Mystery at the heart of life

_{News
December 21, 2014

Cell biology, Intelligent Design, News

1}_{Categories
Cell biology
Intelligent Design
News}

Share: Facebook; Twitter/X; LinkedIn; Flipboard; Print; Email

By Biologic Institute’s Ann Gauger, at Christianity Today’s Behemoth, the secret life of cells:

Our bodies are made up of some 100 trillion cells. We tend to think of cells as static, because that’s how they were presented to us in textbooks. In fact, the cell is like the most antic, madcap, crowded (yet fantastically efficient) city you can picture. And at its heart lies a mystery—or I should say, several mysteries—involving three special kinds of molecules: DNA, RNA, and proteins.

These molecules are assembled into long chains called polymers, and are uniquely suited for the roles they play. More importantly, life absolutely depends upon them. We have to have DNA, RNA, and protein all present and active at the same time for a living organism to live.

How they work together so optimally and efficiently is not merely amazing, but also a great enigma, a mystery that lies at the heart of life itself. More. Paywall soon after. May be worth it.

Follow UD News at Twitter!

Comments

Information Processing at the Cellular Level: Beyond the Dogma Alberto Riva http://link.springer.com/chapter/10.1007%2F978-3-642-30574-0_2 [...] it has become clear that the information stored in DNA is only a small portion of the total, and that the overall picture is much more complex than the one outlined by the dogma. The cell is, at its core, an information processing machine based on molecular technology, but the variety of types of information it handles, the ways in which they are represented, and the mechanisms that operate on them go far beyond the simple model provided by the dogma.
This is a repeat. News posted a reference to this paper on April 10th, 2014, under the OP title "Information killed the Central Dogma too".Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
07:44 PM
7
07
44
PM
PDT}

Cell Type-Specific Responses to Wingless, Hedgehog and Decapentaplegic Are Essential for Patterning Early Eye-Antenna Disc in Drosophila Won J-H, Tsogtbaatar O, Son W, Singh A, Choi K-W, Cho K-O (2015) Cell Type-Specific Responses to Wingless, Hedgehog and Decapentaplegic Are Essential for Patterning Early Eye-Antenna Disc in Drosophila. PLoS ONE 10(4): e0121999. doi:10.1371/journal.pone.0121999 Since ead is composed of six embryonic head segments, the distinct cell types are most likely originated from different embryonic segments. When the location of the six embryonic segments in the L1 ead is identified, it will become possible to link the embryonic ead to cell types in larval ead and ultimately to adult head structures. By the same token, it will be possible to identify the cell types that are responsible for the formation of retina. Combination of clonal analysis in both PE and DP layers, expression pattern of various proteins, and mutant analysis will help understand how the complicated adult head structures are generated from a small disc with only ~20 cells at the beginning. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121999
Work in progress... stay tuned.Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
03:22 PM
3
03
22
PM
PDT}

#617 follow up Why did they write "Strikingly"? What's striking about finding that "piRNA targets can be stably silenced across generations"? Can someone explain this to me? Thank you.Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
03:02 PM
3
03
02
PM
PDT}

piRNAs: from biogenesis to function doi: 10.1242/dev.094037 Development 2014 141, 3458-3471. http://dev.biologists.org/content/141/18/3458.full Recently, several studies have started to uncover the hitherto unknown mechanisms of piRNA biogenesis. Further investigation into this previously uncharacterised cytoplasmic piRNA-mediated silencing mode should provide tremendously exciting results. Strikingly, results from studies on transgene silencing have shown that piRNA targets can be stably silenced across generations. When and how such heritable silencing is initiated is another exciting avenue for investigation, [...] Understanding the piRNA target spectrum provides further challenges, in particular in systems where piRNAs are not perfectly complementary to transposable elements. Further insights into the spatial and temporal compartmentalisation of the piRNA machinery will be required to fully appreciate how correct targeting can be achieved. Future in-depth studies of these and other examples will greatly contribute to our understanding of the significant roles played by Piwi proteins and their associated small RNAs. We look forward to these and many other exciting findings yet to be made in the piRNA field.
Work in progress... stay tuned.Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
01:59 PM
1
01
59
PM
PDT}

