The Higher Dimensional Analysis of Embryonic Development

[BillTre]

TL;DR Summary

It is now possible to obtain almost complete information of important aspects of embryonic development. This includes location and movement of all cells in a embryo as well as which genes are active in each cell. Important information in any attempt to understand ow embryos make adult forms.

I recently read this article in Science magazine: "The 200-year effort to see the embryo." by John B. Wallingford. Sadly it is probably not open access.
This article reviews the history increasingly detailed information available on developing embryos.

Recent technological advances in optical, data, combined with increasingly powerful computer technology has allowed scientists to track every cell through particular stages of embryology in particular animals that are well suited to such viewing. The cell tracking also yields cell lineage information about which cell is related (by cell division) to which cells and when the cell divisions occurred.
It also makes the point that it has recently become possible to determine which genes are expressed (turned on) in each cell in a developing embryo.

Both of these achievements are important landmarks in that they are getting down to the lowest level of detail in these two important areas of biological analysis (cells and genes).

In the grand view of biology, embryonic forms and the processes that generate them are an important intermediary between the inherited genetic instructions (full genomic sequences) and the adult (or other) forms where many analyses of adaptation of inherited genes are made.

That a higher dimensionality developmental analysis is required for understanding a developmental system is extensively made in this article. (Imaging in Systems Biology, Sean Magason and Scott Fraser), which came out more than 10 years ago and is open access.
They refer to the “xyztg data universe” as an ideal of modern developmental biology, which would describe the state of the entire genome (g) across time (t) in all three cardinal axes of space (x, y, z). The entire genome (the “g” part) would (I guess) include an n-dimensional array of expression values (n = 20,000 to 30,000 genes), for each cell (1 to thousands or millions of cells). Lots of information. In theory, all of this is now collectable in particularly well suited research model organisms, like C. elegans (almost microscopic worm), Drosophila melanogaster (fruit fly), and Danio rerio (zebrafish).

Additional useful information could include single cell optical physiological sensors and more detailed cell structure information.

 

[trurle]

Summary: It is now possible to obtain almost complete information of important aspects of embryonic development. This includes location and movement of all cells in a embryo as well as which genes are active in each cell. Important information in any attempt to understand ow embryos make adult forms.

I recently read this article in Science magazine: "The 200-year effort to see the embryo." by John B. Wallingford. Sadly it is probably not open access.
This article reviews the history increasingly detailed information available on developing embryos.

Recent technological advances in optical, data, combined with increasingly powerful computer technology has allowed scientists to track every cell through particular stages of embryology in particular animals that are well suited to such viewing. The cell tracking also yields cell lineage information about which cell is related (by cell division) to which cells and when the cell divisions occurred.
It also makes the point that it has recently become possible to determine which genes are expressed (turned on) in each cell in a developing embryo.

Both of these achievements are important landmarks in that they are getting down to the lowest level of detail in these two important areas of biological analysis (cells and genes).

In the grand view of biology, embryonic forms and the processes that generate them are an important intermediary between the inherited genetic instructions (full genomic sequences) and the adult (or other) forms where many analyses of adaptation of inherited genes are made.

That a higher dimensionality developmental analysis is required for understanding a developmental system is extensively made in this article. (Imaging in Systems Biology, Sean Magason and Scott Fraser), which came out more than 10 years ago and is open access.
They refer to the “xyztg data universe” as an ideal of modern developmental biology, which would describe the state of the entire genome (g) across time (t) in all three cardinal axes of space (x, y, z). The entire genome (the “g” part) would (I guess) include an n-dimensional array of expression values (n = 20,000 to 30,000 genes), for each cell (1 to thousands or millions of cells). Lots of information. In theory, all of this is now collectable in particularly well suited research model organisms, like C. elegans (almost microscopic worm), Drosophila melanogaster (fruit fly), and Danio rerio (zebrafish).

Additional useful information could include single cell optical physiological sensors and more detailed cell structure information.

People like simplifications, but limitations of simplified approach also should be mentioned. Unfortunately, xyztg mapping do not describe fully developmental state for indeterminate cleavage embryos (which include all chordates).

 

[BillTre]

People like simplifications, but limitations of simplified approach also should be mentioned. Unfortunately, xyztg mapping do not describe fully developmental state for indeterminate cleavage embryos (which include all chordates).

What do you base this statement on?
Regulative embryos are not exempt from an xyztg type of analysis, as far as I can tell.

 

[trurle]

What do you base this statement on?
Regulative embryos are not exempt from an xyztg type of analysis, as far as I can tell.

You can apply any form of analysis you want, but results may be in error; in this particular case xyztg analysis will not describe properly single-egg twins.

 

[BillTre]

You can apply any form of analysis you want, but results may be in error; in this particular case xyztg analysis will not describe properly single-egg twins.

