From Phys.org:
The transition from an egg to a developing embryo is one of life’s most remarkable transformations. Yet little is known about it. Now Whitehead Institute researchers have deciphered how one aspect—control of the all-important translation of messenger RNAs (mRNAs) into proteins—switches as the egg becomes an embryo. That shift is controlled by a beautiful mechanism, which is triggered at a precise moment in development and automatically shuts itself off after a narrow window of 20 to 90 minutes.
As an egg develops, it stockpiles mRNAs from the mother because it will not have time to create new mRNAs during the rapid development of a very early embryo. When fertilized the egg becomes an embryo, the stashed maternal mRNAs are pressed into service for a brief window before the embryo starts transcribing its own mRNAs. This change occurs very early; in humans, only two to four cell divisions occur before this transition is executed. Whitehead Member Terry Orr-Weaver studies the control of translation of maternal mRNAs in the model organism Drosophila, or the fruit fly, because its developmental strategy offers experimental advantages. More.
A reader writes to note that the “beautiful mechanism” is described as a
negative feedback loop,” with the same function as those designed in engineering control systems: Furthermore, the activity of PNG kinase leads to the destruction of GNU, and this feedback loop limits this kinase’s activity to the narrow window of time in which it is needed.
“Active PNG leads to decreased GNU protein levels. This makes a negative feedback to shut down PNG kinase activity, thereby ensuring PNG kinase activity is constrained to the short developmental window of the oocyte-to-embryo transition
Another reader who forwarded this item points out that the authors let in the “d” word (and I don’t mean “Darwin”…. ):
The design of this transition could tell scientists more about how human cells work and embryos develop. For example, the switch could be a model for how cells massively and globally change mRNA translation. Also, similar kinase activity during early development has been noted in worms, which may mean that a comparable approach is used in other organisms, including humans.
Well, if the researchers’ careers take a beating for mentioning design, they will need to join the Free the Universities movement. After a while language Stalinism starts t collapse from its own uncommunicativeness and one must peak clearly again.
See also: Cells communicate to navigate a crowded embryo
Interesting paper. Thanks.
Complex complexity
Complex complexity
Complex complexity
Complex complexity
Did somebody say “Strikingly”?
Complex complexity
Elegant switch controls translation in transition from egg to embryo
http://wi.mit.edu/news/archive.....egg-embryo
perhaps when they write ‘design’ they really mean ‘appearance’?
appearances can be deceiving, can’t they? 🙂
Functional Amyloids in Reproduction
Aveline Hewetson 1, Hoa Quynh Do 1, Caitlyn Myers 1, Archana Muthusubramanian 1, Roger Bryan Sutton 2, Benjamin J. Wylie 3 and Gail A. Cornwall
Biomolecules 2017, 7(3), 46;
doi:10.3390/biom7030046
“nature favors the amyloid fold for these processes”?
“nature favors”?
huh?
Complex functional complexity
Complex functional complexity
Complex functional complexity
Complex functionally specified informational complexity.
🙂
“The future of genetic codes and BRAIN codes”
Presentation by professor George M. Church at NIH
2017-Feb-08 @3pm
https://videocast.nih.gov/summary.asp?Live=21803&bhcp=1
@55:30 [in response to a question]
@56:15
Had we remained in Eden, none of this would have been an issue at all. Too late now.
Complex functionally specified informational complexity
Had we remained in Eden, none of this would have been an issue at all. Too late now.
Complex functionally specified informational complexity
Had we remained in Eden, none of this would have been an issue at all. Too late now.
Complex functionally specified informational complexity
Had we remained in Eden, none of this would have been an issue at all. Too late now.
Complex functionally specified informational complexity
Had we remained in Eden, none of this would have been an issue at all. Too late now.
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Had we stayed in Eden, none of this would have been an issue at all. Too late now.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Did somebody say “surprising”? 🙂
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say “One of the challenges of the next century”? Next century?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
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Complex functionally specified informational complexity
Dionisio everywhere: Incredible contributions. Brilliant. Thank you.