Intrinsic and extrinsic mechanisms regulating satellite cell function doi: 10.1242/dev.114223 May 1, 2015 Development 142, 1572-1581. http://dev.biologists.org/content/142/9/1572.full [...] a complex balance between extrinsic cues and intrinsic regulatory mechanisms is needed to tightly control satellite cell cycle progression and cell fate determination. different cell states, namely quiescence, commitment, differentiation and self-renewal. many intrinsic mechanisms are required to regulate the cell cycle and cell fate determination
Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
12:21 PM
12
12
21
PM
PDT}

The ureteric bud epithelium: Morphogenesis and roles in metanephric kidney patterning Vidya K. Nagalakshmi and Jing Yu DOI: 10.1002/mrd.22462 http://onlinelibrary.wiley.com/doi/10.1002/mrd.22462/full Molecular Reproduction and Development Volume 82, Issue 3, pages 151–166, March 2015 [...] our knowledge into the molecular and cellular mechanisms underpinning kidney formation has expanded greatly over the past decades. Yet, these studies also revealed the gaps in our understanding of and generated more questions regarding the formation of the metanephric kidney. What cellular mechanisms mediate differential RET activity-regulated nephric duct cell migration? What is the function of mitosis-associated cell dispersal of the ureteric bud cells? How are the fates between the ureteric tip and the ureteric trunk or between the ureteric trunk and the collecting ducts determined? How does the renal interstitium regulate renal medulla elongation?
[...] these studies also revealed the gaps in our understanding of and generated more questions [...] Outstanding questions answered, new questions raised. a never-ending story...Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
12:12 PM
12
12
12
PM
PDT}

WT1 targets Gas1 to maintain nephron progenitor cells by modulating FGF signals doi: 10.1242/dev.119735 Development 2015 142, 1254-1266. http://dev.biologists.org/content/142/7/1254.
Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
08:59 AM
8
08
59
AM
PDT}

Box @612 Thank you so much for translating their speculative "bottom up" wishful thinking. Perhaps people with that kind of prolific imagination could produce top bestselling books in the fiction genre relatively easy. I think "wow!" is a gross understatement. Those exotic ideas deserve a loud "WOW!!!" on steroids. :) Nevertheless, I agree with you on appreciating the tremendous effort made by these scientists in their interesting research, which at the end of the day is what counts. The facts they discover are very valuable to shed light on the big picture of the elaborate molecular and cellular choreographies orchestrated within the biological systems. We just read carefully their personal interpretations of the found evidences. I'm interested in the detailed raw data describing some complex biological systems, not so much on what someone could infer from every discovery. That's why sometimes I write about two fundamental requirements for all the papers to meet: "Where's the beef?" and "Show me the money!" :)Dionisio_{June 22, 2015
June
06
Jun
22
22
2015
08:50 AM
8
08
50
AM
PDT}

Dionisio #605,
Belief in cells? What’s that?
Karl Friston et al propose that there is (somehow) a complete model of the adult organism in each cell. And their next proposal is that, from this model, each cell can infer a "belief" (expectation) about what kind of signals to expect from neighboring cells at any given particular place in the adult organism. Wow! An elaborate self-locating system. Next the cell will know what to do, how to differentiate, what signals to send and so forth ....
Friston: we can now functionally talk about a cell's beliefs and actions in the following way: each cell possesses a generative model [complete model of adult organism] that encodes (genetic) beliefs [expectations] about the chemotactic signals it should sense and express if it occupied a particular place in the target form.[adult organism] [my additions]
Yes, indeed, this is all crazy, but that is where bottom-up explanations take us. I do appreciate Friston's brave efforts though.Box_{June 22, 2015
June
06
Jun
22
22
2015
01:51 AM
1
01
51
AM
PDT}

Emerging picture of the distinct traits and functions of microvesicles and exosomes doi: 10.1073/pnas.1502590112 PNAS March 24, 2015 vol. 112 no. 12 3589-3590 http://www.pnas.org/content/112/12/3589.extract The ability of a cell to receive signals from other cells and then translate them into changes in cell behavior plays crucial roles in development and tissue homeostasis. However, the deregulation of these carefully orchestrated events underlie the onset or progression of several diseases in the adult organism, highlighting the need to better understand the mechanisms through which cells communicate with each other.
Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
06:20 PM
6
06
20
PM
PDT}

