s one of our big hypotheses, because of the role timing plays in deciding the fates of cells. The idea is that development starts with a certain timeline. If a cell does not make it to a certain stage on time, its cell fate can change, and it’s typically thrown out of the tissue. It’s expelled and it dies.

"In a paper in Nature Genetics in 2016, for instance, we identified nearly 150 new genes, many of which were retroviral, that get expressed very early on in human stem cells. Then, when we turned some of the retroviral genes off, we found it changed the fate of the cells. Instead of becoming embryonic stem cells — which ultimately give rise to the fetus — the cells could only contribute to the trophectoderm layer, which gives rise to the tissues that attach the embryo to the uterus. The trophectoderm is made up in part of “bad” cells that won’t make it as part of the fetus.

"Which means that part of the puzzle on timing and which cells become part of the embryo and which become part of the extra-embryonic tissue depends on human-specific sequences that we inherited from retroviral integration.

Q: That seems surprising — that viral DNA would play such an important role so early in development.

Over the course of evolution, viruses have been in us and on us and changing us continually. We wrote another paper in Nature with Joanna Wysocka at Stanford, suggesting that these viral sequences have another, second effect: that they not only contribute to cell fate but also help the embryo get rid of viral infections.

In both cases, then, it seems like we have a cleanup system early in development that’s viral-based.

Q: You also study factors that determine whether or not cells will become germ cells. What’s at play there?

"In a paper published in Nature Cell Biology in April, we identified a triad of proteins that interact to help form primordial germ cells and maintain the primordial germ cell fate.

"We knew that the protein OCT4 is one of the master regulators of embryonic development and cell fate. But how do you tell if an embryonic cell will form a primordial germ cell, given that both express OCT4? We thought OCT4 could be acting with different partners in specific ways to enable the birth of the germ line.
"
That’s what a decision looks like in cells. You can think of it as a fulcrum: The stem cell sits in the middle, and if OCT4 and the other proteins are acting in concert, that fulcrum will tilt toward the germ line. If one of the proteins isn’t present in the right amount, we found that the cells instead become ectoderm, embryonic tissue that typically gives rise to neurons. It’s a delicate balance. We’re now starting to unpack each protein’s actual function in embryonic and germ cell development, and we’re studying how other transcription factors might be involved."

Comment: Darwin could not comment about embryology, as the science didn't exist. But the intricacies of embryology in timing of various tissues in production and requirement in 3-D for proper placement of the geography of a whole organism is still mostly a mystery. An embryo is not like a new auto on a production line, where one section is added at a time. In embryology the whole organism is having all different parts all at the same time, once the basic stem cells are organized in position. All of this requires design. Chance attempts won't work.

Magic embryology: tight controls, including death

by David Turell @, Wednesday, June 15, 2022, 23:37 (56 days ago) @ David Turell

When cells wander off course they self-distruct:

https://phys.org/news/2022-06-cells-self-destruct.html

"The new research identifies the mechanisms that ensure that any wayward, wandering cells will self-destruct through a specific form of cell death called anoikis. Interestingly, resistance to anoikis is a precursor to many types of metastatic cancers. Understanding the pathways that guide healthy anoikis may ultimately provide insight into how cancers metastasize and why they invade certain parts of the body.

"'Cell death is a normal, healthy part of development," Stathopoulos says. "The migrating cell has to constantly be making decisions and figuring out if it is in the in the right place in the body. If it's not in the right place, it needs to self-destruct. We have now determined the pathways through which the cell can do this."

***

"The CVM cells do not make their long journey through the fruit fly embryo alone. These 40 to 50 cells follow a kind of track that is made up of a different cell type called trunk visceral mesoderm (TVM). TVM cells emit a chemical signal called fibroblast growth factor (FGF), which lets a CVM cell know that it is in the right place.

"At the midpoint of their migration, the CVM cells must navigate around a sharp bend in the embryo, which is roughly U-shaped. At this juncture, CVM cells start proliferating in anticipation of soon being at the end of their journey, when it will be time to start building muscle. The problem is, when cells start multiplying, some begin to drift off of the TVM track. Researchers have previously observed that this is the point where these lost cells will undergo anoikis and self-destruct.

"A gene called hid (short for head involution defective) is responsible for anoikis. When hid is expressed in a cell, the cell will die. In the new work, Macabenta found that CVM cells begin to express hid as they make the turn around the bend in the embryo, but they do not die—unless they fall off of the TVM track.

"The team found that this is possible thanks to the FGF signals, which act as the antidote to hid: If a cell falls off of the track and therefore stops receiving FGF signals, it will die; it can stay alive despite hid being expressed as long as it stays on track. In this way, the embryo can make sure that any wayward cells will self-destruct, while properly functioning cells are spared.

"Finally, the team also discovered that a particular pathway, called the bone morphogenetic protein (BMP) pathway, controls the timing of when the cells begin to proliferate. BMP signaling initiates just as cells navigate the U-shaped turn, roughly at the midpoint of their migration. It is this signal that allows cells to divide and grow in number.

"Cells have an internal "clock," known as the cell cycle, which controls the timing of growth, DNA replication, and cell division (mitosis). The team found that the timing of hid expression is linked to progression of the cell cycle, and when this is disrupted, hid is no longer expressed at the right point during cell migration. BMP signaling is necessary to allow the cell cycle to move forward through mitosis and is therefore also necessary for timing the precise expression of hid, as cells that fail to divide are not able to express hid in a timely manner to eliminate lost cells.

It is crucial that cells are able to have these programmed quality control mechanisms because wayward cells can be damaging to the proper development of the rest of the organism.
(My bold)

Comment: As embryos develop, cells must follow precise paths directed by precise signals, in order to end up as duplicate copies of parents. Here we see nothing but guide signals. It cannot be like herding cats. This shows how cells can operate fully by chemical signals in all cellular operations incuding epigenetics. The Speciation mechanism is totally unknown

Magic embryology: both genes and physical forces

by David Turell @, Wednesday, July 13, 2022, 21:52 (28 days ago) @ David Turell

The physical forces of cell growth help form an embryo:

https://www.quantamagazine.org/embryo-cells-set-patterns-for-growth-by-pushing-and-pull...

"... Amy Shyer, a developmental biologist at Rockefeller University. In her view, physical forces of contraction and compression that act on cells as they grow and divide could also play a central role.

***

"And now she has proof of it. In a paper published in Cell in May, Shyer, her co-senior author and fellow developmental biologist Alan Rodrigues and their colleagues showed that mechanical forces could induce embryonic chicken skin to create follicles for growing feathers. Just as surface tension can pull water into spherical beads on a glass surface, so too can the physical tensions within an embryo set up patterns that guide growth and gene activity in developing tissues.

"As an organism grows and develops, the cells in its tissues pull and push on each other and on the supportive protein scaffolding (extracellular matrix) to which they are intricately linked. Some researchers have suspected that these forces, coupled with changes in the pressure and rigidity of the cells, might direct the formation of complicated patterns

"In the laboratory of morphogenesis at Rockefeller University that they jointly lead, Shyer and Rodrigues removed the skin from a chicken embryo and disintegrated the tissue to pull apart the cells. Then they placed a drop of the cellular solution into a petri dish and let it grow in culture. They watched as the skin cells self-organized into a ring on the floor of the dish — like a 2-D version of the ball of cells that the embryo normally becomes. Pulsating and contracting, the cells pulled on collagen fibers in the extracellular matrix that they assembled around themselves. Over 48 hours, the fibers gradually rotated, bunched together and then pushed each other apart, forming bunches of cells that would become feather follicles.

***

"...by adjusting the rate of cell contraction and other variables, the researchers showed that physical tension in the embryonic mass directly affected the pattern. “I think the biggest surprise was the way the cells interacted with the extracellular matrix in this very dynamic way, in order to create these patterns,” Rodrigues said. “We realized that it is a reciprocal dance between the two.”

“"This suggests that contractility could be sufficient to drive pattern formation,” Camley said. “That’s a really new essential piece.”

***

"In 2017, they took small slices of chicken embryo skin and watched closely as the tissue bunched up in preparation to form a follicle. Meanwhile, they tracked the activation of the genes involved in follicle formation. What they found was that gene expression happened around the same time that the cells bunched up — but not before.

“'Instead of ‘gene expression first, then mechanics later,’ it was sort of like mechanics was generating these shapes,” said Shyer. Later, they showed that even removing some of the gene-regulating chemicals didn’t disrupt the process. “That opened a door to say, ‘Hey, something else might be going on here,’” she said.

***

“'We are realizing that all of the molecular gene expression, signaling and the production of forces in cell movement are just inextricably coupled to one another,” said Edwin Munro, a molecular biologist at the University of Chicago who was not involved in the study.

"Munro thinks the role of the extracellular matrix is more important than scientists currently realize, though recognition of its more central role in development is building. Recent research has linked forces in the extracellular matrix to the development of fruit fly eggs, for example.

"Rodrigues agreed. “It’s like the cells and the extracellular matrix are forming a material in and of itself,” he said. He describes this coupling of contractile cells and extracellular matrix as “active soft matter” and thinks that it points to a new way of thinking about the regulation of embryonic development happening through extracellular forces. In future work, he and Shyer hope to elucidate more details of physical forces in development and to merge them with the molecular view.

“'We used to think if we just studied the genome with more and more depth and rigor, all of this would be clear,” Shyer said, but “the answers to the important questions might not be at the level of the genome.” Once it seemed that developmental decisions were made through the interplay of genes and their products within cells, but the emerging truth is that “the decision-making can be happening outside of the cell, through the physical interactions of cells with each other.'” (my bold)

Comment: Think of the intricacies of this design. Genes driving cell growth in a pattern that produces form. The genes drive the cell growth which ends up in the desired shape as an indirect effect. This is well beyond chance development.

Magic embryology: What guides cell development, placement?

by David Turell @, Friday, March 15, 2019, 01:12 (1245 days ago) @ Balance_Maintained

There must be a blueprint, but where is it? Cells seem to make optimal decisions based on many stimuli that are chemical, physical force and positional:

https://www.quantamagazine.org/the-math-that-tells-cells-what-they-are-20190313/

"It’s now known that some form of positional information makes genes variously switch on and off throughout the embryo, giving cells distinct identities based on their location. But the signals carrying that information seem to fluctuate wildly and chaotically — the opposite of what you might expect for an important guiding influence.

***

"The same precision and reproducibility emerge from a sea of noise again and again in a range of cellular processes. That mounting evidence is leading some biologists to a bold hypothesis: that where information is concerned, cells might often find solutions to life’s challenges that are not just good but optimal — that cells extract as much useful information from their complex surroundings as is theoretically possible.

***

"For decades, scientists have been studying fruit fly larvae for clues about how development unfolds. Some details became apparent early on: A cascade of genetic signals establishes a pattern along the larva’s head-to-tail axis. Signaling molecules called morphogens then diffuse through the embryonic tissues, eventually defining the formation of body parts.

"Particularly important in the fly are four “gap” genes, which are expressed separately in broad, overlapping domains along the axis. The proteins they make in turn help regulate the expression of “pair-rule” genes, which create an extremely precise, periodic striped pattern along the embryo. The stripes establish the groundwork for the later division of the body into segments.

***

"That prompted a group at Princeton University, led by the biophysicists Thomas Gregor and William Bialek, to suspect something else: that the cells could instead get all the information they needed to define the positions of pair-rule stripes from the expression levels of the gap genes alone, even though those are not periodic and therefore not an obvious source for such precise instructions.

"And that’s just what they found.

***

"Even given the limited number of molecules and underlying noise of the system, the varying concentrations of the gap genes was sufficient to differentiate two neighboring cells in the head-to-tail axis — and the rest of the gene network seemed to be transmitting that information optimally.

"But new work shows if the cells can make optimal use of the information available, they can determine their location early, from the gap genes expression alone.

***

"How the cells do it remains a mystery. Right now, “the whole thing is kind of wonderful and magical,” said John Reinitz, a systems biologist at the University of Chicago.

***

'The findings provide a fresh perspective on Waddington’s idea of a developmental landscape. According to Gregor, their work indicates that there’s no need for 20 questions or a gradual refinement of knowledge after all. The landscape “is steep from the beginning,” he said. All the information is already there.

***

"if these regulatory regions need to perform an optimal decoding function, that potentially limits how they can evolve — and in turn, how an entire organism can evolve. “We have this one example … which is the life that evolved on this planet,” Kondev said, and because of that, the important constraints on what life can be are unknown. Finding that cells show Bayesian behavior could be a hint that processing information effectively may be “a general principle that makes a bunch of atoms stuck together loosely behave like the thing that we think is life.”

***

“'I don’t think optimization is an aesthetic or philosophical idea. It’s a very concrete idea,” Bialek said. “Optimization principles have time and again pointed to interesting things to measure.” Whether or not they are correct, he considers them productive to think about.

“'Of course, the difficulty is that in many other systems, the property being decoded is more difficult than one-dimensional position [along the embryo’s axis],” Walczak said. “The problem is harder to define.”

"That’s what made the system Bialek and his colleagues studied so tantalizing. “There aren’t many examples in biology where a high-level idea, like information in this case, leads to a mathematical formula” that is then testable in experiments on living cells, Kondev said."

Comment: Note the important use of information which is guiding the making of an embryo. A blueprint exists in an orchestrated mass of stimuli. As in a symphony, it has to written by a composer.

Magic embryology: What guides nerve pathways to muscles?

by David Turell @, Saturday, March 23, 2019, 17:48 (1236 days ago) @ David Turell

Controls are described:

https://medicalxpress.com/news/2019-03-mountaineers-nerves-expert-guidance.html

"...the nervous system relies on elaborate timing and location of guidance cues for neuronal axons—threadlike projections—to successfully reach their destinations in the body. Now, Salk Institute researchers discover how neurons navigate a tricky cellular environment by listening for directions, while simultaneously filtering out inappropriate instructions to avoid getting lost.

"'There are 100 trillion connections in the nervous system governed by 20,000 genes, of which roughly 10 gene families are known to be involved in controlling axon guidance. We wanted to understand the clever genetic systems nature has employed to wire the most complicated biological machine in the universe," says Salk Professor Samuel Pfaff, senior author and a Howard Hughes Medical Institute investigator. "Thus, we set out to examine how motor neurons find their connections with muscles in the body, which is critical for our brain to relay information to our muscles to allow for movement."

"The brain controls hundreds of different muscles to allow for precise movement. During development, motor neurons in the spinal cord extend their axons outside of the central nervous system to connect with muscle cells in the body. Every motor neuron relies on a set of genes to ensure the axon grows correctly to the muscle.

***

"Upon closer investigation, the scientists found that these motor neurons climbed up the edge of the spinal cord rather than properly exiting to meet their muscle targets. The team pinpointed the gene causing this detrimental mutation as p190, which was previously known to play a role in cancer suppression, but had not been implicated in establishing neuronal connections during development.

"The researchers set up a series of experiments to examine how p190 affects axons leaving the spinal cord. They found that, although axons are normally attracted to a protein in the spinal cord called netrin, during a short time window p190 acts as a blinder, so the axons disregard netrin and are led outside of the spinal cord. After the axons safely leave the central nervous system, this blinder is removed. Without p190, the axons are attracted to netrin and do not properly leave the spinal cord, so never connect with muscles.

"Pfaff, holder of the Benjamin H. Lewis Chair, adds, "These results provide mechanistic insight into the unimagined complexity that cells use to communicate with one another.'"

Comment: Another feedback loop to control development which still has to show how an exact path to the correct muscles is fully controlled over the distance: in a six-foot human flexing his big toe the route is roughly six feet!

Magic embryology: guiding body orientation

by David Turell @, Sunday, May 19, 2019, 18:55 (1179 days ago) @ David Turell

The zygote, as a ball of symmetrical cells, must establish head, tail, left and right to develop any organism in the correct shape. Controls found:

https://www.sciencedaily.com/releases/2019/05/190517115147.htm

"Even before the fertilised egg or zygote can start dividing into daughter cells that form the future tissues and organs during the development of a multicellular organism, the symmetrical zygote needs to become asymmetrical or polarised in shape and molecular organisation. The master switch that triggers the symmetry breaking process in the zygotes of the nematode worm, Caenorhabditis elegans (C. elegans), was identified in a recent study,

***

"Structurally, cells acquire top and bottom or front and rear surfaces, while at the molecular level, special protein groups called polarity regulators move to distinct regions in the cell cortex (a layer beneath the cell membrane). As a result, different cell regions acquire specific architectures and functions.

***

"... his team previously revealed how forces generated on the cortex by the contractions of the actin cytoskeleton (a filamentous framework made of actin and myosin proteins) could direct the movement of polarity regulators to their destined locations. Shortly after fertilisation, actomyosin contractions in the cortex puts the surface of the zygote under tension. Upon symmetry breaking, spatially-controlled inhibition of actomyosin contractions lead to an imbalance in the surface tension, causing the cortical cytoskeletal networks to flow and transport the polarity regulators.

***

"After using a technique called RNA interference to block the synthesis of specific proteins involved in the polarisation process, and observing the effects in live zygotes, they singled out a protein called Aurora-A (AIR-1 in C. elegans) as the master switch for symmetry breaking.

"Aurora-A is a kinase (a type of protein that regulates the activity of other proteins by adding a phosphate molecule to them) that has well-known roles in controlling cell division by assembling centrosomes -- a cellular organelle that organises microtubule filaments and facilitates cell-cycle progression.