[emphasis added]
Complex functionally specified informational complexity
Complex functionally specified informational complexity
TWSYF @64:
It’s my pleasure. However, all I’m doing is referencing a small subset of the enormous volume of biology-related research information available out there.
The real work is done by many seriously dedicated scientists who are trying to figure out how the biological systems work. Unfortunately many of them have been brainwashed with the Darwinian obscenities inserted in otherwise interesting textbooks, thus poisoning the minds of many students.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Off topic?
https://uncommondescent.com/plants/photosynthesis-genes-source-still-unclear/#comment-636305
Those who would like to learn basic biology concepts associated with development, may benefit from watching MIT free courses by professor Hazel Sive.
Lecture 21 Development 1
Lecture 22 Development 2
Lecture 23 Stem Cells
Lecture 24 Nervous System 1
Lecture 25 Nervous System 2
Lecture 26 Nervous System 3
https://ocw.mit.edu/courses/biology/7-013-introductory-biology-spring-2013/video-lectures/lecture-21-development-1/
You may download the videos and watch them offline at your own convenience.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Work in progress… stay tuned.
Biology researchers should focus in on understanding how the marvelous biological systems function, instead of wasting time on OOL pseudoscientific hogwash.
Complex functionally specified informational complexity
As the researchers will dig deeper into their reductionist evo-devo framework, eventually they could realize that the currently-accepted metaphysical models can’t explain the “surprising” and “unexpected” discoveries they’ll make.
Complex functionally specified informational complexity
casual? Did the author mean “causal” instead?
How many people read the abstract of this paper before it was approved for publishing? Proofreaders? Peer-reviewers? Did they read the text carefully?
They seem struggling with complex functionally specified informational complexity. Poor things.
casual? Did the author mean “causal” instead?
How many people read the abstract of this paper before it was approved for publishing? Proofreaders? Peer-reviewers? Did they read the text carefully? At least the abstract? Do they pay attention to details? How much attention? Do they know that “casual” means something different than “causal” ?
They seem struggling with complex functionally specified informational complexity. Poor things.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
This was over 4 years ago. What’s the situation now?
This was over 4 years ago. What’s the situation now?
This was over 4 years ago. What’s the situation now?
This was over 4 years ago. What’s the situation now?
This was over 4 years ago. What’s the situation now?
This was over 4 years ago. What’s the situation now?
This was over 4 years ago. What’s the situation now?
This was 2 years ago. What’s the situation now?
Turing, please can you explain this for us? 🙂
This was 2 years ago. What’s the situation now?
Did somebody say ‘design’? 🙂
This was 2 years ago. What’s the situation now?
Work in progress… stay tuned.
This was 2 years ago. What’s the situation now?
Did somebody say “biological engineering strategies”?
This was 2 years ago. What’s the situation now?
Complex functionally specified informational complexity
Did somebody say ‘orchestrate’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Biological Cybernetics
Advances in Computational Neuroscience
https://link.springer.com/journal/422
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
gpuccio,
Would it be interesting to analyze the information in the proteins mentioned @116-117: Tpr, Nup153 and Nup98 ?
Thank you.
Dionisio:
Nucleoporins are a rather heterogeneous group of proteins. Most of them have some important information jump in vertebrates, and another one between amphibia and reptiles. However, they differ a lot in the amount of human-conserved information present in pre-vertebrates, which can range from almost 0 to about 1.8 bits per AA.