Differential fates of biomolecules delivered to target cells via extracellular vehicles doi: 10.1073/pnas.1418401112 PNAS March 24, 2015 vol. 112 no. 12 E1433-E1442 http://intl.pnas.org/content/112/12/E1433.abstract EVs are heterogeneous and there are many outstanding questions associated with biogenesis, uptake, and the fate of transferred molecules in recipient cells. In fact, the function, characterization, and even the nomenclature of EVs are being refined.
Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
06:10 PM
6
06
10
PM
PDT}

Biological properties of extracellular vesicles and their physiological functions Journal of Extracellular Vesicles 2015, 4: 27066 - http://dx.doi.org/10.3402/jev.v4.27066 http://www.journalofextracellularvesicles.net/index.php/jev/article/view/27066 [...] the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. [...] research on EV-mediated maintenance of homeostasis and regulation of physiological functions remains less studied. More detailed studies comparing different injection sites, donor cells and healthy and disease conditions are necessary to establish the clearance and the organ uptake of the various EV populations. [...] the extent to which vesicular localization of cytokines affects conventional cytokine measurements remains a key issue that has yet to be addressed. The observation that miRISCs accumulate at sites of MVBs suggests that a regulatory circuit of miRISC activity and/or miRNA exosome loading may exist. [..] currently it is difficult to distinguish between the effects triggered by mRNAs and various non-coding RNAs that are abundant components of exosomal RNAs and to assess the extent to which individual mRNAs contribute to these effects. Furthermore, it is not yet clear what proportion of a cell's transcriptome in EVs consists of intact mRNAs that can be translated in the recipient cells and which mRNA fragments may play regulatory roles One of the central processes of embryogenesis is the coordination of cell positioning and fate acquisition in response to the morphogens gradient [...] the composition of these EVs is complex and the specific molecular processes and mechanisms by which EVs help sperm cells in vivo on their way to the oocyte have yet to be elucidated. [...] the distribution of morphogens during embryogenesis is a complex process combining different routes, such as passive diffusion of soluble proteins and the active transport by lipoprotein particles or by EVs. It remains to be established how the sorting of morphogens between these routes is regulated and what the specific impact of each particular route is in the embryonic development. EVs are likely to be involved in the regulation of main routes of embryonic development, including the regulation of morphogen gradients, collective cell migration and tissue polarity. However, this still remains an emerging field with many unanswered questions, which need further investigation. Further research in other liver resident cells (e.g. hepatic sinusoidal cells) and studies involving the co-culture of combinations of different cell types in controlled conditions are required to further unravel the physiological role of the network of EVs established in the liver. Future studies may help to establish how widespread the phenomenon of EV-mediated cross-kingdom communication is. More extensive research to establish a deeper understanding of the physiological relevance of EVs in different homeostatic changes is now warranted.
Work in progress... stay tuned.Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
05:51 PM
5
05
51
PM
PDT}

Geometric control of tissue morphogenesis Celeste M. Nelson doi:10.1016/j.bbamcr.2008.12.014 http://www.sciencedirect.com/science/article/pii/S0167488908004370
Kind of old, but perhaps some interesting concepts, though maybe off target, considering newer papers?Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
04:27 PM
4
04
27
PM
PDT}

A Conceptual Model of Morphogenesis and Regeneration Acta Biotheoretica March 2015 A. Tosenberger, N. Bessonov, M. Levin, N. Reinberg, V. Volpert, N. Morozova This two-level organization of the model organism, with global regulation of stem cells and local regulation of tissues, allows its reproducible development and regeneration. http://link.springer.com/article/10.1007/s10441-015-9249-9
Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
04:11 PM
4
04
11
PM
PDT}

On a Model of Pattern Regeneration Based on Cell Memory http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118091 Bessonov N, Levin M, Morozova N, Reinberg N, Tosenberger A, Volpert V (2015) On a Model of Pattern Regeneration Based on Cell Memory. PLoS ONE 10(2): e0118091. doi:10.1371/journal.pone.0118091 While the field is rapidly accumulating high-resolution data on the genetic networks and molecular components necessary for this process, fundamental insight into complex shape homeostasis is lacking. At this time, no quantitative model of target morphology during pattern formation exists.
Cell memory?Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
04:00 PM
4
04
00
PM
PDT}