"The researchers identified a two-stage process by which Aurora-A influences actomyosin contraction to initiate symmetry breaking and establish cell polarity. In the first stage, Aurora-A accumulates around centrosomes and suppresses actomyosin contractions locally in the surrounding cortex. This creates force differences along different regions of the cortex, and the resulting cortical flow transports myosins and other polarity proteins to the front of the zygote, thereby creating front-rear asymmetry. In the second stage, Aurora-A diffuses into the cytoplasm and suppresses actomyosin contractions across the entire cortex. This prevents further cortex flows or movement of polarity regulators, effectively locking them in place.

***

"The single master switch, Aurora-A, creates 'polar lights' that cover one of the cell poles for symmetry breaking."

"Intriguingly, the research team discovered that the role of Aurora-A in cell polarisation was independent of its role in centrosome assembly and cell-cycle progression. Through fruitful collaborations with colleagues at NUS, including Associate Professor Yusuke Toyama (MBI) and Professor Thorsten Wohland (NUS Department of Biological Sciences), who brought their expertise in laser ablation and fluorescence correlation spectroscopy respectively, they demonstrated that the local accumulation of Aurora-A was sufficient to induce symmetry breaking via its kinase activity, regardless of the involvement of centrosomes."

Comment: This is a complex process, which had to have been designed, or the embryos would not proceed properly. No way it could have been developed by chance trial. The Aurora-A is an enzyme which has two roles, which is unusual in itself. Further it should be realized any enzyme is a giant molecule, and one must ask how does an unguided chance evolutionary hunt and find such an exact protein molecule? Only a designer fits.

Magic embryology: What guides cell development, placement?

by David Turell @, Monday, August 12, 2019, 17:42 (1094 days ago) @ David Turell

More mechanical and spatial factors are recognized:

https://www.quantamagazine.org/for-embryos-cells-size-can-determine-fate-20190812/

"The developing embryo is a finely tuned machine. Its cells know what to do, and when to do it. They know to grow or shrink, to divide or lie dormant, to come together into a beating heart or hurtle through the bloodstream in search of a distant invader. And they know to do all that without a central command station or an objective map of their surroundings to guide them.

"Instead, cells are left to devise their own strategies for calculating precisely where to go and what to become. Those calculations depend on a veritable cocktail of signals, some of which have long been established as obviously important — chemical and electrical gradients, the activity of gene networks, patterns of overlap between spreading fields of molecules.

"But recently experts have also started to pay attention to another, often overlooked set of factors: physical constraints such as size. In new work published today in Nature Physics, a team of researchers reported that during the early development of the roundworm Caenorhabditis elegans, a mechanism based on the size of embryonic cells helps to determine the type of mature tissues they will eventually produce.

"While examining the biochemical process that triggers cells to divide either asymmetrically or symmetrically, the scientists discovered that size was the ruling element — namely, that the size of the cells dictated the pattern that led to one kind of division or another, and ultimately to one kind of lineage or another. “The biology is actually exploiting this fact … to generate a set of outcomes that are required for the development of the organism,” said Martin Howard, ... In this case, cells used innate constraints on their size to specify the lineage that would later give rise to the worm’s sex cells. But more broadly, the findings also point to the possibility of a role for physical cues in the behavior of stem cells and the operation of other developmental systems.

***

"For instance, when the worm embryo is still a single cell, proteins on its outer membrane create two uneven, yin-and-yang-like domains that tell the cell where to split. That system for designating asymmetric cell division is called polarity. One lineage of embryonic cells in C. elegans (known as the P lineage) uses polarity to divide asymmetrically four times; the fifth division is then symmetric, permanently establishing the germline responsible for egg and sperm cells.

***

"By controlling the sizes of the initial embryos, the team was then able to show that there was a minimum size threshold for the P lineage cells, below which they could not set up the polarization pattern. Those smaller cells lost the ability to polarize after just three cell divisions, not four. “Just by manipulating the size of the embryo, we’ve taken a cell that normally would be able to polarize and divide asymmetrically and turned it into a cell that doesn’t polarize and divides symmetrically,” Goehring said.

***

"Cells have seemingly evolved to take advantage of the intrinsic limitations of their patterning process — using it as a ruler of sorts — to determine whether to become germ cells. “The specification [of the germ cells] is a kind of self-organized property of the patterning system,” Howard said.

"And that’s a “genuinely interesting” way to think about the system, said Timothy Saunders, a biophysicist at the Mechanobiology Institute of the National University of Singapore who was not involved in the study. “This idea, that by just simply making things smaller you can naturally switch the type of division, is very neat.”

"These findings come at a time when scientists are widening their view of what controls biological systems to encompass more than genetics alone. “The gene does not exist in a vacuum,” Saunders said. “And we’re realizing more and more that the mechanical environment in which those genes are operating matters” — including for decisions about cell fate."

Comment: It is obvious embryonic cells are controlled by chemical and physical influences. but an overall body plan has to exist. Darwin does not explain the development of embryology in any of his theories. It is magical and strongly suggests that only design fits.

Magic embryology: What guides limbs? electric patterns

by David Turell @, Tuesday, October 08, 2019, 05:08 (1038 days ago) @ David Turell

A new discovery for the guidance of form:

https://phys.org/news/2019-10-voltage-gated-calcium-channels-electric.html

"Prior studies have shown remarkable electrical patterns in developing embryos, some of which act like blueprints of the tissues and organs that eventually take shape as the embryo matures. The electrical patterns are created by cells pumping charged ions into and out of the cell membrane, creating a voltage potential across the membrane barrier. In analogy to cells of the nervous system, the membrane voltage potentials spread via electrical synapses and provide a way for cells to communicate with their neighbors and coordinate activity.

"The new study, conducted in mouse and chicken embryos, demonstrates that a voltage gated calcium channel (VGCC) embedded in the cell membrane, and triggered by voltage to allow calcium ions (Ca2+) to flow into the cell, sets off the expression of genes that guide differentiation to mature cells.

***

"The study now points to a role for VGCCs in 'reading out' the bioelectric patterns of an embryo to set the genetic and protein expression machinery in play for body development.
The researchers looked at the developing limbs of both mice and chicken embryos and found that while the limb bud is initially hyperpolarized, with 1000-fold more calcium ions outside cells than inside, the core of the growing limb becomes depolarized as cartilage forms; (calcium ions flow into the cells to neutralize voltage). They found that the depolarization is mediated by VGCCs, allowing calcium ions to flow inward, which in turn activate a genetic transcription factor called NFATc1, which in turn initiates expression of other genes required for differentiation into mature cartilage cells. The VCGG studied (Cav1.2) was found to be essential for normal cartilage formation, while NFATc1 was confirmed to promote the differentiation of cartilage cells in vitro.

"Looking at the role of Cav1.2 more closely, the researchers discovered that it primarily plays a part in the early stages of cell differentiation into cartilage. Other VGCCs may be involved at later stages of development, and other transcription factors may be activated by the increase in intracellular calcium during the process of cartilage and bone formation, according to the researchers.

"'It's clear that while we have discovered an essential role for voltage gated calcium channels in reading the embryo's bioelectric pattern, we will need to continue work to understand the role of many different ion channels and genetic factors throughout all stages of development," said Cliff Tabin, associate of the Allen Discovery Center at Tufts and chairman of the Depertment of Genetics in the Blavatnik Institute at Harvard Medical School.

"'We are just beginning to understand how the 'software' of embryonic development (the electrical patterns) are created and interpreted by the 'hardware' (the cells' genes and proteins) to enable the cells to cooperate and organize into a highly-patterned body," said Michael Levin, Vannevar Bush Professor of Biology in the School of Arts & Sciences and director of the Allen Discovery Center at Tufts."

Comment: Embryos just don't grow. They are design coded to follow designed plans electrically laid out..

Magic embryology: developing an immune and blood systems

by David Turell @, Wednesday, October 09, 2019, 18:32 (1036 days ago) @ David Turell

Early stem cells are tracked in embryos to learn how the systems develop:

https://medicalxpress.com/news/2019-10-cell-human-liver-reveals-blood.html

"In a world first, scientists have created the human developmental liver cell atlas that provides crucial insights into how the blood and immune systems develop in the foetus. It maps changes in the cellular landscape of the developing liver between the first and second trimesters of pregnancy, including how stem cells from the liver seed other tissues to support the high demand for oxygen needed for growth.

***

"Until now, it was unknown precisely how the blood and immune systems develop in humans—a process known as haematopoiesis. As adults, it is bone marrow that creates our blood and immune cells. But in early embryonic life, the yolk sac and liver play a major role in making blood and immune cells. These cells subsequently seed peripheral tissues such as skin, kidney and finally bone marrow.

***

"A developing foetus requires huge amounts of oxygen to fuel growth. The research discovered that during development, 'mother' haematopoietic stem cells stay in the liver. But as the liver alone cannot supply sufficient red blood cells, the next generation 'daughter' cells—known as progenitor cells—travel to other tissues. They mature in places such as the skin, where they develop into red blood cells to help meet the high demand for oxygen.

"Dr. Elisa Laurenti, a senior author from the Wellcome—MRC Cambridge Stem Cell Institute and the Department of Haematology at the University of Cambridge, said: "We knew that as adults age our immune system changes. This study shows how the liver's ability to make blood and immune cells changes in a very short space of time, even between seven and 17 weeks post-conception. If we can understand what makes the stem cells in the liver so good at making red blood cells, it will have important implications for regenerative medicine.'"

Comment: these early cells are following a planned outline of development. Embryology is the science of understanding how sex produces multicellular organisms. When life was single celled, splitting was a simple sort of reproduction. Having two individuals contribute genes requires that a design plan be set up for each new reproduction of an individual which is not different from the parents, but of course, it might produce some variability. That is a point Darwin used, the variability, but Darwin simply accepted sexual reproduction, and could not explain how a chance evolutionary process could create such a complex mechanism like embryology.It had to be designed.

Magic embryology: developing brain neuron clusters

by David Turell @, Wednesday, October 09, 2019, 18:48 (1036 days ago) @ David Turell

More evidence of design planning in creating an embryo's brain:

https://www.sciencedaily.com/releases/2019/10/191009095826.htm

"Neurons are not randomly arranged in the human brain. In the cortex, they are organized in interconnected clusters with high intrinsic connectivity. This modular connectivity structure, in which clusters eventually serve as functional units, is formed in early phases of development. The underlying self-organization process is regulated by neuronal activity but the detailed mechanisms are still poorly understood. Based on in vitro studies and computational modeling, neuroscientists ....show how neuronal outgrowth and migration interact in shaping network architecture and the degree of modularity in mature networks.

***

"Neurons are sociable cells that, on the long run, die in isolation. During development, they therefore grow out cellular processes, termed neurites, to establish synaptic connections with other neurons. Once they receive sufficient or too much synaptic input, however, they stop growing or shrink. By this, neurons avoid long-term over-excitation. It is widely assumed among researchers that neuronal growth is hereby controlled to stabilize neuronal activity at a specific target level.

"Yet, to increase the probability of connections, neurons cannot only grow out their neurites but are also able to migrate towards other neurons. "In computer simulations we show that migration and neurite outgrowth may interact to shape specific mesoscale network architectures" says Samora Okujeni. The interaction regulates the relation between local connectivity within clusters and long-range inter-cluster connectivity and thereby the degree of network modularity. "This, in turn, influences the generation and spatiotemporal patterns of spontaneous activity." Such interdependencies may be crucial for the proper development of the cortex.

***

"'Cytoskeletal dynamics are not directly controlled by action potential activity but indirectly through an associated calcium influx that influences the balance between growth and degradation." Okujeni explains. "Modularity increased the overall rate of action potentials but decreased their synchronization across the network that effectively determines the calcium influx per action potential. Given this dependence, we estimated that all network structures attain a similar target level of calcium influx during development.'"

Comment: more evidence of a highly designed plan for neurons to follow, ending up in a highly coordinated functional clusters, helping to explain how the brain works so efficiently.

Magic embryology: how stem cells follow genetic instructions

by David Turell @, Friday, November 08, 2019, 19:36 (1006 days ago) @ David Turell

It is all automatic:

https://www.sciencedaily.com/releases/2019/11/191107122638.htm

"All cells in the body contain the same genetic material. The difference between cells therefore depends solely on which genes are expressed or 'turned on'. Now, researchers have gained new insights into how genes are turned on and off and how the cells ''forget their past'' while developing into a specific cell in the body. This new knowledge will be crucial for stem cell therapy and potentially treating people with cancer.

***

"'We previously thought that transcription factors drive the process that determines whether a gene is expressed and subsequently translated into the corresponding protein. Our new results show that transcription factors may be more analogous to being the memory of the cell. As long as the transcription factors are connected to a gene, the gene can be read (turned on), but the external signals received by the cells seem to determine whether the gene is turned on or off. As soon as the transcription factors are gone, the cells can no longer return to their point of origin," explains Josh Brickman, Professor and Group Leader, DanStem, University of Copenhagen.

***

"The researchers developed a stem cell model to mimic a cell's response to signaling and used it to, for first time, precisely determine the sequence of the events involved in a gene being turned on and off in response to a signal in stem cells. The researchers were able to describe how genes are turned on and off and under what circumstances a cell can develop in a certain direction but then elect to return to the starting-point.

***

"'Transcription factors are still a key signal, but they do not drive the process, as previously thought. Once they are there, the gene can be read, and they remain in place for a while after the gene is read. And when they are gone, the window in which the gene can be read can be closed again. You can compare it with the vapour trails you see in the sky when an airplane has passed. They linger for a while but slowly dissipate again," explains first author, William Hamilton, Assistant Professor at DanStem."

Comment: All an automatic process, which is the way cells work

Magic embryology: little understood

by David Turell @, Monday, December 09, 2019, 15:38 (975 days ago) @ David Turell

Specific software must underlie embryological formation of a form from the fertilized egg. New species must have new software to run the show:

https://www.the-scientist.com/critic-at-large/opinion--interdisciplinary-approach-neede...

Physicists, geneticists, computer scientists, and biologists are working together to gain a full appreciation of the intricacies of organismal growth and form.

***

"Over the past 20 years, researchers have made tremendous progress in identifying specific genes necessary for development, mostly by chronicling mutations or deletions of genes that lead to the onset of diseases and anatomical defects. But this information is just the tip of the iceberg. While the genome specifies the crucial “parts list” for individual cells, researchers have much to learn about the signaling events that coordinate the collaborative cellular processes to create and repair complex anatomies.

"In the post-genomic era, it is becoming clear that the next step beyond identifying the genetically specified hardware of the body involves understanding the physiological software: the mechanisms that enable cells and tissues to make decisions and implement swarm dynamics that remodel organ-level structure. Often, the same anatomical outcome can arise from a range of diverse starting conditions. For example, normal frog faces can arise even when tadpole faces have their craniofacial tissues in scrambled positions. To understand this anatomical convergence toward the correct target morphology, researchers must incorporate the deep insights of physics and computer science into cell and developmental biology and remember that evolution exploits physical forces such as biomechanics and bioelectrics. (my bold)

***

"...we work to identify new scientific hypotheses (for example, the idea that anatomical goals are represented by biophysical “memories” in tissues) and experimental tools that will reveal entirely new areas of life science. The dynamic control of biological shape is a problem that requires cross-disciplinary collaboration and the synthesis of data from an array of model systems.

***

"Our core mission is to uncover and exploit the computational layer between the genome and resulting anatomy." (my bold)

Comment: These quotes are from an article that explains how a new lab is working on morphogenesis. The key points show that the missing ingredient is how the software makes new forms, and this can be applied to embryology and to the creation of new species. It requires the development of new software. It is not really magic. It must be new software, that is new information as the term 'computational layer' implies in computer terms. Those changed instructions must be put into stem cells, but also be centrally located to coordinate the whole new construction. New software must be created by precise planning and code-writing. Only a mind can create the new software.

Magic embryology: video egg to organism in 6 minutes

by David Turell @, Monday, December 23, 2019, 15:01 (961 days ago) @ David Turell

Magic embryology: signals that connect neurons

by David Turell @, Monday, December 23, 2019, 19:08 (961 days ago) @ David Turell

Neurons send branches to many other neurons to make the interpretive networks. Chemical signals are used:

"The brain's complex tangle of interconnected nerve cells processes visual images, recalls memories, controls motor function, and coordinates countless other functions. A major goal of neuroscience is understanding how the brain is "wired"—in other words, how do all of its neurons know how they should connect to each other to achieve optimum function?

***

"In the 1960s, Caltech neuroscientist and Nobel Laureate Roger Sperry proposed that neural circuit assembly is guided by interactions between cell-surface proteins—proteins that sit on the outer surface of neurons and other cells. Sperry's hypothesis, which was based on his experiments on optic pathways in frog and fish brains, was that these proteins act like signposts, labeling individual neurons in the brain as appropriate targets for neurons in the eye. The new work from the Zinn laboratory identifies brain and eye cell-surface proteins in Drosophila that have these signpost functions.

"Several years ago, researchers at Stanford and in the Zinn group at Caltech expressed each of 200 different Drosophila cell-surface proteins in lab dishes and characterized all the binding reactions among these proteins that occur in a test tube (about 40,000 possible combinations).

"The work revealed that two families of cell-surface proteins, dubbed Dprs and DIPs, have a particular affinity for one another and that members of both families are found on the surfaces of neurons. Researchers in the Zinn laboratory have been trying to understand how this interaction plays a role in neural development.

***

"They found that, when neural connections are being made in the developing visual system, the target neurons are generated in excess and compete for their photoreceptor partners. This matching is possible because of the interaction between Dpr11 on the photoreceptors and DIP-gamma on the target neurons. Thus, if the two proteins were not both expressed (as was the case, for example, in flies with mutations in either the dpr11 or DIP-gamma genes), the target neurons died and the neural circuit did not develop correctly. Analysis of the neural connections in mutant flies suggests that they should have defects in color vision.