That said, the three proteins you mention are rather similar in their behaviour:
TPR (P12270): length: 2563 AAs
human-conserved information in pre-vertebrates: 0.4646636 baa
jump to vertebrates:
0.676259 baa, 1598 bits
NUP 98-96 complex (P52948): length 1817 AAs
human-conserved information in pre-vertebrates: 0.5701706 baa
jump to vertebrates:
0.5365988 baa, 975 bits
NUP 153 (P49790): length 1475 AAs
human-conserved information in pre-vertebrates: 0.1566102 baa
jump to vertebrates:
0.5023729 baa, 741 bits
As you can see, all of them exhibit a vertebrate jump slightly greater than 0.5 baa (about one quarter if the total potential information in the protein), which translates into absolute bit jumps ranging from 741 to 1598, according to the protein length.
While the first two proteins start with some amount of human-conserved information even in pre-vertebrates (about 0.5 baa), the third one differs, because it shows almost no human-conserved information before the vertebrate jump (0.15 baa).
However, the vertebrate jump in these proteins (ranging from 0.50 to 0.67 baa) is about double than the mean vertebrate jump in the human proteome (0.28796 baa)
Complex functionally specified informational complexity.
gpuccio,
Thank you for the detailed analysis of the given proteins.
Very interesting indeed.
Complex functionally specified informational complexity.
Did somebody say ‘Surprisingly’? 🙂
Complex functionally specified informational complexity.
Work in progress… stay tuned.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Did somebody say ‘surprisingly’?
Work in progress… stay tuned.
Complex functionally specified informational complexity.
Work in progress… stay tuned.
But I don’t like knowledge gaps, because every new discovery points to designed biological systems.
Complex functionally specified informational complexity.
Did somebody say ‘zip code’? 🙂
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Did somebody say ‘unexpected’?
Did they expect something else or nothing at all?
Complex functionally specified informational complexity.
Why largely unstudied? Lack of recourses? lack of time?
Complex functionally specified informational complexity.
Work in progress… stay tuned.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Why are they often omitted or not discussed in depth?
Can somebody provide a valid reason?
Is it lack of resources?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Work in progress… stay tuned.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
If we don’t know their function, then they must not be important.
If they don’t appear in all biological systems, then they must not be important.
Haven’t we read that kind of nonsense before?
Complex functionally specified informational complexity.
Did somebody say ‘entangled’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
This is a 4-year old paper. Let’s see how much more information on this subject has been gathered since then.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
No room for reductionist solutions?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Did somebody say ‘orchestrated’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Did somebody say ‘surprisingly’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Why does it have to be like known regulators? Where is such a rule written in?
Complex functionally specified informational complexity.
A new class of regulators?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Did somebody say ‘coordinated’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
A new regulator?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Dionisio, Heh:),
of the 202 comments so far, you have authored 200. Are you on medication?
You are interrupted twice by, Truth Will Set You Free, @64, and, gpuccio @119, other than that it is a ‘Dionisio’ love fest.
This is not a good look for ID, it points to a kind of Narcissistic personality disorder; were you bullied?
Do you even realise that there is no feedback. Afterall, we speak so as to be heard. If there are no listeners, why speak?
From all ofyour output, am I to take it that you think, all life is sacred from conception?
I disagree strongly, so your effort is wasted. The courts also agree with me. You have God and the Bible. Let’s see which is stronger?
Did somebody say ‘unexpectedly’?
What else did they expect? Why?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
“future studies will be necessary”
“it will be important to uncover the mechanisms”
As outstanding questions get answered, new questions are raised. In biology, the more we know, more is there to learn.
Complex functionally specified informational complexity.
Did somebody say ‘unexpected’?
“Our work paves the way to unveil the molecular mechanisms”
How long is that way? How much ‘paving’ work remains to be done?
Work in progress… stay tuned.
Complex functionally specified informational complexity.
Did somebody say ‘coordinate’?
Complex functionally specified informational complexity.
Did somebody say ‘controls’?
alternative mechanism? another one?
Did somebody say ‘coordinates’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
“at the right time, at the right place and in the correct number”
Did somebody say ‘strikingly’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Did somebody say ‘coordinated’?