Box @597 RE: #595 What do you think they meant in their closing statements?:
It is likely that this is just a first step on an important roadmap to formalize the notion of belief and information-processing in cells towards the efficient, top-down control of pattern formation for regenerative medicine and synthetic bioengineering applications.
Belief in cells? What's that?Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
03:46 PM
3
03
46
PM
PDT}

BA77 The information you posted is indeed very interesting. Thank you. I believe we're going to see much more of this kind of information in the days ahead, as research gets deeper into the intricacies of the elaborate cellular and molecular choreographies orchestrated within the biological systems. It's a fascinating time to watch what's going on in biology research. The more outstanding questions get answered, the more novel issues will appear.Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
08:51 AM
8
08
51
AM
PDT}

Endogenous Gradients of Resting Potential Instructively Pattern Embryonic Neural Tissue via Notch Signaling and Regulation of Proliferation Vaibhav P. Pai, Joan M. Lemire, Jean-François Paré, Gufa Lin, Ying Chen, and Michael Levin The Journal of Neuroscience, 2015, 35(10): 4366-4385; doi: 10.1523/JNEUROSCI.1877-14.2015 http://www.jneurosci.org/content/35/10/4366.short Biophysical forces play important roles throughout embryogenesis, but the roles of spatial differences in cellular resting potentials during large-scale brain morphogenesis remain unknown.
Work in progress... stay tuned.Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
08:37 AM
8
08
37
AM
PDT}

BA77 Thank you for the insightful comments.Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
07:50 AM
7
07
50
AM
PDT}

Box @597 Thank you for the interesting commentary. BTW, How are the cells setup to produce (via signal secretion or however else) the right EF gradients and all that stuff spatiotemporally correct? Any detailed info on that? The party has just started... the fun part is still ahead... we ain't seen nothing yet... this is just the tip of the iceberg... we'll see more papers like these in the near future. The big data avalanche can't be contained. They have to figure out better algorithms to process all that information. Any thoughts on this?Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
07:48 AM
7
07
48
AM
PDT}