***

"Though the researchers have discovered that this specific Dpr/DIP pairing is critical for proper neural-circuit formation, any given neuron expresses about 250 different cell-surface proteins, making the analysis of how cell-surface proteins control connectivity very complex. Future work will continue to study how synaptic connectivity is determined by pairings between Dprs and DIPs and other cell-surface proteins, with the ultimate goal of understanding the information required to create the entire wiring diagram of the fly brain."

Comment: Another complex arrangement to guide development of neuronal connections, all pre-planned by instructions that produce these specific protein signals and make each new brain about the same. There must be an underlying plan to be followed. this cannot be designed by chance.

Magic embryology: rules for growing a new fetus

by David Turell @, Tuesday, January 21, 2020, 22:14 (932 days ago) @ David Turell

Partly involves 3-D mechanical pressures, but the whole process is very poorly understood:

https://www.sciencedirect.com/science/article/pii/S0079610716300542?via%3Dihub

From the abstract:
"We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis—currently an elusive goal—will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences."

In the conclusion, which admits no one yet knows how this all works, they add the following comment about t he comparative anatomy of related groups (homology):

"...there are currently no other causative global mechanical models of morphogenesis extant in the modern literature. The causal account that the model provides for the development of complex vertebrate morphology is necessarily presented by a speculative series of schematic images representing sequences of key mechanical events during embryogenesis, akin to a series of blueprints. The vast—and largely non-pictorial—literature on this subject does not offer a global mechanism to explain the rise of diverse forms of animal phyla. Though highly speculative, the model offered here may suggest just such a mechanism. The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry. Accordingly, the choices available to natural selection may be limited to the possible variations in proportions of the body parts of otherwise relatively conservative and invariant phyletic forms, rather than simply provided by random genetic mutations resulting from errors in transcription. Animal form may thus be seen as the product of physical forces—or biases—acting upon cells and populations of cells with very specific and constrained geometric properties, rather than arising solely from the vagaries of chance. " (my bolds)

Comment: Note the bolded comments, which imply there are underlying physical principles that guide these processes as well as genetic instructions, and therefore any chance events are not allowed. Certainly sounds designed by a designer.

Magic embryology: rules for growing a new fetus

by dhw, Wednesday, January 22, 2020, 14:35 (931 days ago) @ David Turell

QUOTE: The vast—and largely non-pictorial—literature on this subject does not offer a global mechanism to explain the rise of diverse forms of animal phyla. Though highly speculative, the model offered here may suggest just such a mechanism. The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry. Accordingly, the choices available to natural selection may be limited to the possible variations in proportions of the body parts of otherwise relatively conservative and invariant phyletic forms, rather than simply provided by random genetic mutations resulting from errors in transcription. Animal form may thus be seen as the product of physical forces—or biases—acting upon cells and populations of cells with very specific and constrained geometric properties, rather than arising solely from the vagaries of chance. " (David’s bolds)

DAVID: Note the bolded comments, which imply there are underlying physical principles that guide these processes as well as genetic instructions, and therefore any chance events are not allowed. Certainly sounds designed by a designer.

Your second bold is a clear indication that the author believes changing environmental conditions influence the behaviour of cell communities (he calls them “populations), though their “constrained properties” can hardly explain innovation. It is perfectly possible that your “underlying physical principles” may be guided by underlying mental activities. I am not sufficiently au fait with the terminology to understand your first bold, but I’d have thought that all the resemblances were EVIDENCE of common descent. Since you have bolded it, perhaps you can summarize the gist for me. As you know, I am as sceptical as you about “chance” being the driving force of evolution.

Magic embryology: rules for growing a new fetus

by David Turell @, Wednesday, January 22, 2020, 16:27 (931 days ago) @ dhw

QUOTE: The vast—and largely non-pictorial—literature on this subject does not offer a global mechanism to explain the rise of diverse forms of animal phyla. Though highly speculative, the model offered here may suggest just such a mechanism. The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry. Accordingly, the choices available to natural selection may be limited to the possible variations in proportions of the body parts of otherwise relatively conservative and invariant phyletic forms, rather than simply provided by random genetic mutations resulting from errors in transcription. Animal form may thus be seen as the product of physical forces—or biases—acting upon cells and populations of cells with very specific and constrained geometric properties, rather than arising solely from the vagaries of chance. " (David’s bolds)

DAVID: Note the bolded comments, which imply there are underlying physical principles that guide these processes as well as genetic instructions, and therefore any chance events are not allowed. Certainly sounds designed by a designer.

dhw: Your second bold is a clear indication that the author believes changing environmental conditions influence the behaviour of cell communities (he calls them “populations), though their “constrained properties” can hardly explain innovation. It is perfectly possible that your “underlying physical principles” may be guided by underlying mental activities. I am not sufficiently au fait with the terminology to understand your first bold, but I’d have thought that all the resemblances were EVIDENCE of common descent. Since you have bolded it, perhaps you can summarize the gist for me. As you know, I am as sceptical as you about “chance” being the driving force of evolution.

Homologies are similar formations in structure and for common descent he assumes the lookalikes are all set up by the same physical shaping forces all through time.

Magic embryology: rules for growing a new fetus

by dhw, Thursday, January 23, 2020, 10:01 (931 days ago) @ David Turell

QUOTE: The vast—and largely non-pictorial—literature on this subject does not offer a global mechanism to explain the rise of diverse forms of animal phyla. Though highly speculative, the model offered here may suggest just such a mechanism.The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry. Accordingly, the choices available to natural selection may be limited to the possible variations in proportions of the body parts of otherwise relatively conservative and invariant phyletic forms, rather than simply provided by random genetic mutations resulting from errors in transcription.bAnimal form may thus be seen as the product of physical forces—or biases—acting upon cells and populations of cells with very specific and constrained geometric properties, rather than arising solely from the vagaries of chance." (David’s bolds)

DAVID: Note the bolded comments, which imply there are underlying physical principles that guide these processes as well as genetic instructions, and therefore any chance events are not allowed. Certainly sounds designed by a designer.

dhw: Your second bold is a clear indication that the author believes changing environmental conditions influence the behaviour of cell communities (he calls them “populations), though their “constrained properties” can hardly explain innovation. It is perfectly possible that your “underlying physical principles” may be guided by underlying mental activities. I am not sufficiently au fait with the terminology to understand your first bold, but I’d have thought that all the resemblances were EVIDENCE of common descent. Since you have bolded it, perhaps you can summarize the gist for me. As you know, I am as sceptical as you about “chance” being the driving force of evolution.

DAVID: Homologies are similar formations in structure and for common descent he assumes the lookalikes are all set up by the same physical shaping forces all through time.

Thank you, but I understand “homologies” – it’s the “topogical trajectory” etc. that I don’t understand. But we agree about chance and common descent, so let’s leave it at that.

Magic embryology: rules for growing a new fetus

by David Turell @, Thursday, January 23, 2020, 22:34 (930 days ago) @ dhw

QUOTE: The vast—and largely non-pictorial—literature on this subject does not offer a global mechanism to explain the rise of diverse forms of animal phyla. Though highly speculative, the model offered here may suggest just such a mechanism.The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry. Accordingly, the choices available to natural selection may be limited to the possible variations in proportions of the body parts of otherwise relatively conservative and invariant phyletic forms, rather than simply provided by random genetic mutations resulting from errors in transcription.bAnimal form may thus be seen as the product of physical forces—or biases—acting upon cells and populations of cells with very specific and constrained geometric properties, rather than arising solely from the vagaries of chance." (David’s bolds)

DAVID: Note the bolded comments, which imply there are underlying physical principles that guide these processes as well as genetic instructions, and therefore any chance events are not allowed. Certainly sounds designed by a designer.

dhw: Your second bold is a clear indication that the author believes changing environmental conditions influence the behaviour of cell communities (he calls them “populations), though their “constrained properties” can hardly explain innovation. It is perfectly possible that your “underlying physical principles” may be guided by underlying mental activities. I am not sufficiently au fait with the terminology to understand your first bold, but I’d have thought that all the resemblances were EVIDENCE of common descent. Since you have bolded it, perhaps you can summarize the gist for me. As you know, I am as sceptical as you about “chance” being the driving force of evolution.

DAVID: Homologies are similar formations in structure and for common descent he assumes the lookalikes are all set up by the same physical shaping forces all through time.

dhw: Thank you, but I understand “homologies” – it’s the “topogical trajectory” etc. that I don’t understand. But we agree about chance and common descent, so let’s leave it at that.

Sorry about that. 'Topological trajectories' means shaping forms of organs and bodies from forces in tissues already in prior existence resulting in forcing more directional cell growth.

Magic embryology: rules for growing a new fetus

by dhw, Friday, January 24, 2020, 11:41 (929 days ago) @ David Turell

QUOTE: The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry.

DAVID: Homologies are similar formations in structure and for common descent he assumes the lookalikes are all set up by the same physical shaping forces all through time.

dhw: Thank you, but I understand “homologies” – it’s the “topogical trajectory” etc. that I don’t understand. But we agree about chance and common descent, so let’s leave it at that.

DAVID: Sorry about that. 'Topological trajectories' means shaping forms of organs and bodies from forces in tissues already in prior existence resulting in forcing more directional cell growth.

Thank you. Topology = the anatomy of any specific bodily area, structure or part. So if I may put this in plain English, they are saying that the similar formations are due to the fact that changes take place in existing structures though these remain basically the same. In that case, the similarities are not “due” partly to common descent; the similarities are the evidence for common descent!

Magic embryology: rules for growing a new fetus

by David Turell @, Friday, January 24, 2020, 20:39 (929 days ago) @ dhw

QUOTE: The homologous morphological resemblance among the phyla may, in fact, be due as much to the inevitable topological trajectory of the confined expansion of a primordial spherical membrane as it is to common ancestry.

DAVID: Homologies are similar formations in structure and for common descent he assumes the lookalikes are all set up by the same physical shaping forces all through time.

dhw: Thank you, but I understand “homologies” – it’s the “topogical trajectory” etc. that I don’t understand. But we agree about chance and common descent, so let’s leave it at that.

DAVID: Sorry about that. 'Topological trajectories' means shaping forms of organs and bodies from forces in tissues already in prior existence resulting in forcing more directional cell growth.

dhw: Thank you. Topology = the anatomy of any specific bodily area, structure or part. So if I may put this in plain English, they are saying that the similar formations are due to the fact that changes take place in existing structures though these remain basically the same. In that case, the similarities are not “due” partly to common descent; the similarities are the evidence for common descent!

The forces have to act on what exists in the very early embryo, which generally reflects the past shapes, result, the appearance of common descent as part of the process. We agree.

Magic embryology: requires exact timing for every tissue

by David Turell @, Wednesday, February 05, 2020, 16:55 (917 days ago) @ David Turell

Making an exact copy fetus requires exact programming:

https://www.knowablemagazine.org/article/living-world/2020/how-does-embryo-make-all-its...

"In all sorts of animals, from fruit flies to mice to elephants, cells follow fairly similar sets of steps to grow from embryo to adult. But while these steps follow the same order and often involve the same kinds of genes and molecular signals, they proceed at different rates from species to species.

***

"So what are the timers that keep things trucking along at the right rate for any given organism, ensuring that it grows to the proper size and with all its parts in place?

"Take one lone example among many: motor neurons, the nerves that make muscles contract. These develop from precursor cells over a few days in mice but a week or two in humans — and the same thing happens when the cells are grown in a dish. “We can look at this carefully and demonstrate it’s the same genetic process, the same gene activities, the same mechanisms involved, and it’s just running slower in humans than in mouse embryos,” Briscoe says. “We’re trying to tackle that problem.”

***

"First of all, for bodies to properly form, events must unfold in the right sequence: A before B, and B before C, and so on, at right times all over the developing body.

***

"For example, there’s a crisp order in how Drosophila neurons develop from stem cells in a part of the embryo called the ventral nerve cord. The stem cells produce neurons with different identities, one after the other; all of them develop, from the same pool of stem cells, just at different times, and once it’s time for the later types, there’s no going back to making earlier ones. They’re guided through this process by the sequential rise and fall of activity of a set of key genes.

"The second aspect of timing is far more mysterious: the molecular processes setting the tempo such that clocks run faster or slower in different species.

Scientists already have identified types of clocks in sundry tissues. Speaking generally, such molecular timers either “count up by steadily increasing the levels of a critical regulator until it exceeds a threshold, or count down by gradually decreasing the levels of an inhibitor,” Ebisuya and Briscoe write.

***

"Some clocks run through feedback loops, wherein proteins build up to a certain level and then act to shut down their production — creating cyclical oscillations that cells can harness to drive developmental steps. Vertebrates of all kinds depend on an oscillating clock of this type to create the right number of structures called somites, which later develop into the bones and muscles of the vertebral column.

"And in other cases, cells seem to keep track of how many times they’ve divided, says developmental biologist Mubarak Hussain Syed of the University of New Mexico, who studies the timing of gene activity during Drosophila early brain development. “The cell might be counting, ‘OK, we have done 20 divisions, and now it’s time’ ” for the next step, he says.

***

"Zooming in on details could yield a vast view. Scientists believe that changes in developmental timing — heterochronies, as they are called — had profound roles to play in the evolution of the diversity in body shapes and proportions we see in modern creatures. Snakes, for example, have many more vertebrae than do mice; they achieve this by running their segmentation clock at a faster clip relative to the development of other body parts. Giraffes come by their long necks another way: They have the same number of cervical vertebrae as their closest relatives, okapi, but those vertebrae are given more time to grow large.

"By revealing the molecular clocks that time growth, biologists may start to understand the influences that gave the world mice, humans and elephants to begin with."

Comment: Pure automaticity following a planned development. New cells respond to total controls. If this happens in embryos, as it must, it is easy to conclude all cells in fully developed organisms are are constantly following those overall instructions. No magical cell mental activity, making lone decisions by themselves when the cells turn from development to the regular activities of simply conducting the duties of living.

Magic embryology: requires exact timing for every tissue

by dhw, Thursday, February 06, 2020, 14:36 (916 days ago) @ David Turell

QUOTE: "In all sorts of animals, from fruit flies to mice to elephants, cells follow fairly similar sets of steps to grow from embryo to adult. But while these steps follow the same order and often involve the same kinds of genes and molecular signals, they proceed at different rates from species to species.”

DAVID: Pure automaticity following a planned development. New cells respond to total controls. If this happens in embryos, as it must, it is easy to conclude all cells in fully developed organisms are are constantly following those overall instructions. No magical cell mental activity, making lone decisions by themselves when the cells turn from development to the regular activities of simply conducting the duties of living.

As usual, you leap in with your automaticity once the species is established. Of course everything has to be repeated automatically if the new species is to survive. But this does not explain how speciation – i.e. all the differences between the species – arose in the first place. Similarly, it does not explain how cells adapt to changing conditions in order that the species can remain the same. You always focus on the established “routine” and then ignore every aspect of life’s history when the routine is somehow broken (origin of species, adaptation to new conditions, and innovation – when existing cell communities produce something new).

Nature’s Wonders: Ants
QUOTE: “'Put another way, ants, which have some of the most sophisticated and successful social structures in biology, do not practice a ‘shoot first and ask questions later’ social policy.'

DAVID: Note this is very tightly controlled automatic response, no thought involved, and indicates most animal responses are quite automatic.

And again as usual, you focus on the modes of perception rather than the mental processes that follow on from the perception. How do you imagine ants created their sophisticated and successful social structures and policies in the first place? Most human responses are also quite automatic. It’s what we and our fellow animals do with the information that suggests we are intelligent.

Magic embryology: requires exact timing for every tissue

by David Turell @, Friday, February 07, 2020, 01:27 (916 days ago) @ dhw

QUOTE: "In all sorts of animals, from fruit flies to mice to elephants, cells follow fairly similar sets of steps to grow from embryo to adult. But while these steps follow the same order and often involve the same kinds of genes and molecular signals, they proceed at different rates from species to species.”

DAVID: Pure automaticity following a planned development. New cells respond to total controls. If this happens in embryos, as it must, it is easy to conclude all cells in fully developed organisms are are constantly following those overall instructions. No magical cell mental activity, making lone decisions by themselves when the cells turn from development to the regular activities of simply conducting the duties of living.

dhw: As usual, you leap in with your automaticity once the species is established. Of course everything has to be repeated automatically if the new species is to survive. But this does not explain how speciation – i.e. all the differences between the species – arose in the first place. Similarly, it does not explain how cells adapt to changing conditions in order that the species can remain the same. You always focus on the established “routine” and then ignore every aspect of life’s history when the routine is somehow broken (origin of species, adaptation to new conditions, and innovation – when existing cell communities produce something new).

Once again I agree with the statement that we do not know how speciation happens. I'm surprised that you do not recognize epigenetics as art of the adaptive mechanism. As for cell committees, no evidence, and extremely unlikely. I'll stick with design.


Nature’s Wonders: Ants
QUOTE: “'Put another way, ants, which have some of the most sophisticated and successful social structures in biology, do not practice a ‘shoot first and ask questions later’ social policy.'

DAVID: Note this is very tightly controlled automatic response, no thought involved, and indicates most animal responses are quite automatic.

dhw: And again as usual, you focus on the modes of perception rather than the mental processes that follow on from the perception. How do you imagine ants created their sophisticated and successful social structures and policies in the first place? Most human responses are also quite automatic. It’s what we and our fellow animals do with the information that suggests we are intelligent.

All we know is the wrong smell makes an enemy. Since odorous compounds are complicated proteins, making them requires design, which I assume were given to the ants.