Did somebody say ‘orchestrated’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Heh:)
wonderful. Don’t stop on my account:)
Can you make 300?
Did somebody say ‘concerted manner’?
Did somebody say ‘complexity’?
Did somebody say ‘controlled’?
Did somebody say ‘fine-tuned coordination’?
Did somebody say ‘coordinating’?
Did somebody say ‘orchestrates’?
Complex functionally specified informational complexity.
Did somebody say ‘orchestrate’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Did somebody say ‘instructions’?
Did somebody say ‘strikingly’?
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Work in progress… stay tuned.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity.
Complex functionally specified informational complexity
Did somebody say ‘preferable strategy’?
Complex functionally specified informational complexity
Did somebody say ‘preferable strategy’?
Complex functionally specified informational complexity
@236-238 the referenced paper apparently deals with plant leaves, which are relatively simpler organs.
The morphogenesis of other more complex organs is a different story, as we have seen described in a number of recent papers, where the diffusion-reaction mechanisms by themselves can’t make the morphogen gradients. Other transport mechanisms have been described in those cases.
Did somebody say ‘Surprisingly’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Where’s the beef? 🙂
Complex functionally specified informational complexity
Where’s the beef?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘programme’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Here’s an example of the fundamental evo-devo problem which has been formulated thus:
Dev(d) = Dev(a) + Delta(a,d)
Where
‘a’ is an ancestor biological system,
‘d’ is a descendant biological system,
Dev(x) is the entire developmental process of the biological system ‘x’
Delta(x,y) is the entire set of spatiotemporal changes required in Dev(x) in order to have Dev(y)
Where’s the beef?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘Strikingly’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
The authors of this paper should have consulted a biochemistry professor who a couple of years ago in this website claimed to know exactly how to cook the whole enchilada. 🙂
But they should have asked “honest questions” (whatever that means) lest he won’t share his secret recipe. 🙂
Complex functionally specified informational complexity
Complex functionally specified informational complexity
The authors of this paper should have consulted a biochemistry professor who a couple of years ago in this website claimed to know exactly how to cook the whole enchilada. 🙂
But they should have asked “honest questions” (whatever that means) lest he won’t share his secret recipe. 🙂
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘programs’?
Complex functionally specified informational complexity
Did somebody say ‘intriguing’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say “microswitches”?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say “coordinated”?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
a new mechanism? another one?
Did somebody say “Surprisingly”?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
The authors of this research paper may want to consult someone who -at least momentarily- claimed -two years ago- to know exactly how morphogen gradients form. 🙂
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
I thought they knew exactly how morphogen gradients are formed. I must have read the wrong memo. 🙂
Complex functionally specified informational complexity
Did somebody say “surprisingly”? Why?
Complex functionally specified informational complexity
Did somebody say ‘timing’?
Complex functionally specified informational complexity
Did somebody say ‘information remembered’?
Did somebody say ‘information interpreted’?
Complex functionally specified informational complexity
The more we know, more is there for us to learn.
Complex functionally specified informational complexity
Did somebody say ‘speculations ‘?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Dionisio, of to the races as of @1.
Write a book. No one will read it as your style lacks grace; “Compex fuctionally specified informational complexity.” Heh:)
Me thinks thou hast supped too much of the teat of Kairos; anon.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘orchestration’?
Complex functionally specified informational complexity
Did somebody say ‘complexity’?
Did somebody say ‘complex machineries’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say “oscillation of […] feedback loops”?
Is this about biology or electronic circuits?
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Reshuffling existing functionality?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Why? Based on what?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Wrong assumption?
Complex functionally specified informational complexity
Did somebody say ‘just in time’?
Complex functionally specified informational complexity
Did somebody say ‘control the timing’?
Did somebody say ‘precisely regulating’?
Complex functionally specified informational complexity
Did somebody say ‘precise’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘surprising’?
Complex functionally specified informational complexity
Did somebody say ‘Surprisingly’?