As to 'especially the face' emitting biophotons, Verses:
Exodus 34:29-30: "Moses didn't realize as he came back down the mountain with the tablets that his face glowed from being in the presence of God. Because of this radiance upon his face, Aaron and the people of Israel were afraid to come near him." Matthew 17:1-2 After six days Jesus took with him Peter, James and John the brother of James, and led them up a high mountain by themselves. There he was transfigured before them. His face shone like the sun, and his clothes became as white as the light.
Also of interest, many Near Death Experiencers give testimony of being in a 'body of light' whilst having their Near Death Experience:
Coast to Coast - Vicki's Near Death Experience (Blind From Birth) part 1 of 3 http://www.youtube.com/watch?v=e65KhcCS5-Y Quote from preceding video: 'I was in a body and the only way that I can describe it was a body of energy, or of light. And this body had a form. It had a head. It had arms and it had legs. And it was like it was made out of light. And 'it' was everything that was me. All of my memories, my consciousness, everything.' - Vicky Noratuk
Moreover, biophotons are quantum in nature. i.e. Biophotons are not reducible to classical explanations for light:
Quantum criticality in a wide range of important biomolecules Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say. That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.” The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552 Symphony of Life, Revealed: New Imaging Technique Captures Vibrations of Proteins, Tiny Motions Critical to Human Life - Jan. 16, 2014 Excerpt: To observe the protein vibrations, Markelz' team relied on an interesting characteristic of proteins: The fact that they vibrate at the same frequency as the light they absorb. This is analogous to the way wine glasses tremble and shatter when a singer hits exactly the right note. Markelz explained: Wine glasses vibrate because they are absorbing the energy of sound waves, and the shape of a glass determines what pitches of sound it can absorb. Similarly, proteins with different structures will absorb and vibrate in response to light of different frequencies. So, to study vibrations in lysozyme, Markelz and her colleagues exposed a sample to light of different frequencies and polarizations, and measured the types of light the protein absorbed. This technique, , allowed the team to identify which sections of the protein vibrated under normal biological conditions. The researchers were also able to see that the vibrations endured over time, challenging existing assumptions. "If you tap on a bell, it rings for some time, and with a sound that is specific to the bell. This is how the proteins behave," Markelz said. "Many scientists have previously thought a protein is more like a wet sponge than a bell: If you tap on a wet sponge, you don't get any sustained sound." http://www.sciencedaily.com/releases/2014/01/140116084838.htm Photocount distribution of photons emitted from three sites of a human body - 2006 Excerpt: Signals from three representative sites of low, intermediate and high intensities are selected for further analysis. Fluctuations in these signals are measured by the probabilities of detecting different numbers of photons in a bin. The probabilities have non-classical features and are well described by the signal in a quantum squeezed state of photons. Measurements with bins of three sizes yield same values of three parameters of the squeezed state. http://www.ncbi.nlm.nih.gov/pubmed/16520060
Also of related interest to Biophotons, the image on the Shroud of Turin was formed by a quantum process. i.e. The image on the Shroud of Turin was not formed by a classical process:
The absorbed energy in the Shroud body image formation appears as contributed by discrete values – Giovanni Fazio, Giuseppe Mandaglio – 2008 Excerpt: This result means that the optical density distribution,, can not be attributed at the absorbed energy described in the framework of the classical physics model. It is, in fact, necessary to hypothesize a absorption by discrete values of the energy where the ‘quantum’ is equal to the one necessary to yellow one fibril. http://cab.unime.it/journals/index.php/AAPP/article/view/C1A0802004/271 “It is not a continuum or spherical-front radiation that made the image, as visible or UV light. It is not the X-ray radiation that obeys the one over R squared law that we are so accustomed to in medicine. It is more unique. It is suggested that the image was formed when a high-energy particle struck the fiber and released radiation within the fiber at a speed greater that the local speed of light. Since the fiber acts as a light pipe, this energy moved out through the fiber until it encountered an optical discontinuity, then it slowed to the local speed of light and dispersed. The fact that the pixels don’t fluoresce suggests that the conversion to their now brittle dehydrated state occurred instantly and completely so no partial products remain to be activated by the ultraviolet light. This suggests a quantum event where a finite amount of energy transferred abruptly. The fact that there are images front and back suggests the radiating particles were released along the gravity vector. The radiation pressure may also help explain why the blood was “lifted cleanly” from the body as it transformed to a resurrected state.” Kevin Moran – optical engineer Scientists say Turin Shroud is supernatural – December 2011 Excerpt: After years of work trying to replicate the colouring on the shroud, a similar image has been created by the scientists. However, they only managed the effect by scorching equivalent linen material with high-intensity ultra violet lasers, undermining the arguments of other research, they say, which claims the Turin Shroud is a medieval hoax. Such technology, say researchers from the National Agency for New Technologies, Energy and Sustainable Economic Development (Enea), was far beyond the capability of medieval forgers, whom most experts have credited with making the famous relic. “The results show that a short and intense burst of UV directional radiation can colour a linen cloth so as to reproduce many of the peculiar characteristics of the body image on the Shroud of Turin,” they said. And in case there was any doubt about the preternatural degree of energy needed to make such distinct marks, the Enea report spells it out: “This degree of power cannot be reproduced by any normal UV source built to date.” http://www.independent.co.uk/news/science/scientists-say-turin-shroud-is-supernatural-6279512.html
Quote and Music:
"There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy." Shakespeare - Hamlet A Mighty Fortress Is Our God - Orchestra https://www.youtube.com/watch?v=oHkLyeD6I1Q
bornagain77_{June 21, 2015
June
06
Jun
21
21
2015
06:52 AM
6
06
52
AM
PDT}