Magic embryology: requires exact timing for every tissue

by dhw, Friday, February 07, 2020, 13:09 (915 days ago) @ David Turell

DAVID: Pure automaticity following a planned development. New cells respond to total controls. If this happens in embryos, as it must, it is easy to conclude all cells in fully developed organisms are are constantly following those overall instructions. No magical cell mental activity, making lone decisions by themselves when the cells turn from development to the regular activities of simply conducting the duties of living.

dhw: As usual, you leap in with your automaticity once the species is established. Of course everything has to be repeated automatically if the new species is to survive. But this does not explain how speciation – i.e. all the differences between the species – arose in the first place. Similarly, it does not explain how cells adapt to changing conditions in order that the species can remain the same. You always focus on the established “routine” and then ignore every aspect of life’s history when the routine is somehow broken (origin of species, adaptation to new conditions, and innovation – when existing cell communities produce something new).

DAVID: Once again I agree with the statement that we do not know how speciation happens. I'm surprised that you do not recognize epigenetics as art of the adaptive mechanism. As for cell committees, no evidence, and extremely unlikely. I'll stick with design.

Intelligent cell communities ARE a theory of “design”. Where is your evidence for divine dabbling and/or preprogramming? What on earth makes you think I don’t recognize epigenetics as part of the adaptive system? How is this supposed to invalidate the concept of intelligent cells responding to the needs and opportunities of the environment by changing their structures? As for your “cell committees” (your term, not mine), do you deny the existence of cell communities, and do you deny that those communities are in constant contact with one another in all multicellular organisms?

Nature’s Wonders: Ants
QUOTE: “'Put another way, ants, which have some of the most sophisticated and successful social structures in biology, do not practice a ‘shoot first and ask questions later’ social policy.'”

DAVID: Note this is very tightly controlled automatic response, no thought involved, and indicates most animal responses are quite automatic.

dhw: And again as usual, you focus on the modes of perception rather than the mental processes that follow on from the perception. How do you imagine ants created their sophisticated and successful social structures and policies in the first place? Most human responses are also quite automatic. It’s what we and our fellow animals do with the information that suggests we are intelligent.

DAVID: All we know is the wrong smell makes an enemy. Since odorous compounds are complicated proteins, making them requires design, which I assume were given to the ants.

That is not all we know. We know that they have created sophisticated and successful social structures and policies and strategies to deal with both friends and enemies once their automatically operating senses have perceived who is who. Just like humans in fact. But apparently God had to preprogramme all this 3.8 billion years ago or come and do a dabble, because you know ants are automatons and only seem to be intelligent.

Magic embryology: requires exact timing for every tissue

by David Turell @, Friday, February 07, 2020, 21:23 (915 days ago) @ dhw


dhw: As usual, you leap in with your automaticity once the species is established. Of course everything has to be repeated automatically if the new species is to survive. But this does not explain how speciation – i.e. all the differences between the species – arose in the first place. Similarly, it does not explain how cells adapt to changing conditions in order that the species can remain the same. You always focus on the established “routine” and then ignore every aspect of life’s history when the routine is somehow broken (origin of species, adaptation to new conditions, and innovation – when existing cell communities produce something new).

DAVID: Once again I agree with the statement that we do not know how speciation happens. I'm surprised that you do not recognize epigenetics as art of the adaptive mechanism. As for cell committees, no evidence, and extremely unlikely. I'll stick with design.

dhw: Intelligent cell communities ARE a theory of “design”. Where is your evidence for divine dabbling and/or preprogramming? What on earth makes you think I don’t recognize epigenetics as part of the adaptive system?

Note this statement of yours:"it does not explain how cells adapt to changing conditions in order that the species can remain the same".

dhw: How is this supposed to invalidate the concept of intelligent cells responding to the needs and opportunities of the environment by changing their structures? As for your “cell committees” (your term, not mine), do you deny the existence of cell communities, and do you deny that those communities are in constant contact with one another in all multicellular organisms?

Cells are constantly in communication running the automatic processes of life. Only changes in germ cell DNA can speciate. These are the only cells to which you can reasonably refer, and they do not think and plan designs. A thinking mind must be present to design needed future changes.

Nature’s Wonders: Ants
QUOTE: “'Put another way, ants, which have some of the most sophisticated and successful social structures in biology, do not practice a ‘shoot first and ask questions later’ social policy.'”

DAVID: Note this is very tightly controlled automatic response, no thought involved, and indicates most animal responses are quite automatic.

dhw: And again as usual, you focus on the modes of perception rather than the mental processes that follow on from the perception. How do you imagine ants created their sophisticated and successful social structures and policies in the first place? Most human responses are also quite automatic. It’s what we and our fellow animals do with the information that suggests we are intelligent.

DAVID: All we know is the wrong smell makes an enemy. Since odorous compounds are complicated proteins, making them requires design, which I assume were given to the ants.

dhw: That is not all we know. We know that they have created sophisticated and successful social structures and policies and strategies to deal with both friends and enemies once their automatically operating senses have perceived who is who. Just like humans in fact. But apparently God had to preprogramme all this 3.8 billion years ago or come and do a dabble, because you know ants are automatons and only seem to be intelligent.

We can only tell they act intelligently, just as from the outside of cells all we can see is activity that looks intelligent or is the result of intelligently planned in automatic responses.

Magic embryology: requires exact timing for every tissue

by dhw, Saturday, February 08, 2020, 15:28 (914 days ago) @ David Turell

DAVID: I'm surprised that you do not recognize epigenetics as part of the adaptive mechanism. As for cell committees, no evidence, and extremely unlikely. I'll stick with design.

dhw: Intelligent cell communities ARE a theory of “design”. Where is your evidence for divine dabbling and/or preprogramming? What on earth makes you think I don’t recognize epigenetics as part of the adaptive system?

DAVID: Note this statement of yours:"it does not explain how cells adapt to changing conditions in order that the species can remain the same".

Why must I note my own statement? Why don’t you note it? Epigenetics does not explain how cells adapt! My proposal is that the cells themselves have the intelligent autonomous ability to adapt. Why did you raise the subject of epigenetics in the first place?

dhw: As for your “cell committees” (your term, not mine), do you deny the existence of cell communities, and do you deny that those communities are in constant contact with one another in all multicellular organisms?

DAVID: Cells are constantly in communication running the automatic processes of life.

Thank you. The cells run the show,whether automatic or non-automatic, and maybe it was your God who gave them the ability to do so. You’re cottoning on at last. Except that you refuse to see it, as follows:

DAVID: Only changes in germ cell DNA can speciate. These are the only cells to which you can reasonably refer, and they do not think and plan designs. A thinking mind must be present to design needed future changes.

There we go again. How do you know they don’t think? And I am tempted to carry out my threat and fill a page with the statement you keep ignoring:
MY THEORY IS THAT CELLS DO NOT PLAN DESIGNS NEEDED FOR FUTURE CHANGES. CELLS RESPOND TO NEEDS AS THEY ARISE. THEY DO NOT ANTICIPATE NEEDS.

DAVID re ants: We can only tell they act intelligently, just as from the outside of cells all we can see is activity that looks intelligent or is the result of intelligently planned in automatic responses.

Yes, yes, we’ve been over this a thousand times. They act intelligently, and you say there is a 50/50 chance that they are intelligent or they are automatons obeying your God’s instructions. You refuse to allow even a 50/50 chance of your being wrong, and so you reject 100% the possibility that they are intelligent.

Magic embryology: requires exact timing for every tissue

by David Turell @, Saturday, February 08, 2020, 18:59 (914 days ago) @ dhw

DAVID: I'm surprised that you do not recognize epigenetics as part of the adaptive mechanism. As for cell committees, no evidence, and extremely unlikely. I'll stick with design.

dhw: Intelligent cell communities ARE a theory of “design”. Where is your evidence for divine dabbling and/or preprogramming? What on earth makes you think I don’t recognize epigenetics as part of the adaptive system?

DAVID: Note this statement of yours:"it does not explain how cells adapt to changing conditions in order that the species can remain the same".

dhw: Why must I note my own statement? Why don’t you note it? Epigenetics does not explain how cells adapt! My proposal is that the cells themselves have the intelligent autonomous ability to adapt. Why did you raise the subject of epigenetics in the first place?

To answer, epigenetics is the only proven mechanism we know. As you seem to point out, we don't know how the mechanism is managed with the organisms, but, as I view it, it must be germ cells changing the next generations through reproduction. At your theory level they receive pleading messages from somatic cells to please fix things.


dhw: As for your “cell committees” (your term, not mine), do you deny the existence of cell communities, and do you deny that those communities are in constant contact with one another in all multicellular organisms?

DAVID: Cells are constantly in communication running the automatic processes of life.

dhw: Thank you. The cells run the show,whether automatic or non-automatic, and maybe it was your God who gave them the ability to do so. You’re cottoning on at last.

See comment above.

DAVID: Only changes in germ cell DNA can speciate. These are the only cells to which you can reasonably refer, and they do not think and plan designs. A thinking mind must be present to design needed future changes.

dhw: There we go again. How do you know they don’t think? And I am tempted to carry out my threat and fill a page with the statement you keep ignoring:
MY THEORY IS THAT CELLS DO NOT PLAN DESIGNS NEEDED FOR FUTURE CHANGES. CELLS RESPOND TO NEEDS AS THEY ARISE. THEY DO NOT ANTICIPATE NEEDS.

I fully know and understand your theory which I totally reject. Again note my concept above dtaht germ cells have to respond, if they can. I think God speciates directly.


DAVID re ants: We can only tell they act intelligently, just as from the outside of cells all we can see is activity that looks intelligent or is the result of intelligently planned in automatic responses.

dhw: Yes, yes, we’ve been over this a thousand times. They act intelligently, and you say there is a 50/50 chance that they are intelligent or they are automatons obeying your God’s instructions. You refuse to allow even a 50/50 chance of your being wrong, and so you reject 100% the possibility that they are intelligent.

As always I agree they act as if intelligent, but their intelligence is not proven, only an outsider's impression!

Magic embryology: managing DNA/chromosomes

by David Turell @, Saturday, February 29, 2020, 23:16 (893 days ago) @ David Turell

They are purposely handled in a 3-D manner:

https://phys.org/news/2020-02-gps-chromosomes-genome.html

"The spatial arrangement of genetic material within the cell nucleus plays an important role in the development of an organism.

***

" The reason why cells develop differently is that only parts of their chromosomes are read. This results in some genes being active while others, in contrast, are silent.

For gene activation, both the way the genes are packaged as well as their spatial organization in the cell nucleus play a decisive role.

***

"...chromosome domains segregated into two compartments, active and inactive. "During early embryogenesis, however, the chromosomes are organized differently," says Ahilya Sawh, first author of the study. "In the early embryo, they are organized into an unconventional barbell-like structure, with inactive compartments separated by a central active region." The researchers discovered that the nuclear lamina—a protein mesh lining the inner surface of the cell nucleus—is required to achieve this barbell arrangement. The lamina is attached to the inactive sections and stretches the chromosome.

"'Only at a later stage of embryonic development, when the germ layers develop, we actually see the well-known segregation into an active and inactive region," explains Mango. "Using chromosome tracing, we were able to map the whole 3-D chromosome architecture and could show for the first time that chromosomes rearrange during early development, a maturation process that requires the nuclear lamina."

"The reorganization of the chromosomes accompanies cell maturation and represents a milestone in the development of a complex organism. The correct chromosomal architecture is crucial to prevent developmental disorders."

Comment: This kind of 3-D control is a highly designed mechanism. It cannot be developed by chance. That is the choice: chance or design by a designer.

Magic embryology: rapid stem cell differentiation

by David Turell @, Sunday, April 19, 2020, 22:58 (843 days ago) @ David Turell

It occurs earlier than thought:

https://phys.org/news/2020-04-stem-cells-human-embryos-commit.html

"Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation.

***

"As part of the research, published in Cell Stem Cell, Crick scientists found that embryonic stem cells differentiate unexpectedly early, irreversibly committing to become each of the more than 200 cell types in the body.

They showed this was as a result of a newly identified small group of genes becoming activated, which they named 'early-commitment genes'.

"'Working with stem cells and mathematical models, we've identified a new class of genes which are responsible for regulating one of the earliest stages of human development," says Silvia Santos, author and group leader in the Quantitative Cell Biology Laboratory at the Crick.

"'Once these genes are activated, it's a question of minutes before the cells fully commit to differentiation. The speed of this is incredibly surprising, especially if you consider how the first signs of differentiation, that's the embryo developing the first embryonic germ layers, take about three days. These layers ultimately give rise to all the tissues in the growing foetus weeks later."

"The researchers focused on one early-commitment gene, called GATA3. When this gene was activated experimentally in the lab, embryonic stem cells quickly committed to differentiation. On the other hand, when this gene was deleted, this process was sluggish and not quite right.

"'GATA3 is crucial to the healthy, timely differentiation of stem cells. Once it's switched on, this gene triggers a positive feedback loop, which helps it stay active. In turn, this ensures that the cells remain differentiated, and do not reverse back to a stem cell state," says Alexandra Gunne-Braden, co-lead author and postdoc in the Quantitative Cell Biology Laboratory at the Crick.

Comment: when life was single-celled, reproduction was simply cells splitting. The evolution of sexual reproduction has never been explained by evolution theory. It is high complex, and must be tightly controlled to avoid errors, noting the high speed of the process. This research tells us something of how it works, not how it was created. Design is required by a designer.

Magic embryology: rapid stem cell differentiation

by dhw, Monday, April 20, 2020, 15:19 (842 days ago) @ David Turell

QUOTE: "Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation.
"Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation
.

DAVID: when life was single-celled, reproduction was simply cells splitting. The evolution of sexual reproduction has never been explained by evolution theory. It is high complex, and must be tightly controlled to avoid errors, noting the high speed of the process. This research tells us something of how it works, not how it was created. Design is required by a designer.

I have always suspected that stem cells were the foundation stones of evolution, thanks to their ability to differentiate. Exciting stuff! And yes, I have always acknowledged the case for design, which is a major reason why I am not an atheist. You already know the reasons why I am not a theist either.

Magic embryology: rapid stem cell differentiation

by David Turell @, Monday, April 20, 2020, 16:15 (842 days ago) @ dhw

QUOTE: "Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation.
"Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation
.

DAVID: when life was single-celled, reproduction was simply cells splitting. The evolution of sexual reproduction has never been explained by evolution theory. It is highly complex, and must be tightly controlled to avoid errors, noting the high speed of the process. This research tells us something of how it works, not how it was created. Design is required by a designer.

dhw: I have always suspected that stem cells were the foundation stones of evolution, thanks to their ability to differentiate. Exciting stuff! And yes, I have always acknowledged the case for design, which is a major reason why I am not an atheist. You already know the reasons why I am not a theist either.

Correction. Stem cells are programmed to be exact copiers, not evolvers. That job is in the germ cells DNA to carry over new changes, but we do not know exactly how it works for new species.

Magic embryology: rapid stem cell differentiation

by dhw, Tuesday, April 21, 2020, 13:08 (841 days ago) @ David Turell

QUOTE: "Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation."

DAVID: when life was single-celled, reproduction was simply cells splitting. The evolution of sexual reproduction has never been explained by evolution theory. It is highly complex, and must be tightly controlled to avoid errors, noting the high speed of the process. This research tells us something of how it works, not how it was created. Design is required by a designer.

dhw: I have always suspected that stem cells were the foundation stones of evolution, thanks to their ability to differentiate. Exciting stuff! And yes, I have always acknowledged the case for design, which is a major reason why I am not an atheist. You already know the reasons why I am not a theist either.

DAVID: Correction. Stem cells are programmed to be exact copiers, not evolvers. That job is in the germ cells DNA to carry over new changes, but we do not know exactly how it works for new species.

According to my science dictionary, the stem cell is “an undifferentiated cell, particularly in an embryo, capable of unlimited division and of producing daughter cells that develop into different cell types, which in turn give rise to different tissues and organs.” How this comes to mean that they are “exact copiers” I really don’t know, and a cell that can give rise to different tissues and organs sounds to me like the perfect foundation for evolution.

Magic embryology: rapid stem cell differentiation

by David Turell @, Tuesday, April 21, 2020, 19:24 (841 days ago) @ dhw

QUOTE: "Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation."

DAVID: when life was single-celled, reproduction was simply cells splitting. The evolution of sexual reproduction has never been explained by evolution theory. It is highly complex, and must be tightly controlled to avoid errors, noting the high speed of the process. This research tells us something of how it works, not how it was created. Design is required by a designer.

dhw: I have always suspected that stem cells were the foundation stones of evolution, thanks to their ability to differentiate. Exciting stuff! And yes, I have always acknowledged the case for design, which is a major reason why I am not an atheist. You already know the reasons why I am not a theist either.

DAVID: Correction. Stem cells are programmed to be exact copiers, not evolvers. That job is in the germ cells DNA to carry over new changes, but we do not know exactly how it works for new species.

dhw: According to my science dictionary, the stem cell is “an undifferentiated cell, particularly in an embryo, capable of unlimited division and of producing daughter cells that develop into different cell types, which in turn give rise to different tissues and organs.” How this comes to mean that they are “exact copiers” I really don’t know, and a cell that can give rise to different tissues and organs sounds to me like the perfect foundation for evolution.

Your dictionary is correct. The stem cells follow what instructions the germ cells give in their DNA. The are bound by those instructions to exactly reproduce what came before: horse makes horse, fox makes fox, robin makes robin. An unwanted mutation in an embryo stem cell can create a monster.