Did somebody say ‘unanticipated level of control’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘dialogue’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘dialogue’?
Did somebody say ‘coherent’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘machinery’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
There yet?
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Reshuffling existing genetic/epigenetic information?
Embedded Variability Framework (EVF)?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
There yet?
Work in progress… stay tuned.
Complex functionally specified informational complexity
Necessary but not sufficient?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
How is citokinin controlled?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘coordinated’?
Did somebody say ‘program’?
Complex functionally specified informational complexity
Do they mean that this is not the end of the story?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say “reconsider morphogenetic gradient theory” in 2017?
Didn’t a distinguished biochemistry professor claim two years ago, here in this website, that all is known about morphogen gradient formation?
Why reconsider it now?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘orchestrates’?
Did somebody say ‘programs’?
Complex functionally specified informational complexity
Did somebody say ‘communicate’?
Did somebody say ‘coordinate’?
Complex functionally specified informational complexity
Did somebody say ‘new paradigms’?
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Did somebody say ‘instruct’?
Complex functionally specified informational complexity
Did somebody say ‘coordinate’?
Complex functionally specified informational complexity
A Turing-like mechanism doesn’t seem to explain the observed facts?
an integrated model is required to fully understand these processes?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Did somebody say ‘orchestration’?
Complex functionally specified informational complexity
Did somebody say ‘concerted action’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Work in progress… stay tuned.
Complex functionally specified informational complexity
Did somebody say ‘unexpected’?
Complex functionally specified informational complexity
Did somebody say ‘Surprisingly’?
Did somebody say ‘puzzling’?
Complex functionally specified informational complexity
Complex functionally specified informational complexity
What they have to understand is the fundamental evo-devo problem formulated thus:
Dev(d) = Dev(a) + Delta(a,d)
Where,
Dev(a) is the entire developmental process of the ancestor ‘a’
Dev(d) is the entire developmental process of the descendant ‘d’
Delta(a,d) is the collection of all the required spatiotemporal changes in Dev(a) in order to get Dev(d).
Note that entire developmental process includes the whole enchilada, i.e. all the ingredients and cooking recipes.
Complex functionally specified informational complexity
Complex functionally specified informational complexity
Complex functionally specified informational complexity
@385-392: juicy
Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root.
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
Yesudhas, Dhanusha & Batool, Maria & Anwar, Muhammad Ayaz & Panneerselvam, Suresh & Choi, Sangdun. (2017). Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes. 8. . 10.3390/genes8080192.
Background
Enhancers are DNA regulatory elements that influence gene expression. There is substantial diversity in enhancers’ activity patterns: some enhancers drive expression in a single cellular context, while others are active across many. Sequence characteristics, such as transcription factor (TF) binding motifs, influence the activity patterns of regulatory sequences; however, the regulatory logic through which specific sequences drive enhancer activity patterns is poorly understood. Recent analysis of Drosophila enhancers suggested that short dinucleotide repeat motifs (DRMs) are general enhancer sequence features that drive broad regulatory activity. However, it is not known whether the regulatory role of DRMs is conserved across species.
Results
We performed a comprehensive analysis of the relationship between short DNA sequence patterns, including DRMs, and human enhancer activity in 38,538 enhancers across 411 different contexts. In a machine-learning framework, the occurrence patterns of short sequence motifs accurately predicted broadly active human enhancers. However, DRMs alone were weakly predictive of broad enhancer activity in humans and showed different enrichment patterns than in Drosophila. In general, GC-rich sequence motifs were significantly associated with broad enhancer activity, and consistent with this enrichment, broadly active human TFs recognize GC-rich motifs.
Conclusions
Our results reveal the importance of specific sequence motifs in broadly active human enhancers, demonstrate the lack of evolutionary conservation of the role of DRMs, and provide a computational framework for investigating the logic of enhancer sequences.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-017-3934-9) contains supplementary material, which is available to authorized users.