The Real Bioinformatics Revolution - Proteins and Nucleic Acids 'Singing' to One Another? Excerpt: the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see' and ‘hear' each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).,,, More than 1 000 proteins from over 30 functional groups have been analysed. Remarkably, the results showed that proteins with the same biological function share a single frequency peak while there is no significant peak in common for proteins with different functions; furthermore the characteristic peak frequency differs for different biological functions.,,, The same results were obtained when regulatory DNA sequences were analysed. http://www.i-sis.org.uk/TheRealBioinformaticsRevolution.php The Puzzling Role Of Biophotons In The Brain - Dec. 17, 2010 Excerpt: In recent years, a growing body of evidence shows that photons play an important role in the basic functioning of cells. Most of this evidence comes from turning the lights off and counting the number of photons that cells produce. It turns out, much to many people’s surprise, that many cells, perhaps even most, emit light as they work. In fact, it looks very much as if many cells use light to communicate. There’s certainly evidence that bacteria, plants and even kidney cells communicate in this way. Various groups have even shown that rats brains are literally alight thanks to the photons produced by neurons as they work.,,, ,,, earlier this year, one group showed that spinal neurons in rats can actually conduct light. ,, Rahnama and co point out that neurons contain many light sensitive molecules, such as porphyrin rings, flavinic, pyridinic rings, lipid chromophores and aromatic amino acids. In particular, mitochondria, the machines inside cells which produce energy, contain several prominent chromophores. The presence of light sensitive molecules makes it hard to imagine how they might not be not influenced by biophotons.,,, They go on to suggest that the light channelled by microtubules can help to co-ordinate activities in different parts of the brain. It’s certainly true that electrical activity in the brain is synchronised over distances that cannot be easily explained. Electrical signals travel too slowly to do this job, so something else must be at work.,,, (So) It’s a big jump to assume that photons do this job. http://www.technologyreview.com/view/422069/the-puzzling-role-of-biophotons-in-the-brain/ Using light to control cell (protein) clustering - February 12, 2013 Excerpt: Results of the study,, show how blue light can be used as a switch to prompt targeted proteins to accumulate into large clusters.,, "Our study shows a new use for using energy, in this case light, as a tool to understand and control cellular function. In this study, we demonstrated a new method for turning specific cell signaling pathways on and off with spatial and temporal precision, and use this to help better understand the dynamics of the pathway. At the same time, our technique can be used to control certain cell functions," Kane and Schaffer said.,,, http://phys.org/news/2013-02-cell-clustering.html A look at some systemic properties of self-bioluminescent emission - 2008 Excerpt: There is an apparent consensus in the literature that emission in the deep blue and ultraviolet (150-450nm) is related to DNA / RNA processes while emission in the red and near infrared (600-1000nm) is related to mitochondria and oxidative metabolisms,,, http://adsabs.harvard.edu/abs/2008SPIE.7057E...8C Watching a protein as it functions - March 15, 2013 Excerpt: When it comes to understanding how proteins perform their amazing cellular feats, it is often the case that the more one knows the less one realizes they know. For decades, biochemists and biophysicists have worked to reveal the relationship between protein structural complexity and function, only to discover more complexity.,,, A signaling protein usually responds to a messenger or trigger, such as heat or light, by changing its shape, which initiates a regulatory response in the cell. Signaling proteins are all-important to the proper functioning of biological systems, yet the rapid sequence of events, occurring in picoseconds, had, until now, meant that only an approximate idea of what was actually occurring could be obtained.,, The team identified four major intermediates in the photoisomerization cycle. ,,, By tracking structurally the PYP photocycle with near-atomic resolution, the team provided a foundation for understanding the general process of signal transduction in proteins at nearly the lightning speed in which they are actually happening. http://phys.org/news/2013-03-protein-functions.html
Finding light to play a regulatory role in turning specific cell signaling pathways on and off is no small thing to consider since cell signaling pathways are extremely complex with many different proteins involved in a highly integrated fashion in each specific pathway,,,
Signaling Pathways and Tables http://www.cellsignal.com/reference/pathway/index.html Cell Signals - 3-D animation video http://www.youtube.com/watch?v=89W6uACEb7M
You can see a human emitting biophotonic laser light here:
Strange! Humans Glow in Visible Light - Charles Q. Choi - July 22, 2009 Schematic illustration of experimental setup that found the human body, especially the face, emits visible light in small quantities that vary during the day. B is one of the test subjects. The other images show the weak emissions of visible light during totally dark conditions. The chart corresponds to the images and shows how the emissions varied during the day. The last image (I) is an infrared image of the subject showing heat emissions. http://i.livescience.com/images/i/000/006/481/original/090722-body-glow-02.jpg?1296086873 http://www.livescience.com/7799-strange-humans-glow-visible-light.html
bornagain77_{June 21, 2015
June
06
Jun
21
21
2015
06:51 AM
6
06
51
AM
PDT}