Magic embryology: rapid stem cell differentiation

by dhw, Wednesday, April 22, 2020, 11:47 (841 days ago) @ David Turell

DAVID: Correction. Stem cells are programmed to be exact copiers, not evolvers. That job is in the germ cells DNA to carry over new changes, but we do not know exactly how it works for new species.

dhw: According to my science dictionary, the stem cell is “an undifferentiated cell, particularly in an embryo, capable of unlimited division and of producing daughter cells that develop into different cell types, which in turn give rise to different tissues and organs.” How this comes to mean that they are “exact copiers” I really don’t know, and a cell that can give rise to different tissues and organs sounds to me like the perfect foundation for evolution.

DAVID: Your dictionary is correct. The stem cells follow what instructions the germ cells give in their DNA. The are bound by those instructions to exactly reproduce what came before: horse makes horse, fox makes fox, robin makes robin. An unwanted mutation in an embryo stem cell can create a monster.

Obviously, but the definition tells us that stem cells can produce cells which give rise to different tissues and organs, and the article you quoted says: "Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation.” I’ve also read that stem cells are used in various treatments to repair defects, as they can adopt different “identities”. If our whole history can be traced back to stem cells, which are capable of giving rise to different organs, doesn’t that suggest that they provide the foundations for evolution? I’m asking, not telling. You are the scientist.

Magic embryology: rapid stem cell differentiation

by David Turell @, Wednesday, April 22, 2020, 23:22 (840 days ago) @ dhw

DAVID: Correction. Stem cells are programmed to be exact copiers, not evolvers. That job is in the germ cells DNA to carry over new changes, but we do not know exactly how it works for new species.

dhw: According to my science dictionary, the stem cell is “an undifferentiated cell, particularly in an embryo, capable of unlimited division and of producing daughter cells that develop into different cell types, which in turn give rise to different tissues and organs.” How this comes to mean that they are “exact copiers” I really don’t know, and a cell that can give rise to different tissues and organs sounds to me like the perfect foundation for evolution.

DAVID: Your dictionary is correct. The stem cells follow what instructions the germ cells give in their DNA. The are bound by those instructions to exactly reproduce what came before: horse makes horse, fox makes fox, robin makes robin. An unwanted mutation in an embryo stem cell can create a monster.

dhw: Obviously, but the definition tells us that stem cells can produce cells which give rise to different tissues and organs, and the article you quoted says: "Our biological history can be traced back to a small group of cells called embryonic stem cells, which through cell division, give rise to cells that specialise to perform a specific role in the body—a process known as differentiation.” I’ve also read that stem cells are used in various treatments to repair defects, as they can adopt different “identities”. If our whole history can be traced back to stem cells, which are capable of giving rise to different organs, doesn’t that suggest that they provide the foundations for evolution? I’m asking, not telling. You are the scientist.

You are trying to stretch a definition. Stick with my quote above. The zygote, formed from the junction of sperm and egg carry all the genome instructions and stem cells follow the definitive rules.

Magic embryology: guiding limb formation

by David Turell @, Wednesday, June 03, 2020, 21:51 (798 days ago) @ David Turell

A special gradation of molecular action:

https://phys.org/news/2020-06-essential-limb-formation-embryonic.html

Researchers at the Centro Nacional de Investigaciones Cardiovasculares (CNIC) have discovered a system that provides cells with information about their position within developing organs. This system, studied in developing limbs, tells cells what anatomical structure they need to form within the organ.

***

Embryonic development is one of the most fascinating processes in nature and has aroused scientific interest since the time of Aristotle. The generation of millions of cells from a single progenitor and their organization to produce the precise anatomy of each species is one of the most astounding examples of a self-organizing system.

***

The positional information theory, first proposed more than 50 years ago by the British scientist Lewis Wolpert, hypothesized a mechanism through which cells obtain information about their position in the embryo. "This system can be compared to the GPS geolocation systems used by cell phones," Dr. Torres continued. "GPS systems consist of an external reference—the satellite signals—and a mechanism for interpreting these signals, housed in each of our cell phones. In biological systems, the positional information in each cell triggers a distinct and specific developmental plan at each location."

The CNIC team, working with partners at the National Institutes of Health in the U.S., analyzed the molecular basis of limb formation. The scientists discovered how cells obtain information about their position on the proximodistal axis of the limb bud, or primordium (the rudimentary state of a developing organ.)

Study first author Dr. Irene Delgado said, "Our work shows that the signal that tells cells where they are is the growth factor FGF." FGF molecules are produced exclusively by a small group of cells at the distal tip of the limb bud, furthest away from the body trunk.

The strength of the signal received by cells depends on how close they are to the FGF-producing cells. In other words, explained Dr. Delgado, "the more distal a cell is, the stronger the FGF signal it receives, whereas more proximal cells receive a weaker signal."

The researchers demonstrated that the molecule in receptor cells that interprets FGF signals is a transcription factor called Meis. This transcription factor is distributed in a linear abundance gradient, so that it is highly abundant in proximal cells (close to the body trunk) and becomes progressively less abundant in more distal positions. In other words, clarified Dr. Torres, "the amount of Meis in each cell reflects the amount of FGF received, and thus marks the cell's position along the proximodistal axis of the developing limb."

Transcription factors regulate the function of the genome, modulating cell behavior by switching some genes on and switching others off. Depending on the amount of Meis in a cell, specific groups of genes, including Hox genes, are activated, corresponding to the cell's position along the proximodistal axis. "Cells that receive an instruction that their position is proximal are programmed to generate the shoulder, whereas more distal cells are programmed to form the hand, and cells in an intermediate position form the upper arm, elbow, or forearm," said Delgado.

comment: The embryo must become an exact copy of its parents. This is a highly designed system that requires a designer.

Magic embryology: epigenetic controls

by David Turell @, Tuesday, August 04, 2020, 21:37 (736 days ago) @ David Turell

A new study of these controls:

https://www.sciencedaily.com/releases/2020/08/200804111532.htm

"A research team at the Max Planck Institute for Molecular Genetics in Berlin has explored the role of factors in embryonic development that do not alter the sequence of DNA, but only epigenetically modify its "packaging." In the scientific journal Nature, they describe how regulatory mechanisms contribute to the formation of different tissues and organs in early mouse embryos.

***

"Epigenetic regulator factors are part of this molecular mechanism and act to modify the "packaging" of the DNA molecule without altering the underlying genetic information. Specifically, they act to bookmark the DNA and control what parts can be accessed in each cell.

***

"'The same regulator is present in all cells, but can have very different tasks, depending on cell type and time of development," says Stefanie Grosswendt, one of the first authors of a new study in the scientific journal Nature.

***

"An eight-day-old mouse embryo looks a bit like a seahorse and does not have any organs yet. "From the outer appearance of an early embryo, one can often only guess which structures and organs will form and which will not," say bioinformatician Helene Kretzmer and biologist Zachary Smith, who are also both first authors of the publication. "Our sequencing allows for a much more precise and high resolution view."

"The single-cell analysis gave them a highly detailed view over the first nine days of mouse development. Often, switching off a single regulator led to ripple effects throughout the network of interacting genes, with many differentially activated or inactivated genes over the course of development.

"Removing the epigenetic regulator Polycomb (PRC2) had a particularly striking impact. "Without PRC2, the embryo looks egg-shaped and very small after eight and a half days, which is very unusual," says Kretzmer. "We see vast changes to how DNA is packaged that happens much earlier, long before the embryo develops morphological abnormalities."

***

"The researchers found that PRC2 is responsible for limiting the amount of germline progenitor cells -- the cells that later become sperm and eggs. Without PRC2, the embryo develops an excessive number of these cells, loses its shape, and dies after a short time.

Comment: Obviously, since many tissues are so different in form and functions, there have to be regulators to active that portion of DNA that for each specific cell type. This degree of complexity has to be designed. Not by chance.

Magic embryology: constantly influenced by the biome

by David Turell @, Thursday, August 27, 2020, 19:11 (713 days ago) @ David Turell

The microbiome is always a part of embryological development:

https://phys.org/news/2020-08-environment-microbiome-jointly-body.html

"All multicellular living beings are colonized by an unimaginably large number of microorganisms and have developed together with them from the very beginning of multicellular life. The natural microbiome, i.e. the totality of these bacteria, viruses and fungi that live in and on a body, is of fundamental importance for the entire organism: it supports, for example, the absorption of nutrients or fends off pathogens. The individual development of a living being, on the other hand, was long regarded as a purely genetically determined process that is independent of external factors. For some time now, however, it has become clear that developmental processes do not take place autonomously either. Most living beings have developed strategies to recognize changes in their environment and to adapt their individual growth and thus also the resulting body shape to the prevailing conditions. But how this so-called phenotypic plasticity is controlled and how environmental factors including microbial influences are recognized and integrated into genetic development programs has only recently become the subject of research.

***

"The researchers were able to identify two Hydra specific genes and demonstrate their involvement in a signaling pathway central to development, which together control the response of the polyp to cues from its environment.

***

"The effects of phenotypic plasticity can thus be traced back to Hydra-specific genes that regulate the adaptation to external influences in this organism. The study thus provides an example of the importance of such genetic information, also known as 'orphan genes' due to the lack of corresponding genes in other species. These rapidly evolving genes allow different organisms to adapt to new energy sources or habitats, for example. "It was already known that these genes intervene, for example, in the developmental program of a living being or are linked to the regulation of its immune system in order to implement an environmental reaction during development," explains co-author Professor Thomas Bosch from Kiel University, head of the Collaborative Research Center 1182. "Our work now reveals an exemplary mechanisms that underlie this recognition of external factors. In this way, we were able to demonstrate which internal processes ultimately lead to the adaptation of a living being's developmental program in response to its environment," Bosch says."

Comment: All of us are inhabited by friendly microbiomes that are integrated with the genetic systems in a cooperative effort. This is as finely tuned as any ecosystem and really is one. As noted before, this is why bacteria are still around, as necessary. Now we can include viruses and fungi. No mistakes here.

Magic embryology: human segmentation is lower

by David Turell @, Thursday, September 17, 2020, 20:35 (692 days ago) @ David Turell

As compared to mice. Gene controls found:

https://phys.org/news/2020-09-humans-slowly-mice-chemistry.html

"In the early phase of the development of vertebrates, the embryo develops into a series of 'segments' that eventually differentiate into different types of tissues, such as muscles or the ribs. This process is known to be governed by an oscillating biochemical process, known as the segmentation clock, which varies between species. For example, it is about two hours in mice, and about five hours in humans. Why the length of this cycle varies between species has remained a mystery, however.

To solve this mystery, the group began experiments using embryonic stem cells for mice and induced pluripotent stem (iPS) cells which they transformed into presomitic mesoderm (PSM) cells, the cells that take part in the segmentation clock.

***

"'Failing to show a difference in the genes left us with the possibility that the difference was driven by different biochemical reactions within the cells." They looked at whether there were differences in factors such as the degradation rate of the HES7 protein, an important factor in the cycle. They looked at a number of processes including how quickly mouse and human proteins were degraded and found, confirming the hypothesis, that both proteins were degraded more slowly in human cells than in mouse cells. There were also differences in the time it took to transcribe and translate HES7 into proteins, and the time it took for HES7 introns to be spliced. "We could thus show," says Ebisuya, "that it was indeed the cellular environment in human and mouse cells that is the key to the differential biochemical reaction speeds and thus differential time scales."

"She continues, "Through this we have come up with a concept that we call developmental allochrony, and the present study will help us to understand the complicated process through which vertebrates develop. One of the key remaining mysteries is exactly what is difference between the human and mouse cells that drives the difference in reaction times, and we plan to do further studies to shed light on this.'"

Comment: With our degree of complexity, it is not surprising we have a different segmentation rate. That it is so complex suggests it is finely complexly designed.

Magic embryology: human development is slower

by David Turell @, Saturday, September 19, 2020, 18:21 (690 days ago) @ David Turell

Control mechanisms are found:

https://www.sciencedaily.com/releases/2020/09/200917181310.htm

"All mammals follow the same steps to grow from embryo to adult. This involves the same series of events, in the same sequence, using similar genes and molecular signals. However, the speed of progress through these steps differs considerably from one species to another. For instance, motor neurons -- the nerve cells that control muscle movement -- take about three days to develop in mice, but over a week to develop in humans.

***

"...the researchers discovered that differences in the speed at which proteins are broken down and replaced explains the difference in speed between the two species. Proteins are constantly turned over -- made and dismantled -- in cells, and this happens twice as fast in mouse cells compared to human cells. This faster rate of protein turnover in mouse cells accounts for the faster pace of motor neuron formation.

"Teresa Rayon explained, "Human and mouse motor neurons use the same genes and molecules for their embryonic development, it just takes longer for the process to play out in humans. Proteins are simply more stable in humans than mouse embryos and this slows the rate of human development."

"'It's as if mouse and human embryos are reading the same musical score and playing the same tune but the metronome ticks more slowly in humans than in mice. Now that we've found the metronome, we want to understand how to change its speed.'"

Comment: The differences are not surprising, but humans are not the slowest. Gestation in elephants is 22 months.

Magic embryology: mechanical forces reviewed

by David Turell @, Wednesday, January 13, 2021, 19:07 (574 days ago) @ David Turell

Still poorly understood:

https://www.nature.com/articles/d41586-021-00018-x?utm_source=Nature+Briefing&utm_c...

"At first, an embryo has no front or back, head or tail. It’s a simple sphere of cells. But soon enough, the smooth clump begins to change. Fluid pools in the middle of the sphere. Cells flow like honey to take up their positions in the future body. Sheets of cells fold origami-style, building a heart, a gut, a brain.

"None of this could happen without forces that squeeze, bend and tug the growing animal into shape. Even when it reaches adulthood, its cells will continue to respond to pushing and pulling — by each other and from the environment.

"Yet the manner in which bodies and tissues take form remains “one of the most important, and still poorly understood, questions of our time”, says developmental biologist Amy Shyer, who studies morphogenesis

***

"Maître’s group investigated how the initial ball of cells comprising the very early mouse embryo develops a large, fluid-filled cavity called the lumen. As this cavity fills, the cells that will become the fetus are pushed together on one side. This first symmetry-breaking event ensures that the embryo implants into the uterine wall correctly, and also governs which side of the embryo will be the back and which the belly. What wasn’t clear was how the embryo creates and positions the lumen

***

"Later in development, embryos break symmetry in another direction, differentiating head from tail.

***

"They found that the tip of the growing tail was in a state that physicists call ‘fluid’ — the cells flowed freely, and when pressed, the tissue deformed easily. The farther the scientists got from the tail end, the more rigid the tissue became. “We knew that it was solidifying, but we didn’t know the mechanism,” Campàs recalls.

***

"As the cells crowded together, the tissue solidified. Campàs compares the transition to coffee grains being packaged: the grains flow freely into a bag, but become so tightly packed that the filled bag feels like a brick. He plans to investigate whether this mechanism underlies the formation of other embryonic structures, such as limb buds.

***

"Once the developing embryo has mapped itself out, individual organs begin to form. “Fundamentally, we have a poor understanding of how any internal organ forms,” says Timothy Saunders, a developmental biologist at the National University of Singapore.

***

"There’s a crucial event when two pieces of tissue come together to form a tube that will ultimately become the heart. Each piece contains two kinds of heart-muscle cell. The pieces must zip up correctly, pairing like with like, for a healthy heart to emerge. “We often saw misalignment that was then corrected,” says Saunders. “What’s causing the correction?”

***

"Simple cell proliferation can also signal cells to arrange themselves properly, as researchers at the University of Cambridge, UK, discovered in embryos of the clawed frog Xenopus. The team, led by physical biologist Kristian Franze, already knew that as the eye and brain wire up, the eye neurons send out their axons — long projections that neurons use to contact each other — along a pathway defined by the stiffness of the brain tissue. Eye axons follow softer tissues towards a central hub in the developing brain

***

"As in the developing zebrafish tails, the stiffer tissue in the frog brains seemed to contain a greater density of cells. When the team blocked cell division in the developing embryos, the stiffness gradient never appeared — and the axons couldn’t find their way. Packing a space with cells seems to be a quick and effective way to guide the wiring-up of the nervous system."

Comment: All fun and games in research. We see how it happens but have no idea what is guiding the developments, except the general knowledge it must come from the genome. Only a designing mind can create this process of embryological reproduction.

Magic embryology: how the placenta appears

by David Turell @, Thursday, October 01, 2020, 21:19 (678 days ago) @ Balance_Maintained

Certain cells from the original fertilized egg form the placenta:

https://science.sciencemag.org/content/370/6512/19

"The placenta—a Frisbee-size hunk of tissue that chaperones a fetus in the uterus only to be tossed aside in the delivery room—has mysterious beginnings. The organ emerges from cells that develop alongside the embryo, and that have been difficult to grow in the lab. Now, researchers have devised a way to derive and observe early precursors of placental cells in a dish. They have found a method of “reprogramming” adult cells, reverting them to a primitive state, that can prompt them to become trophoblast stem cells (TSCs), which give rise to placental cells.

***

"Those steps begin just days after a sperm and egg join. “The first decision in human life is to set aside the placental, supportive cells,” says Kathy Niakan, a developmental biologist at the Francis Crick Institute, whose team reported key molecular signals for that initial step in Nature last week. These cells go on to form the trophoblast, a multilayered ring that surrounds the embryo and helps it implant into the wall of the uterus. Some of these cells, TSCs, then give rise to cell types that will make up the bulk of the placenta, which enables mother and fetus to exchange nutrients and gases and helps protect the fetus from the mother's immune system.