L. Colbran, Laura & Chen, Ling & A. Capra, John. (2017). Short DNA sequence patterns accurately identify broadly active human enhancers. BMC Genomics. 18. . 10.1186/s12864-017-3934-9.
Convolutionary neural networks (CNN) has been widely used for DNA motif discovery due to its high accuracy. To employ CNN for DNA motif discovery task, the input DNA sequences are required to be encoded as numerical values and represented as either vector or multi-dimensional matrix. This paper evaluates the simple and more compact ordinal encoding method versus the popular one-hot encoding for DNA sequences. We compare the performances of both encoding methods using three sets of datasets enriched with DNA motifs. We found that the ordinal encoding performs comparable to the one-hot encoding method but with significant reduction in training time. In addition, the one-hot encoding performance is quite consistent across various datasets but would require suitable CNN configuration to perform well. The ordinal encoding with matrix representation performs best in some of the evaluated datasets. This study implies that the performance of CNN for DNA motif discovery depends on the suitable design of the sequence encoding and representation. In addition, the CNN architecture and configuration require some tuning to suit different encoding methods.
Choong, Allen & Lee, Nung Kion. (2017). Evaluation of Convolutionary Neural Networks Modeling of DNA Sequences using Ordinal versus one-hot Encoding Method. BIORXIV/2017/186965. . 10.1101/186965.
For identifying the genes that are regulated by a transcription factor (TF), we have established an analytical pipeline that combines genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq and RNA-Seq. Here, SELEX was used to select DNA fragments from an Aspergillus nidulans genomic library that bound specifically to AmyR, a TF from A. nidulans. High-throughput sequencing data were obtained for the DNAs enriched through the selection, following which various in silico analyses were performed. Mapping reads to the genome revealed the binding motifs including the canonical AmyR-binding motif, CGGN8CGG, as well as the candidate promoters controlled by AmyR. In parallel, differentially expressed genes related to AmyR were identified by using RNA-Seq analysis with samples from A. nidulans WT and amyR deletant. By obtaining the intersecting set of genes detected using both gSELEX-Seq and RNA-Seq, the genes directly regulated by AmyR in A. nidulans can be identified with high reliability. This analytical pipeline is a robust platform for comprehensive genome-wide identification of the genes that are regulated by a target TF.
Kojima, Takaaki & Kunitake, Emi & Ihara, Kunio & Kobayashi, Tetsuo & Nakano, Hideo. (2016). A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq. PLOS ONE. 11. e0159011. 10.1371/journal.pone.0159011.
In the past decade, various transcriptional activators of cellulolytic enzyme genes have been identified in Ascomycete fungi. The regulatory system of cellulolytic enzymes is not only partially conserved, but also significantly diverse. For example, Trichoderma reesei has a system distinct from those of Aspergillus and Neurospora crassa—the former utilizes Xyr1 (the Aspergillus XlnR ortholog) as the major regulator of cellulolytic enzyme genes, while the latter uses CLR-2/ClrB/ManR orthologs. XlnR/Xyr1 and CLR-2/ClrB/ManR are evolutionarily distant from each other. Regulatory mechanisms that are controlled by CLR-2, ClrB, and ManR are also significantly different, although they are orthologous factors. Expression of clr-2 requires the activation of another transcription factor, CLR-1, by cellobiose, while CLR-2 is constitutively active for transactivation. By contrast, ClrB activation requires cellobiose. While ClrB mainly regulates cellulolytic genes, ManR is essential for the activation of not only cellulolytic but also mannanolytic enzyme genes. In this review, we summarize XlnR/Xyr1- and CLR-2/ClrB/ManR-dependent regulation in N. crassa, A. nidulans, A. oryzae, and T. reesei and emphasize the conservation and diversity of the regulatory systems for cellulolytic enzyme genes in these Ascomycete fungi. In addition, we discuss the role of McmA, another transcription factor that plays an important role in recruiting ClrB to the promoters in A. nidulans.