Can you explain why not?

Seems like it should be able to to me.
It would involve regulatory processes that adjust for the abnormal situation to produce a smaller but somewhat normal embryo.

Regulatory processes also are found in the development of more determinative type embryos the you are distinguishing from the "indeterminate cleavage embryos".
C. elegans, whose embryos are very stereotypic in their development have regulatory processes underlying even apparently stereotypic processes.

Please provide references. Your responses look like uniformed conjectures.

 

[trurle]

Regulatory processes also are found in the development of more determinative type embryos the you are distinguishing from the "indeterminate cleavage embryos".
C. elegans, whose embryos are very stereotypic in their development have regulatory processes underlying even apparently stereotypic processes.

Please provide references. Your responses look like uniformed conjectures.

Yes, "regulatory processes" imply the existence of other variables (input parameters) beyond xyztg. Most important are effects from cell contacts affecting development. In indeterminate type embryos signals from cell contacts have priority over xyztg, and this priority mechanism allows twins (or exogastrulation anomaly). Other factors are also known, in particular i should point out on classical experiments with temperature gradients across egg.

Regarding references, i just remember standard embryology and histology textbooks. You stubborn promotion of actually very simplified and limited-application xyztg model lead me actually to suspect a conflict of interests.

 

[BillTre]

Yes, "regulatory processes" imply the existence of other variables (input parameters) beyond xyztg. Most important are effects from cell contacts affecting development. In indeterminate type embryos signals from cell contacts have priority over xyztg, and this priority mechanism allows twins (or exogastrulation anomaly). Other factors are also known, in particular i should point out on classical experiments with temperature gradients across egg.

Variables like cell contacts come out of an analysis of the position of the different cells in an embryo.
These are not beyond the scope of xyztg type of analysis. The expression of particular genes in particular cells which would be required for those cells to sense whether or not they are in contact with particular cells. The expression of the proper genes would allow particular cells to do these things.
Signals from cell contacts don't have priority over nor are they beyond the positions of cells and different genes expressed by different cells.
They are a result of them!
This does not seem separate from the xyztg approach to me.
Have you read the references I linked to?

Similarly, other molecular processes would underlie other regulatory events, such a cell's sensing of its position in a chemical gradient. The proper genes being expressed allows them to properly sense and respond to their position in the embryo.

 

[trurle]

Have you read the references I linked to?

I read. Historical and technical part was entertaining (i did not knew light sheet fluorescent microscopy before for example), although in last 2 paragraphs authors of Science paper jump to ambiguous conclusion setting that over-simplified "xyztg approach". It is very similar in attitude to enthusiasts of 3D printing. Not many of real-world shapes could be 3D printed, and not many organisms are adequately described in the xyztg space. It will take years of trial and failures to separate hopes from reality.

 

[BillTre]

Not many of real-world shapes could be 3D printed,

Well, not true. Jet engine.

not many organisms are adequately described in the xyztg space

Of course not. It is something that is being developed.
Now only in the most amenable model organisms.
https://www.ge.com/reports/mad-props-3d-printed-airplane-engine-will-run-year/

 

[trurle]

Well, not true. Jet engine.Of course not. It is something that is being developed.
Now only in the most amenable model organisms.
https://www.ge.com/reports/mad-props-3d-printed-airplane-engine-will-run-year/

The last citation states "more than third of the jet engine is 3D printed". Again, please separate hopes (100% 3D printed engine or 100% applicability of xyztg mapping) and reality.
Well, i am watching the topic closely. For example, Merlin engine had 40% of 3D printed parts by mass, and this may be a "bleeding edge technology", proceeding only because development cost of large engines is prohibitively high. For example, for 3D printing is nearly impossible to form pre-stressed components, and mapping of embryos may soon stumble on similar problems. Like "We mapped the embryonic development of zebra fish. But results are valid only for egg lying on borosilicate glass at 21C temperature and salinity 37 promille."

 

[BillTre]

This objection:

The last citation states "more than third of the jet engine is 3D printed". Again, please separate hopes (100% 3D printed engine or 100% applicability of xyztg mapping) and reality.

is quite different from your original one:

Not many of real-world shapes could be 3D printed,

I guess those 67% of the engine parts were not real world parts!

Just like this claim:

mapping of embryos may soon stumble on similar problems

is quite different from this one:

In indeterminate type embryos signals from cell contacts have priority over xyztg, and this priority mechanism allows twins (or exogastrulation anomaly).

You have provided zero references for anything you have claimed.
Your changing claims have danced around the subject, but are supported by nothing but your opinion.
You have only responded to counter arguments by changing what you say.
Your arguments amount to you don't believe it can be done.
Fine. That's your opinion, but don't pretend it is something more.