***

"Polo's team reported that these induced TSCs could develop into two major types of trophoblast cells and, like the cells surrounding an embryo, secrete human chorionic gonadotropin, a hormone whose signals are key to maintaining a pregnancy. David, a co-author on that paper, separately used gene expression data from human embryos to estimate that his own group's lab-derived TSCs are equivalent to those seen 8 to 10 days after fertilization, the team reported on 15 September in a preprint on bioRxiv."

Comment: Still not completely understood, but a highly complex process. Live birth requires this arrangement as there is no feeding yolk for food supply. The m other has to be the supplier. The placenta itself is very complex in its parts and actions. This had to be designed.

Magic embryology: how the placenta appears

by David Turell @, Sunday, October 25, 2020, 18:13 (654 days ago) @ David Turell

More on the genetics and stem cell changes:

https://www.nature.com/articles/d41586-020-02914-0

"The placenta is a defining feature of being a mammal, and its formation is one of the first steps in mammalian development. The embryo begins to make its placenta without direct guidance from its mother — rather, it follows a set of molecularly encoded, do-it-yourself assembly instructions. (my bold)

***

"...studies established that the ball-shaped mouse embryo develops an external ‘rind’ of cells fated to become placenta about three days after fertilization. These cells, called the trophectoderm, encircle a group of inner cells that are considered pluripotent — they possess the capacity to produce all cell types of the body, [ i.e., stem cells]

"In mouse embryos, this first cellular differentiation involves the polarization of trophectoderm cells along one axis, known as the apical–basal axis. Cell-polarity proteins accumulate on the apical side of trophectoderm cells, repressing signalling through the HIPPO pathway. By contrast, HIPPO signalling is active in the pluripotent cells, because they are unpolarized. In the pluripotent cells, HIPPO signalling prevents the transcription factor YAP1 from moving to the nucleus. In trophectoderm cells, nuclear YAP1 promotes the expression of the trophectoderm genes Cdx2 and Gata3, and represses the pluripotency gene Sox2

***

"...the authors analysed gene expression in human and cow embryos, and demonstrated that YAP1 localization and GATA3 gene expression are conserved between species as the trophectoderm emerges. Next, they disrupted cell polarization in each species by inhibiting atypical protein kinase C (aPKC), a key polarization protein. This prevented nuclear localization of YAP1, and disrupted GATA3 expression. These observations point to a conserved gene-regulatory module that governs the first cell-fate decision in mouse, cow and human embryos

***

"Discoveries in mouse and human embryos contribute directly to our understanding of stem-cell biology. Cultured stem cells were first derived from both pluripotent and trophectoderm cells of the mouse embryo, paving the way for the establishment of stem-cell lines from human embryos."

Comment: Note the reference to informative instructions in my bold in the first paragraph. Only a designer could supply them

Magic embryology: first breath controls

by David Turell @, Sunday, December 06, 2020, 00:07 (613 days ago) @ David Turell

Placental embryos don't have to breath, but after birth a fist breath and thereafter automatic breathing must occur. this is under neural control:

https://www.sciencedaily.com/releases/2020/12/201204110218.htm

"A new discovery reveals how something amazing happens when a baby takes a first breath.

"A team of researchers led by UVA's Yingtang Shi, MD; Patrice Guyenet, PhD; and Douglas A. Bayliss, PhD, have discovered a signaling system within the brainstem that activates almost immediately at birth to support early breathing. That first gasp that every parent cherishes appears to trigger this support system.

"'Birth is traumatic for the newborn, as the baby has to independently take control over various important body functions, including breathing," said Bayliss, chairman of UVA's Department of Pharmacology. "We think that activation of this support system at birth provides an extra safety factor for this critical period."

***

"Bayliss and his colleagues at UVA, working with researchers at the University of Alberta and Harvard University, found that a specific gene is turned on immediately at birth in a cluster of neurons that regulate breathing selectively in mice. This gene produces a peptide neurotransmitter -- a chain of amino acids that relays information between neurons. This transmitter, called PACAP, starts to be released by these neurons just as the baby emerges into the world.

"The scientists determined that suppressing the peptide in mice caused breathing problems and increased the frequency of apneas, which are potentially dangerous pauses in breathing. These apneas further increased with changes in environmental temperature.

***

"PACAP is the first signaling molecule shown to be massively and specifically turned on at birth by the breathing network,"

Comment: obviously some specific safety system of this sort had to exist. Certainly more evidence of design. Live birth could not have started unless this was already in place.

Magic embryology: master gene controls in embryo forming

by David Turell @, Tuesday, December 22, 2020, 18:54 (596 days ago) @ David Turell

From a study of Caenorhabditis elegans:

https://phys.org/news/2020-12-roundworms.html

"Transforming a fertilized egg into a fully functional adult is a complicated task. Cells must divide, move, and mature at specific times. Developmental genes control that process, turning on and off in a choreographed way. However, the environment influences development. A team of researchers ...reported December 22, 2020 in the journal Current Biology how gene activity matches nutrient levels. They found a master switch developing worms use to pause growth when nutrients are scarce. When the environment improves, animals continue developing. The switch adjusts gene activity to match nutrient levels.

***

"'This always happens the same way. You always get 959 cells, and the patterns of those divisions that give you those cells are always done in the same manner between one animal and the next."

"The genes that direct this flexible program switch on and off in predictable patterns as an embryo morphs through several larval stages into a fully formed worm.

"In the wild, developing worms can't always depend on comfortable temperatures and plentiful food. Sometimes, development must pause until conditions improve. Hammell's team discovered a protein called BLMP-1 that adjusts gene activity (transcription) to keep pace with development. When conditions are good, BLMP-1 levels increase and unravel stretches of DNA, so genes are more accessible. Activators then switch on the genes at the right time. "This is an anticipatory mechanism to say 'everything's okay, make development as robust as possible,'" Hammell explains. If conditions are not optimal, BLMP-1 levels go down, leaving genes packed tightly away, slowing or even stopping development.

"The team's experiments revealed BLMP-1 as a master regulator of thousands of genes that cycle on and off during development. Hammell says that was a surprise since his team initially set out to investigate this process in just a handful of developmental genes. BLMP-1 is unique in that it coordinates many different kinds of processes."

Comment: The development of any embryo is an engineering project that must follow a designed plan. The secret is in DNA with certain controlling genes. How they really work is totally unknown. How evolution developed it is also totally mysterious. Only a designer mind can do this.

Magic embryology: sticky cells group together

by David Turell @, Friday, December 25, 2020, 18:54 (593 days ago) @ David Turell

Magic embryology is a system that is under tight instructions:

https://www.eurekalert.org/pub_releases/2020-12/tu-ptd122420.php

"Scientists have long observed that not-yet-specialized cells move in a way that ensures that cell groups destined for a specific tissue stay together. In 1964, American biologist Malcolm Steinberg proposed that cells with similar adhesiveness move to come in contact with each other to minimize energy use, producing a thermodynamically stable structure. This is known as the differential adhesion hypothesis.

***

"'Our study showed, for the first time, that cell sorting is regulated by changes in adhesion."

"Kuranaga and her team conducted experiments in fruit fly pupae, finding that a gene, called Toll-1, played a major role in this adhesion process.

"As fruit flies develop from the immature larval stage into the mature adult, epithelial tissue-forming cells, called histoblasts, cluster together into several 'nests' in the abdomen. Each nest contains an anterior and a posterior compartment. Histoblasts are destined to replace larval cells to form the adult epidermis, the outermost layer that covers the flies. The cells in each compartment form discrete cell populations, so they need to stick together, with a distinct boundary forming between them.

"Using fluorescent tags, Kuranaga and her team observed the Toll-1 protein is expressed mainly in the posterior compartment. Its fluorescence also showed a sharp boundary between the two compartments.

"Further investigations showed Toll-1 performs the function of an adhesion molecule, encouraging similar cells to stick together. This process keeps the boundary between the two compartments straight, correcting distortions that arise as the cells divide to increase the number.

"Interestingly, Toll proteins are best known for recognizing invading pathogens, and little is known about their work beyond the immune system. "Our work improves understanding of the non-immune roles of Toll proteins," says Kuranaga. She and her team next plan to study the function of other Toll genes in fruit fly epithelial cells."

Comment: this is all under tight instructions from an intelligent design. Developmental embryology is a complete refutation of Darwin's theory. A chance development of this process is impossible.

Magic embryology: placenta like no other organ

by David Turell @, Wednesday, March 10, 2021, 18:23 (518 days ago) @ David Turell

Has many mutations and seems to screen for them:

https://medicalxpress.com/news/2021-03-placenta-dumping-ground-genetic-defects.html

"In the first study of the genomic architecture of the human placenta, scientists at the Wellcome Sanger Institute, the University of Cambridge and their collaborators have confirmed that the normal structure of the placenta is different to any other human organ and resembles that of a tumor, harboring many of the same genetic mutations found in childhood cancers.


"The study, published today in Nature, found evidence to support the theory of the placenta as a 'dumping ground' for genetic defects, whereas the fetus corrects or avoids these errors. The findings provide a clear rationale for studying the association between genetic aberrations and birth outcomes, in order to better understand problems such as premature birth and stillbirth.

***

"It has long been known that the placenta is different from other human organs. In one to two percent of pregnancies, some placental cells have a different number of chromosomes to cells in the fetus—a genetic flaw that could be fatal to the fetus, but with which the placenta often functions reasonably normally.

***

"'Our study confirms for the first time that the placenta is organized differently to every other human organ, and in fact resembles a patchwork of tumors. The rates and patterns of genetic mutations were also incredibly high compared to other healthy human tissues."

***

"Professor Gordon Smith, a senior author of the study from the University of Cambridge, said: "It was fascinating to observe how such a serious genetic flaw as a chromosomal copy number error was ironed out by the baby but not by the placenta. This error would have been present in the fertilized egg. Yet derivative cell populations, and most importantly those that went on to form the child, had the correct number of copies of chromosome 10, whereas parts of the placenta failed to make this correction. The placenta also provided a clue that the baby had inherited both copies of the chromosome from one parent, which can itself be associated with problems."

***

"Dr. Sam Behjati, a senior author of the study from the Wellcome Sanger Institute, said: "The placenta is akin to the 'wild west' of the human genome, completely different in its structure from any other healthy human tissue. It helps to protect us from flaws in our genetic code, but equally there remains a high burden of disease associated with the placenta. Our findings provide a rationale for studying the association between genetic aberrations in the placenta and birth outcomes at the high resolution we deployed and at massive scale.'"

Comment: Here again we see God saw need for error corrections and provided a mechanism.

Magic embryology: DNA controls over cell migration

by David Turell @, Tuesday, March 30, 2021, 21:48 (498 days ago) @ David Turell

https://www.sciencedaily.com/releases/2021/03/210330081315.htm

Working with fruit flies, scientists at Johns Hopkins Medicine say they have identified a new molecular pathway that helps steer moving cells in specific directions. The set of interconnected proteins and enzymes in the pathway act as steering and rudder components that drive cells toward an "intended" rather than random destination, they say.

***

In experiments with fruit fly embryos carrying an intact Tre1 gene, cells that produce future generations of the organism, called germ cells, migrate correctly to the sex organ, known as the gonad.

"Without the Tre1 gene, however, most of the germ cells failed to meet up with other nongerm cells, or somatic cells, of the gonad," says Andrew. "Correct navigation of germ cells is important to ensure that future generations of the organism will happen."

This is not the first time that scientists noted Tre1's importance in germ cell navigation. Two research teams from Indiana University and the Massachusetts Institute of Technology had previously made the link. However, says Andrew, questions remained about what happens inside germ cells to get cells to the right place once Tre1 activates.

***

At the end of the molecular cascade, a chain of actin proteins forms in a protrusion at the cell's leading edge to exert mechanical forces for movement. (my bold)

***

The scientists also searched for the upstream signal that activates Tre1. They used a genetically engineered protein made by researchers at the University of California, San Francisco to track the location of a signaling protein called Hedgehog, which has previously been linked to germ cell migration, although its role in this process has been disputed.

In germ cells, Hedgehog signaling increases the membrane levels of a protein called Smoothened, which is found in the cells' leading edge protrusion where Tre1 is also found.

Comment: We know the gene in control, but not how control is precisely conducted. We remain on the outside looking into the black box of genome stepwise control. A cascade of of specialize molecules requires design. Note my bold.

Magic embryology: embryo cells have specific instructions

by David Turell @, Monday, April 12, 2021, 19:07 (485 days ago) @ David Turell

This is what happens when you grow a few of them of one type:

https://www.sciencenews.org/article/frog-skin-cells-self-made-living-machines-xenobots

"Using blobs of skin cells from frog embryos, scientists have grown creatures unlike anything else on Earth, a new study reports. These microscopic “living machines” can swim, sweep up debris and heal themselves after a gash.

***

"Scientists removed small clumps of skin stem cells from frog embryos, to see what these cells would do on their own. Separated from their usual spots in a growing frog embryo, the cells organized themselves into balls and grew. About three days later, the clusters, called xenobots, began to swim.

"Normally, hairlike structures called cilia on frog skin repel pathogens and spread mucus around. But on the xenobots, cilia allowed them to motor around. That surprising development “is a great example of life reusing what’s at hand,” says study coauthor Michael Levin, a biologist at Tufts University in Medford, Mass.

***

"Xenobots have no nerve cells and no brains. Yet xenobots — each about half a millimeter wide — can swim through very thin tubes and traverse curvy mazes. When put into an arena littered with small particles of iron oxide, the xenobots can sweep the debris into piles. Xenobots can even heal themselves; after being cut, the bots zipper themselves back into their spherical shapes.

"Scientists are still working out the basics of xenobot life. The creatures can live for about 10 days without food. When fed sugar, xenobots can live longer (though they don’t keep growing). “We’ve grown them for over four months in the lab,” says study coauthor Doug Blackiston, also at Tufts. “They do really interesting things if you grow them,” including forming strange balloon-like shapes."

Comment: This is not puzzling to me. Teh clumps of skin cells are simply following the instructions they have in their DNA.

Magic embryology: embryo cells push and pull others

by David Turell @, Monday, April 12, 2021, 19:43 (485 days ago) @ David Turell

Much physical force is involved as tissues develop:

https://phys.org/news/2021-04-uncover-cells-physical-state-embryonic.html

"Indeed, he explained, embryonic cellular tissue is a "weird material," with each cell consuming chemical energy and using it to apply forces to its neighbors and coordinate their actions. In-vitro studies with cells in synthetic dishes provide only part of the picture, he added; by studying cells in their native environment, the living embryo, they could find out how cells control their collective state and the phase transitions that emerge from their symphony of pushes and pulls.

***

"Embryonic tissue, according to the researchers, behaves physically somewhat like an aqueous foam, a system composed of individual pockets of air clumped together in a liquid. Think soap suds or beer froth.

"'In the case of foam, its structure and dynamics are governed by surface tension," Kim said. Analogous forces are found where cells come into contact with each other in embryonic tissue, on both the inner faces of the cell membranes and between cells.

"'Effective forces acting on cell-to-cell junctions are governed by cortical tension and cell-to-cell adhesion," Kim said, "so the net force at the cell-to-cell contacts can be modeled as an effective surface tension."

"However, unlike the more static forces between cells in typical foams, the forces between cells in embryonic tissue are dynamic.

"'Cells in tissues do not generate static forces, but rather display dynamic pushing and pulling over time," Campàs explained. "And we find that it is actually these tension fluctuations that effectively 'melt' the tissue into a fluid state." It is this fluidity of the tissue that allows cells to reorganize and shape the tissues, he explained.

***

"Their finding that tension fluctuations are responsible for the fluidity of tissue during development stands in contrast to the generally accepted notion that changes in adhesion between cells is the critical factor that controlled the fluidity of the tissue—if the adhesion between cells reached a certain high threshold, the tissue would become fluid.

"'But since cell forces and tensions fluctuate in embryos, it could be that these played an important role in tissue fluidization," Campàs said. "So when we ran the simulations and did the experiments, we realized that actually the jiggling was way more important for the fluidization than the adhesion." The fluid state of the tissue is the result of the dynamics of forces, rather than changes in static cell tension or adhesion."

Comment: Obviously as cells grow there will be pushing and pulling that is part of the new development of the tissue. teh cells follow instructions that take into account the eventual shapes to be formed.

Magic embryology: embryo timekeeper

by David Turell @, Wednesday, April 28, 2021, 18:18 (469 days ago) @ David Turell

A metabolic clock to time repeated events is found and studied:

https://www.nature.com/articles/d41586-021-01086-9?utm_source=Nature+Briefing&utm_c...

"Animal cells bustle with activity, and the pace varies between species. In all observed instances, mouse cells run faster than human cells, which tick faster than whale cells. These differences affect how big an animal gets, how its parts are arranged and perhaps even how long it will live. But biologists have long wondered what cellular timekeepers control these speeds, and why they vary.

"A wave of research is starting to yield answers for one of the many clocks that control the workings of cells. There is a clock in early embryos that beats out a regular rhythm by activating and deactivating genes. This ‘segmentation clock’ creates repeating body segments such as the vertebrae in our spines. This is the timepiece that Ebisuya has made in her lab.

***

"Biologists have been studying the segmentation clock since the 1990s, and they know that it runs about twice as fast in mouse embryos as it does in human embryos. The speed at which an embryo develops, or at which different parts of it develop, has an important influence on the adult body. Ebisuya and others want to understand how differences in developmental pace give rise to organisms with such different bodies and behaviours.

***

"The findings are already overturning some long-held assumptions about how different animals develop. So far, there is no sign of a master gene controlling the speed of the segmentation clock. Instead, its speed seems to be controlled by the differing rates at which proteins are broken down. Scientists had assumed the speed was mostly constant for each protein across animals, so the discovery might require them to revise some molecular-biology textbooks.