Kunitake, Emi & Kobayashi, Tetsuo. (2017). Conservation and diversity of the regulators of cellulolytic enzyme genes in Ascomycete fungi. Current Genetics. 63. . 10.1007/s00294-017-0695-6.
Background
Genome and transcriptome sequencing has greatly facilitated the understanding of biomass-degrading mechanisms in a number of fungal species. The information obtained enables the investigation and discovery of genes encoding proteins involved in plant cell wall degradation, which are crucial for saccharification of lignocellulosic biomass in second-generation biorefinery applications. The thermophilic fungus Malbranchea cinnamomea is an efficient producer of many industrially relevant enzymes and a detailed analysis of its genomic content will considerably enhance our understanding of its lignocellulolytic system and promote the discovery of novel proteins. ResultsThe 25-million-base-pair genome of M. cinnamomea FCH 10.5 was sequenced with 225× coverage. A total of 9437 protein-coding genes were predicted and annotated, among which 301 carbohydrate-active enzyme (CAZyme) domains were found. The putative CAZymes of M. cinnamomea cover cellulases, hemicellulases, chitinases and pectinases, equipping the fungus with the ability to grow on a wide variety of biomass types. Upregulation of 438 and 150 genes during growth on wheat bran and xylan, respectively, in comparison to growth on glucose was revealed. Among the most highly upregulated CAZymes on xylan were glycoside hydrolase family GH10 and GH11 xylanases, as well as a putative glucuronoyl esterase and a putative lytic polysaccharide monooxygenase (LPMO). AA9-domain-containing proteins were also found to be upregulated on wheat bran, as well as a putative cutinase and a protein harbouring a CBM9 domain. Several genes encoding secreted proteins of unknown function were also more abundant on wheat bran and xylan than on glucose. Conclusions
The comprehensive combined genome and transcriptome analysis of M. cinnamomea provides a detailed insight into its response to growth on different types of biomass. In addition, the study facilitates the further exploration and exploitation of the repertoire of industrially relevant lignocellulolytic enzymes of this fungus.
Hüttner, Silvia & Thuy Nguyen, Thanh & Granchi, Zoraide & Chin-A-Woeng, Thomas & Ahrén, Dag & Larsbrink, Johan & Thanh, Vu & Olsson, Lisbeth. (2017). Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea. Biotechnology for Biofuels. 10. . 10.1186/s13068-017-0956-0.
The spinal cord (SC) is the part of the central nervous system (CNS) that is responsible for the motor, somato-sensory, and visceral innervation of the extremities, trunk, and large parts of the neck as well as all inner organs. Spinal nerves of the peripheral nervous system (PNS) serve as connections between the CNS and distal receptors and organs. And just as the SC controls many aspects of locomotion and visceral function, it also serves as an important relay station for incoming, afferent information from the periphery to central brain regions. It thus constitutes the major coordination hub for how humans unconsciously perceive their periphery and how our bodies react to this information, often involuntarily and without involvement of higher brain functions. And while the topography and cytoarchitecture of the human spinal cord is fairly well understood, the functional implications of some well-described structures remain elusive. Because of the central role the spinal cord plays in many forms of CNS impairment, a better understanding of the functional neuroanatomy of this structure is a prerequisite for addressing potential therapeutic approaches. This chapter gives an overview of spinal cord development, topography, cytoarchitecture, and functional assembly with a special focus on two aspects often compromised during spinal cord injury, namely, the control of micturition and the propriospinal neuron networks that hold great promise for the future improvement of therapies for patients suffering from spinal cord injury.
Engelhardt, Maren & Sobotzik, Jürgen-Markus. (2017). Functional Neuroanatomy of the Spinal Cord. Neurological Aspects of Spinal Cord Injury. 19-60. 10.1007/978-3-319-46293-6_2.