***

"Speed matters when it comes to building species. Evolution didn’t give giraffes long necks by adding extra bones; they have the same number of vertebrae as their stubby-necked okapi relatives. Rather, neck vertebrae in giraffes grow over longer periods of time, which allows them to reach bigger sizes.

***

"Pourquié and other biologists have been trying to take the segmentation clock apart and understand how it works, building a long list of genes and proteins that help the clock to keep time. One key gene is Hes7, the mammalian equivalent of the bird gene c-hairy1. Hes7 can repeatedly turn itself on and off, as can several other genes involved in the clock. That makes it “a key pacemaker for the segmentation clock”, says Ryoichiro Kageyama, a developmental biologist at Kyoto University in Japan who has studied the gene for almost two decades.

"But it is still unclear why Hes7 turns on and off at different speeds in different species, and thus how the speed of the segmentation clock is ultimately controlled. A series of studies over the past three years point to an answer.

***

"These studies revealed many similarities between the segmentation clock of humans and those of other animals. Analogues of the same genes and proteins are involved in mice and humans, for instance.

"But there was one striking difference. The human segmentation clock is slow. Each oscillation takes 5–6 hours, twice as long as the 2–3 hours it takes in mouse embryos: a clear example of heterochrony (see ‘Unlocking the segmentation clock’). But why is the human segmentation clock so slow, and what is controlling it?

***

"The in vitro segmentation clock studies could well resolve this question, but also suggest a broader mystery: do human cells run slower than those of other species, not just during specific periods of development, but throughout our lives? If so, that could help to explain why our lifespan is extended compared with that of other species."

Comment: We are all based on the same basic body plans so size of parts plays a big role in what types of species develop. This is highly complex design plan when timing is part of the process. Not by chance.

Magic embryology: control of differentiation

by David Turell @, Monday, June 14, 2021, 19:08 (422 days ago) @ David Turell

A specific molecule tur ns on a specific segment of DNA:

https://phys.org/news/2021-06-cell.html

"A Medical University of South Carolina (MUSC) study in Cell Reports led by Stephen Duncan, D.Phil., examines how an endodermal cell—a type of developing cell—becomes a liver cell and not some other type of cell. Duncan and his team found that the development of naive cells into differentiated liver cells was dependent on the transcription factor GATA6.

"'What we found is that this specific transcription factor, GATA6, has an unusual mechanism because it can recognize regulatory regions on DNA before a specific gene is turned on," explained Duncan. "It doesn't directly turn on expression of a gene but marks a gene as being capable of being turned on if the cell encounters the right developmental cues."

"'We found that, in the absence of GATA6, regions surrounding genes remained closed and inaccessible," said Duncan. "GATA6 can open up chromatin around regulatory regions of genes that are ultimately expressed as the cell begins to differentiate.'"

Comment: this finding is not surprising. We can see what works, but do not know how it works or why it works. Our knowledge of genomics is still on the outside looking in.

Magic embryology: control of head to toe differentiation

by David Turell @, Thursday, June 17, 2021, 21:32 (419 days ago) @ David Turell

The director group of cells are found:

https://phys.org/news/2021-06-trigger-head-to-tail-axis-human-embryo.html

"Scientists have identified key molecular events in the developing human embryo between days 7 and 14—one of the most mysterious, yet critical, stages of our development.

"The second week of gestation represents a critical stage of embryo development, or embryogenesis. Failure of development during this time is one of the major causes of early pregnancy loss. Understanding more about it will help scientists to understand how it can go wrong, and take steps towards being able to fix problems.

***

"In a new study, the team collaborated with colleagues at the Wellcome Sanger Institute to reveal what happens at the molecular level during this early stage of embryogenesis. Their findings provide the first evidence that a group of cells outside the embryo, known as the hypoblast, send a message to the embryo that initiates the development of the head-to-tail body axis.

"When the body axis begins to form, the symmetrical structure of the embryo starts to change. One end becomes committed to developing into the head end, and the other the 'tail'.

"The new results, published today in the journal Nature Communications, reveal that the molecular signals involved in the formation of the body axis show similarities to those in animals, despite significant differences in the positioning and organisation of the cells.

"We have revealed the patterns of gene expression in the developing embryo just after it implants in the womb, which reflect the multiple conversations going on between different cell types as the embryo develops through these early stages," said Professor Magdalena Zernicka-Goetz in the University of Cambridge's Department of Physiology, Development and Neuroscience, and senior author of the report.

"She added: "We were looking for the gene conversation that will allow the head to start developing in the embryo, and found that it was initiated by cells in the hypoblast—a disc of cells outside the embryo. They send the message to adjoining embryo cells, which respond by saying 'OK, now we'll set ourselves aside to develop into the head end.'"

"The study identified the gene conversations in the developing embryo by sequencing the code in the thousands of messenger RNA molecules made by individual cells. They captured the evolving molecular profile of the developing embryo after implantation in the womb, revealing the progressive loss of pluripotency (the ability of the embryonic cells to give rise to any cell type of the future organism) as the fates of different cells are determined."

Comment: It has to be a highly controlled, orchestrated, programmed series of events. Therefore highly designed and never by chance mutations.

Magic embryology: microglia help prune synapses

by David Turell @, Saturday, August 28, 2021, 14:44 (347 days ago) @ David Turell

Study in mouse young brains:

https://science.sciencemag.org/content/373/6558/978.2?utm_campaign=ec_sci_2021-08-26&am...

"A fundamental question in developmental neuroscience is how different cell types wire together with exquisite specificity to ensure the formation of canonical neural circuits. Increasingly, non-neural cells have been implicated as being essential to this process. Microglia-resident immune cells of the brain play crucial roles in refining synaptic connections. Favuzzi et al. show that GABA-receptive microglia interact with inhibitory synapses in developing mice 2 to 3 weeks after birth. Within this population of microglia, GABA promotes the selective pruning of inhibitory connectivity. Perturbing these specialized microglia caused long-lasting defects in inhibitory connectivity without affecting excitatory synapses and led to hyperactivity in adult animals. Thus, distinct microglial populations differentially engage with specific synapse types during development to modulate behavior."

Comment: I view embryology occurring after birth, just as in human development for years after birth. This precise arrangement with cooperating microglia tailoring synapses must have a designer. Not by chance.

Magic embryology: multiple switches guide limb formation

by David Turell @, Wednesday, September 29, 2021, 19:46 (315 days ago) @ David Turell

Any early evolutionary mechanism:

https://phys.org/news/2021-09-robust-gene-networks-depths-evolutionary.html

"A sophisticated system guides the development of our limbs. Researchers at University of Basel have shed new light on the genetic toolkit used during evolution to create a range of different extremities such as fins, wings, hooves, toes and fingers.

"Much can go wrong when a fertilized egg develops into an embryo and ultimately gives rise to a newborn as mutations in the genome that affect development are relatively common. The fact that embryonic development is usually flawless for humans and animals is due to the fact that genetic programs are controlled by series of gene circuits that can back one another up in a self-regulatory fashion. (my bold)

"This robustness of developmental programs is a key interest of the research group led by Professor Rolf Zeller and PD. Dr. Aimée Zuniga at the Department of Biomedicine, University of Basel. They seek to gain insights into this process studying a key regulator of limb development, a protein called "Gremlin1". This protein stops cells from forming bones too early and functions in fine tuning the activity of several signaling networks by connecting them with one another. Most importantly, Gremlin1 is responsible for the correct formation of the so called limb buds, which are the tiny embryonic structure that will give rise to our extremities.

***

"In the scientific journal Nature Communications, they describe a series of "switches" embedded in the genome of all vertebrates which ensures that the correct amount of Gremlin1 is produced at the right place. These switches are called "enhancers".

Zuniga compares the system that she and her team are investigating with a room's lighting system that is controlled by a series of switches. The light enables one to read the instructions to build correctly formed extremities. "In the beginning, we did not know what each individual switch contributes to lighting the room," the researcher explains. "There could be a master switch that turns off all lights, making the instructions impossible to read. Instead, we now know that all switches contribute to the lighting system: if one switch is broken the amount of light is only marginally or not at all affected and the information can still be read. This is why the system is so robust. On the other hand, once too many switches are broken, too little of the information can be read, and in the worst case none at all."

"Indeed, analysis by Ph.D. student Jonas Malkmus and colleagues showed that individual switches can be inactivated without disrupting Gremlin1 or the development of extremities. However, below a certain threshold of functioning switches, the system fails and malformations occur. "The multiple safeguards in the system explain why birth defects due to genetic alterations in Gremlin1 regulation are extremely rare," says Malkmus. (my bold)

"Next, the researchers set out to identify the evolutionary roots of this robust series of switches. They found that the core of this series of switches that ensures the correct amount and distribution of Gremlin1 in human embryos existed in fishes already more than 400 million years ago. "This shows that evolution already had the toolkit for developing extremities even before fins evolved into legs and the first animals went ashore," explains Zuniga. What changed over the course of evolution was the activity of individual enhancers and, as a result, the distribution of Gremlin1. "The activity of the genetic switches and the distribution of Gremlin1 in limb buds prefigures their subsequent development into fins, wings, hooves or hands and feet," explains Zeller.

"If only one switch would regulate the production of Gremlin1, then the evolutionary pressure to keep this switch exactly as it is would be huge. "A system with many switches ensures that the system does not easily fail," says Zuniga. "And it gives evolution room for change." Therefore, individual switches have been able to change without significant pressure, and this has played a part in the development of a wide range of extremities during the history of evolution."

Comment: Note my bolds. This system keeps errors to an extreme minimum. The study fits my theory that God sets up programs early in anticipation of future designs of future evolutionary stages..

Magic embryology: control of differentiation

by David Turell @, Tuesday, November 09, 2021, 15:48 (274 days ago) @ David Turell

Stem cells follow outside controls in differentiation:

https://www.sciencedaily.com/releases/2021/11/211108130842.htm

"Stem cells are true multi-talents. They can develop into any cell type of an organism -- in humans there are over 200 -- and thus perform all vital tasks. Once the stem cells have decided on a task they can no longer be deterred from their goal. The final product, tissues and organs, almost always look the same and consist of defined proportions of different specialised cell types. But how do the cells actually know what they want to become and how many of them are actually allowed to do so?

***

"Using stem cells in a test tube, the researchers were able to show that decision-making does not take place purely randomly at the level of individual cells, as previously assumed, but is communicated within the cell community. (my bold)

***

"If the researchers took away a growth factor that was important for cell development, the cells were no longer able to develop into fruit bladder precursor cells even in the presence of high amounts of GATA. However, the more of the growth factor the cells received, the more fruit bladder precursor cells also developed. Their ability to divide into the right proportions of the two cell types despite disturbances was thus lost. Stem cells must therefore communicate with each other in order to make the right decision.

"'Communication in cell development is like working in a team. If the members choose tasks without consulting each other, some things are done twice and others not at all. A team that communicates well, on the other hand, can solve problems that arise and complete even complex projects reliably and efficiently," Christian Schröter says. "So it's not just the state of the individual cell that decides on its faith, but the functioning communication with the other cells.'"

Comment: In embryology the fetus develops in a standard pattern. The overall plan is fixed, so the result is always the same if no mistakes happen. Under guidance differentiating cell communities cooperate, but end up with a fixed result automatically.

Magic embryology: GPS for forms

by David Turell @, Thursday, November 11, 2021, 18:12 (272 days ago) @ David Turell

Well outlined:

https://theconversation.com/genetic-gps-system-of-animal-development-explains-why-limbs...

"While human body shape and appearance have clearly changed during the course of evolution, some of the genes that control the defining characteristics of different species surprisingly have not. As a biologist studying evolution and development, I have devoted many years to pondering how genes actually make people and other animals look the way they do.

"New research from my lab on how these genes work has shed some light on how genes that have remained unchanged for hundreds of thousands of years can still alter the appearance of different species as they evolve.

***

"Hox genes play an important role in setting up this body plan. This group of genes is a subset of genes involved in anatomical development called homeobox genes. They act like a genetic GPS system, determining what each body segment will turn into during development. They ensure that your limbs grow from your torso instead of from your head by controlling other genes that instruct the formation of specific body parts.

All animals have Hox genes and express them in similar body regions. Furthermore, these genes haven’t changed throughout evolutionary history. How can these genes remain so stable over such vast evolutionary time spans, yet play such pivotal roles in animal development.

***

"The next big question, then, was how exactly do these Hox genes determine the identities of different body regions?

"There have been two schools of thought on how Hox genes work. The first, called the instructive hypothesis, proposes that these shape-controlling genes function as “master” regulatory genes that supply the body instructions on how to develop different body parts.

"The second, proposed by McGinnis, hypothesizes that Hox genes instead provide a positional code that marks particular locations in the body. Genes can use these codes to produce specific body structures at those locations. Over the course of evolution, specific body parts come under the control of a specific Hox gene in a way that would best maximize the organism’s survival. This is why flies develop antennae rather than legs on their heads, and humans have collar bones below instead of above their necks."

Comment: Sexual reproduction always produces the same infant forms. Although the research is still ongoing, we still don't know exact mechanisms of control. But the instructional information always produces the same results with minor variations. This is a pure example of cellular automaticity. Automatic sameness is automaticity in fetal production.

Magic embryology: timing controls

by David Turell @, Tuesday, January 25, 2022, 20:10 (197 days ago) @ David Turell

By a specific set of proteins:

https://phys.org/news/2022-01-lefty-protein-tightens-embryonic.html

"A protein known as Lefty pumps the brakes as human embryos begin to differentiate into the bones, soft tissues and organs that make us.

"This inhibitor protein is key during the early stages of life when the fates of embryonic stem cells are determined by the Nodal signaling pathway, according to Rice University bioscientists.

"Experiments by the lab of Rice's Aryeh Warmflash and led by postdoctoral researcher Lizhong Liu have visualized for the first time the mechanism by which Nodal and Lefty interact to specify the future body plan in a mammalian embryo.

"The study shows not only how Nodal signaling molecules, known as morphogens, are held in check by Lefty but also that Nodal proteins are passed directly from cell to cell, triggering transcription of new Nodals by the recipient. At the same time, a wave of Lefty transcription is transiently triggered in the cells when they first receive Nodal, regulating the speed of the wave.

"'Basically, we show that rather than gradients of protein forming and instructing cells to become different cell types, the molecules involved do not diffuse at all," Warmflash said. "Instead, cells relay the signal so that each cell produces the signal and passes it to its neighbor, which causes the neighbor to produce it and so on. It's kind of like a game of telephone."

***

"Traditionally, patterns are thought to arise because some proteins diffuse faster than others, Liu said. Local Nodal activity could cause production of Lefty, which diffuses farther than Nodal and limits the signal to a territory of a particular size, a theory that he said has not been rigorously tested.

"To the researchers' surprise, the direct observation of endogenous molecules showed no sign of Nodal diffusion. Instead, the wave that moves inward is the result of new Nodal proteins produced by each cell that then triggers its neighbor to do the same.

"The lab was able to prove this is essential for the wave by creating cells that lack the Nodal protein. These cells could receive the signal but not pass it on to their neighbors.

"The researchers also found that while Lefty didn't diffuse in their gastrulation experiments, it can move over much longer range in other contexts."

Comment: Darwin evolution theory has no explanation for this process. It has to be developed all at once by design, since it is irreducibly complex.

Magic embryology: cells using mechanical forces

by David Turell @, Monday, February 14, 2022, 18:04 (177 days ago) @ David Turell

With cells in membranes:

https://phys.org/news/2022-02-cell-groups-cancers.html

"...a new study found in a living embryo that the back ends of moving cell groups push the group forward. This runs contrary to previous findings, where cell groups grown in dishes of nutrients (cultures) pulled themselves forward with their front edges.

***

"Specifically, the study found for the first time in an animal tissue that proteins called integrins on the surfaces of the cells at the rear attach in greater numbers to the membrane as they move along, and exert more force in one direction, than the cells in the group's front. The integrin clusters (focal adhesions) observed in the embryo were smaller than those seen in culture studies, and broke down faster.

***

"The study results are based on mechanisms of cell movement established by past studies. For instance, a protein called actin is known to form the protein "skeleton" of cells, with actin chains able to grow in a certain direction, and apply force that change a cell's shape. Integrins, proteins built into outer cell membranes, interact both with actin networks, and proteins outside of cells. These and other proteins form a system that a cell uses to briefly attach to and "roll along" a basement membrane, a pliable mesh of proteins and sugars. What was unknown going into the current study was how tissues in living animals apply force in groups to generate this motion.

***

"Using "bleached" dots on the basement membrane to measure shape changes (deformations) on a minute scale, and a new software called embryogram to calculate how far the dots move as the primordium "grips" the membrane, the researchers determined how much the cells pulled and pushed on the membrane, "like a tire on pavement." The effect is much like the high school physics experiment where students draw two dots on a rubber band, and calculate the force applied as they stretch the band by measuring the change in distance between the dots.

"With these tools in hand, the team showed that the primordium cells link the force-generating actin-myosin network at the back end of the moving group through integrin clusters on the side closest to the basement membrane. The team theorizes that cells attached to membrane toward the back push on the cells in front of them to move the entire group. The researches also gained new insights on an established mechanism where cells have surface proteins that let them "sense" and follow a guidance cue called a chemokine, from low concentration to high concentration. The new study found, however, that cells toward the back end of the primordium sense the chemokine gradient more strongly.

"Interestingly, the study found that the primordium moved in a "continuous breaststroke" by pushing the basement membrane downward, sideways and backwards, much like the arms of a swimmer. The authors do not know why this is, but speculate that this is the most efficient way to move forward. They note that banana slugs also use the rear edge of the "foot" they apply to the ground, suggesting that evolution favors rear engine propulsions because they are most efficient at different size scales."

Comment: When two parents combine DNA's into one cell, creating a fetus for birth requires a very complex set of controls which on a designer could create. Embryology, itself, proves a designer exists.

Magic embryology: independent early cells

by David Turell @, Tuesday, February 15, 2022, 17:16 (176 days ago) @ David Turell

They start producing proteins very quickly:

https://phys.org/news/2022-02-embryo-cells-gain-independence.html

"It happens in the first hours after fertilization: The cells of the early embryo begin to independently produce proteins, the building blocks for cells and organs. Their own, uniquely composed genetic material serves as the blueprint. In vertebrates, the starting signal for this process comes from three maternal proteins that bind to the DNA of the offspring.

***

"'We have shown how the proteins Pou5f3 and Sox19b function at different time points in embryonic development and in different areas of the embryo," says the biologist of the study's integrative approach.

***

"They induced mutations in the genes for Pou5f3 and Sox19b so that the fish would no longer produce these regulatory proteins. In this way, they succeeded in demonstrating that the two proteins have independent tasks. However, they both act on the DNA by binding to gene regulatory regions and making the genes freely accessible to the cellular machinery.

***

"In addition, the team discovered that Pou5f3 and Sox19b suppress late genetic programs. "They keep important processes in sleep mode so that they do not start until later, when the appropriate step in development approaches," describes Onichtchouk. "This concerns the genes responsible for the development of the organs." However, Pou5f3 and Sox19b appear to be the determining factors for the activation of the genes only on the ventral side of the embryo. On the dorsal side, they are ineffective. Onichtchouk wants to determine the reason for this: "We are curious to find out what takes over this function here and whether these proteins also originate from the mother.'"

Comment: very precise timed actions controlled by genes. Embryology shows the automaticity of living biochemistry.

Magic embryology: differentiation control

by David Turell @, Monday, February 21, 2022, 20:38 (170 days ago) @ David Turell

A control is found:

https://medicalxpress.com/news/2022-02-key-cell-differentiation.html

"Embryonic stem cells and other pluripotent cells divide rapidly and have the capacity to become nearly any cell type in the body. Scientists have long sought to understand the signals that prompt stem cells to switch off pluripotency and adopt their final functional state.

"In a study published in the Proceedings of the National Academy of Sciences, researchers report that they have identified a key regulator of this process. They discovered that a molecule known as BEND3 shuts down expression of hundreds of genes associated with differentiation, maintaining the cell's stem cell-like status. Only when BEND3 is downregulated can cells adopt their final form and function. Once they differentiate, they usually stop actively proliferating.

***

"Prasanth's laboratory focuses on cell cycle regulators. Her early studies identified BEND3 as a potentially important player in the system. Her team found that when BEND3 bound to strategic locales along the chromosome, it reduced or blocked the expression of dozens of genes. When BEND3 was removed, gene expression rebounded.

"'When you do these gene-expression studies, you can see hundreds of genes go up, hundreds down," Prasanth said. "But what does it really mean?"

***

"'The binding of BEND3 to these genes blocks their expression, preventing the cells from entering a differentiated state," Supriya Prasanth said. "And the moment you remove that control, the cells are now moving toward the differentiation pathway."

"BEND3 is not the only regulator of the cell-differentiation pathway; it binds to and interacts with many other molecular regulators of this process, Supriya Prasanth said. But its presence or absence appears critical to determining a cell's fate, making it an attractive target for potential medical interventions when the process goes awry.

"In an accompanying paper published in the journal Genes and Development, the Supriya Prasanth lab and collaborators at the Memorial Sloan Kettering Cancer Center provided structural insights into BEND3-mediated gene regulation.

"The paper is titled "BEND3 safeguards pluripotency by repressing differentiation-associated genes.'"

Comment: developing an embryo must result in an identical reproduction. Obviously tight controls care necessary. Only a carefully designed system will do this.

Magic embryology: how do stem cells reach a destination

by David Turell @, Monday, March 28, 2022, 20:28 (135 days ago) @ David Turell

This is how they migrate by chemical and mechanical signals, but not how they know where they are intended to go:

https://www.quantamagazine.org/cells-blaze-their-own-trails-to-navigate-through-the-bod...

"It starts from the earliest stages of life. When we are embryos just a few weeks old, a special population of “neural crest” cells in our back suddenly spreads through the body to become a wide range of essential tissues — bones, cartilage and nerves in the face, tendons, pigment cells in the skin, parts of the heart and more.

***

"Now researchers have discovered another crucial part of the answer, one that helps explain how cells are directed to their destinations in the neural crest migration and probably other movements as well. The new work shows that in addition to using chemical cues, neural crest cells “feel” their way through the body, creating patterns of physical tension in the surrounding tissue that point them the right way. In effect, the cells create the signals that they use to steer themselves.

"Finding this navigation mechanism doesn’t just clarify how neural crest cells make their vital migration. It also further validates an idea that has been gathering force in just the last few years: that “self-generated gradients” are essential to cell migrations, and that these gradients can be built from all kinds of factors — not just chemicals.

***

"Self-generated gradients have now made sense of perplexing behavior in cancer cells, fish embryos, immune cells, bacteria, slime mold, and more — and findings are accumulating rapidly. “People are opening their eyes, and it’s now seen everywhere, suddenly,” said Jonna Alanko, a postdoc at the Institute of Science and Technology Austria. “I’m pretty sure that this is only the tip of the iceberg.”

***

"Much of the research to date on self-generated gradients has looked at chemical signals, but cells can create gradients in other physical attributes, too, including mechanical properties. The recent paper analyzing migrating neural crest cells revealed a self-generated gradient of stiffness, to the authors’ surprise.

***

"The researchers already knew that the “placode” cells in front of the migrating cells produces a chemical attractant to help draw the cells forward. These placode cells are repelled by the touch of the neural crest cells, so they run in the opposite direction. The newly discovered mechanical gradient works in tandem with the chemical cues to drive the migration of the neural crest cells forward by a “chase and run” mechanism.

***

"The idea is catching on. Once the paper was published, Mayor’s inbox was flooded with messages from other researchers about the same kind of mechanism that seemed to be at work in embryos, immune cells and cancer. Self-generated stiffness gradients will turn out to be common, Mayor predicted. “There are many papers coming out very soon that will show this.'”

Comment: in the exact designed creation of a new embryo, each new cell daughter of the first stem cells must know exactly where it is supposed to go or the embryo would be a jumbled inexact copy of what is intended. This is how they use a system to migrate. Not how they know or decide where to go on their own in advance. I simply imagine each cell has a GPS system with the proper endpoint presented which they must follow. Just like we use in our cars to reach an intended destination. The designer at work.

Magic embryology: asymmetric cell division

by David Turell @, Tuesday, March 29, 2022, 21:45 (134 days ago) @ David Turell

A new not surprising finding:

https://phys.org/news/2022-03-cell-division-embryos-textbook-case.html

"As cell biologists, Université de Montréal professor Greg FitzHarris and his Ph.D. student Lia Paim are very interested in fertility and what happens inside the eggs and embryos of the mice they study in their lab. And sometimes, they spot something unusual … by accident.

"Their latest findings, published in PNAS, could change how one particular aspect of cell division is understood and pave the way for further research on how this might play a role in the viability of the embryo—even a human one

***

"Most of our lab's experiments are about embryo development. We focus on understanding what makes the best embryo and how this relates to the embryo's potential and thus the likelihood of having a successful pregnancy.

"The mouse embryo is also a unique setting for studying cell divisions.

"In one of our experiments, Lia spotted something unusual happening during cell division. In a real-life situation such as a developing embryo in which cells are in close contact with other surrounding cells, she noticed that during the final step of cell division, called cytokinesis, the cell is pinched in two primarily from one side only.

"And she realized that the particular way in which this was occurring had not been seen by researchers before.

"The traditional textbook view of cytokinesis is that it occurs in a symmetric manner, where a pinching of the cell happens equally from both sides to cut the mother cell in two and make two new daughter cells.

"Lia discovered that molecules called cell polarity proteins have a major effect upon cytokinesis in embryos. This is why cytokinesis becomes asymmetric, quite unlike what the textbooks show.

***

"It is well known that cytokinesis sometimes fails in embryos, and that this can threaten the viability of the embryo and thus the likelihood of having a successful pregnancy, in mice as in humans. The asymmetric cytokinesis we discovered could be part of the reason for this, but we would need to do more experiments to test this possibility."

Comment: What the reviewer does not tell us is obvious: the developing embryo has to send cells in three dimensions. An asymmetric cell divisions has the necessary directionality which the modification of standard mitosis supplies. More obvious design.

Magic embryology: setting initial geography

by David Turell @, Saturday, May 14, 2022, 16:26 (88 days ago) @ David Turell

The direction of development is set in the first few cells:

https://www.eurekalert.org/news-releases/952171

"Cells also communicate with their nearest neighbors, and in embryos, nothing is left to chance in the ‘seating plan’ for the first few cells. However, questions remain about the how this process is controlled and how it can influence the overall growth of an organism.

"Building on their previous studies on the development of worm eggs, researchers from Kyoto University Kanagawa Institute of Technology, and the National Institute of Genetics have now precisely modeled the shape of eggshells to show how the space in the egg and the contours of the shell direct the relative positions of cells in the growing embryo. Their findings may provide a theoretical basis for directing the development of stem cells into larger tissues and organs.

***

"When looking under a microscope at eggs of the worm Caenorhabditis elegans, the team previously noticed that in eggs with a longer shape, the first four cells arranged in a line; in contrast, if the shell was round, the cells would bunch up. They also identified an unexplained ‘T-reverse’ pattern in some eggs, where three cells bunch up, making a gap shaped like a T, with one cell in a line at the end.

"The team hypothesized that the formation of this pattern, might be controlled by variations in the eggshell contours. To test this, they applied a more sophisticated ‘phase-field’ mathematical model that could more precisely account for the actual egg shape measured from worms. This new model successfully reproduced the previous findings and now also accounts for the unexplained T-reverse arrangement. The findings show for the first time that the previously ignored local contours of the egg affect the cell patterns.

"In the new way of looking at the embryo, it turns out that it is actually the “space inside the egg” that is a key factor driving the cell patterns. To test this concept further, the researchers examined the eggs of worms that were genetically modified to allow more space for the cells inside. With extra room, the first four cells preferred to spread out in a line rather than bunching up.

"Seirin-Lee said, “Worm eggshells are often treated as a simple oval shape, but the actual shape may be closer to a capsule in some cases. We now understand how important geometric constraints and space are for directing cells, and this concept also applies to human cells. We hope this work will lead us to a better handle on artificially controlling cell differentiation and extend the capabilities of stem cell techniques.'”

Comment: it has been noted before that physical forces play a role in embryo development along with the specific instructions in stem cells individual genomes.

Magic embryology: forming a neural tube

by David Turell @, Monday, May 16, 2022, 20:20 (86 days ago) @ David Turell

A major process for vertebrate embryos:

https://www.sciencedaily.com/releases/2022/05/220516123943.htm

"In the human embryo, the neural tube forms between the 22nd and 26th day of pregnancy. Later, the brain and spinal cord will develop from this tube. The neural tube forms when an elongated flat tissue structure, the neural plate, bends lengthwise into a U shape and closes to form a tube. What drives this development is not yet clear. Researchers...have now been able to show that the surrounding tissue is likely to play a significant role by exerting pressure from the outside.

***

"Until now, scientists assumed that local biochemical signals in the cells of the neural plate lead to the formation of these hingepoints, and that the hingepoints play an active role in the formation of the neural tube. However, there has been no explanation as to why the hingepoints form exactly where they do.

"The ETH researchers now postulate an alternative mechanism, according to which the neural plate does not actively bend itself, driven by the hingepoints, to form a tube. Rather, the neural plate initially adopts a slightly curved shape for anatomical reasons. Subsequently, the tissue lying either side of the neural plate (ectoderm and mesoderm) expands. This applies pressure to the neural plate from the side and causes it to passively form into a tube.

"This showed that the processes were best explained by the expansion of the surrounding tissue. "We use this to demonstrate that hinge points can arise as a result of external pressure. So they are probably not drivers of neurulation, as was previously thought, but a side effect of it," Iber says. Instead, the driver appears to be the surrounding tissue.

"Especially in the upper part of the back, neurulation can be explained by the expansion of the adjacent tissue, because for anatomical reasons the neural plate is slightly pre-bent already. Further down the future back, this initial curvature is absent; the neural plate is flat in this area.

"With their modelling, the ETH scientists were able to show that here, too, neurulation can be explained by external forces: protein fibres and anchor proteins help to pull the neural plate together like a zip. This causes the neural plate to curve and close into a tube.

"According to the researchers, the fact that the mechanisms differ in the upper and lower back could explain why spinal malformations don't occur with the same frequency all along the back. Spina bifida is more common in the lower back, where the surrounding tissues are less supportive."

Comment: this precise sequence of actions require delicate design from the beginning. Sequential chance mutations are incapable of creating this design.

Magic embryology: control over placental growth

by David Turell @, Monday, June 13, 2022, 19:42 (58 days ago) @ David Turell

One specific protein is involved:


https://phys.org/news/2022-06-black-embryonic.html

:DNA regulation is a critical process in a cell that allows it to fulfill its function. This process is key during pregnancy, when embryonic cells must develop into all cell types needed to form an embryo. An international team of researchers from KU Leuven, Babraham Institute, Radboud University, Ghent University and IMBA, have discovered that the first cell fate decision of embryonic development is regulated by a protein known as PRC2. This new insight into human development could help us to understand early pregnancy loss in the future.

"All human beings start their existence as a sperm cell and egg cell. By the fifth or sixth day, the fertilized egg has become a blastocyst, a rapidly dividing cluster of cells, consisting of an inner and outer group of cells. The outer group will form the placenta; the inner cells will develop into an embryo. This development is a complex process whereby every step is critical, and the slightest mistake may end embryonic development.

***

"As early embryonic cells eventually form all cells, researchers have always assumed that early embryonic cells could easily switch genes on and off during development. "The first decision that cells need to take during human embryonic development is if they will form the embryo itself or the placenta. Our results show that this first decision is not as easy as we first thought," explains Professor Vincent Pasque (KU Leuven). "To form the placenta, the outer cells of the blastocyst must turn the correct switches on at the right time. We discovered that cells need to overcome barriers to turn placenta genes on," adds Hendrik Marks, group leader from Radboud University.

***

"'Using this embryo model, we could see that when we remove the protein PRC2, an increased number of placenta cells are present in blastoids. These results show that PRC2 is a barrier for the placenta cells to appear," explains Ph.D. researcher Irene Talon (KU Leuven).

"'Our research opens up the ability to better control stem cell specialization and blastoid development, which is useful for studying in the laboratory how the initial placental cells are formed. In the longer term, the new knowledge might improve our understanding of how embryos successfully implant in the uterus at the earliest stages of pregnancy, and why this can sometimes go wrong," concludes Professor Peter Rugg-Gunn."

Comment: one small step in understanding embryo developemnt automatic controls. How many controlled steps yet to find?

Magic embryology:

by David Turell @, Sunday, July 31, 2022, 23:05 (10 days ago) @ David Turell

Nuclear position controls studied:

https://www.the-scientist.com/news-opinion/how-wandering-nuclei-shape-developing-embryo...

"Early in development, all animal embryos pass through an almost identical stage where they form a blastoderm, which is a hollow ball of a few thousand cells. From that hollow ball, layers of cells start to fold into shapes that will become different parts of the body. Although the behavior of cells and the patterning of the embryo after the blastoderm stage is well-understood, how the blastoderm itself is made has remained a longstanding mystery.

"Now, a team of biologists and applied mathematicians at Harvard University in Massachusetts have developed a framework for understanding the general principles by which cell nuclei move and arrange themselves during the earliest stages of embryonic development to form the blastoderm.

***

"The researchers approached the study with two hypotheses: that the nuclei might push away nearby neighbors, and that each nucleus experiences a force that pulls it away from other nuclei and into empty space. They formalized these two hypotheses with mathematical models and made computer simulations of the developing embryos. Ultimately, the latter hypothesis—that nuclei are somehow pulled into the egg’s remaining empty space—best matched their observations.

***

"So how do the nuclei sense the space around them? The researchers hypothesize that microtubules attach to each nucleus self-assemble and grow outward, preferentially pulling the nuclei toward empty space because they can grow longer in that direction.

"Ensuring that nuclei are where they need to be in the blastoderm sets the foundation for all subsequent development to happen correctly, explains Stefano Di Talia, a developmental biologist at Duke University in North Carolina who didn’t work on the study. “Even more importantly, a lot of the mechanisms that have to do with the formation of the blastoderm are really fundamental cell biological and biophysical questions,” such as how the cell cycle is coordinated with biochemical signals and mechanical forces generated by the cytoskeleton to position things correctly, he says. (my bold)

"Di Talia says the ability of microtubules to pull nuclei into position is a fascinating hypothesis and could be a more general mechanism to explain how cells move during development and morphogenesis. “I think there’s going to be lot of situations where microtubule-driven processes are going to control the positioning of nuclei or organelles,” he says, “and I think the systems where you can really learn the biophysics of how that works are going to be very helpful.'”

Comment: note the bold. The cell nuclei move by following biochemical signals and mechanical forces, but how those signals and forces are coordinated comes from instructions sent by the DNA interpreting the proper information it has. This cannot be developed in step-by-step fashion. It must be designed all at once.

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