Box and Dionisio, if you have not already seen these, here are a few notes that you guys may find interesting and useful:
The (Electric) Face of a Frog - video https://www.youtube.com/watch?v=0VULjzX__OM The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern - July 2011 Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, "When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,",,, "We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It's a jaw dropper.",,, http://www.physorg.com/news/2011-07-frog-time-lapse-video-reveals-never-before-seen.html Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation - January 2013 Excerpt: A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes. http://www.ncbi.nlm.nih.gov/pubmed/23802040 podcast - Jonathan Wells: Is There Biological Information Outside of the DNA?, pt. 3 - Bioelectric code http://intelligentdesign.podomatic.com/entry/2014-06-11T16_35_52-07_00 Not in the Genes: Embryonic Electric Fields - Jonathan Wells - December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels -- which determines the form of the endogenous electric field -- constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html
Besides being a lead player in morphogenesis during embryological development, biophotons are also heavily involved in the cellular communication of an organism throughout an organism's entire life.
Are humans really beings of light? Excerpt: Dr. Popp exclaims, "We now know, today, that man is essentially a being of light.",,, "There are about 100,000 chemical reactions happening in every cell each second. The chemical reaction can only happen if the molecule which is reacting is excited by a photon... Once the photon has excited a reaction it returns to the field and is available for more reactions... We are swimming in an ocean of light." http://viewzone2.com/dna.html Biophotons - The Light In Our Cells - Marco Bischof - March 2005 Excerpt page 2: The Coherence of Biophotons: ,,, Biophotons consist of light with a high degree of order, in other words, biological laser light. Such light is very quiet and shows an extremely stable intensity, without the fluctuations normally observed in light. Because of their stable field strength, its waves can superimpose, and by virtue of this, interference effects become possible that do not occur in ordinary light. Because of the high degree of order, the biological laser light is able to generate and keep order and to transmit information in the organism. http://www.international-light-association.eu/PDF/Biophotons.pdf What are Biophotons? Excerpt: According to a leading researcher of biophotons, German biophysicist Fritz-Albert Popp, light is constantly being absorbed and remitted by DNA molecules within each cell's nucleus. These biophotons create a dynamic, coherent web of light. A system that could be responsible for chemical reactions within the cells, cellular communication throughout the organism, and the overall regulation of the biological system, including embryonic development into a predetermined form. The laser-like coherence of the biophoton field is a significant attribute, making it a prime candidate for exchanging information in a highly functional, efficient and cooperative fashion, lending credence to the idea that it may be the intelligence factor behind the biological processes. An aspect of, or cousin to consciousness, though this remains speculative. http://www.wisegeek.com/what-are-biophotons.htm The mechanism and properties of bio-photon emission and absorption in protein molecules in living systems – May 2012 Excerpt: From the energy spectra, it was determined that the protein molecules could both radiate and absorb bio-photons with wavelengths of less than 3 micrometers and 5–7 micrometers, consistent with the energy level transitions of the excitons.,,, http://jap.aip.org/resource/1/japiau/v111/i9/p093519_s1?isAuthorized=no
bornagain77_{June 21, 2015
June
06
Jun
21
21
2015
06:50 AM
6
06
50
AM
PDT}

Dionisio #595, A very interesting paper by Karl Friston et al. They intend to come up with a bottom-up explanation no matter what.
In this paper, we pursue the notion that morphogenetic selforganization requires each cell to have an implicit model of its place in the final morphology [21]
Picture this: each cell has a complete model of the entire human being. How much info is that?

—and that self-assembly is the process of moving to sample local signals that are predicted by that model.
And from this complete model a cell can predict what kind of signals it will receive from neighboring cells at any given location .... Wow!
In other words, we consider biologically plausible solutions to the inverse problem of how cells attain a target morphology, based upon a forward or generative model of the signals they should sense after they have attained that form [16].
"Plausible!"
One solution to this hard problem of self-assembly is to assume that every (undifferentiated) cell has the same model of the cellular ensemble, which it uses to predict the signals it should encounter at each location in the target form.

At the beginning of morphogenesis, all the cells are thus identical: they possess the same model and implicit (stem-cell like) pluripotentiality, and know nothing about their past locations or their ultimate fate.
Yes. From whence cometh the coordination?
If each cell then minimizes variational free energy then it should, in principle, come to infer its unique place in the ensemble and behave accordingly.
What???
This is guaranteed because the minimum of variational free energy is obtained when each cell is in a unique location and has correctly inferred its place.
Let me get this straight. Variational free energy is minimal when the organism is fully constructed, so all each cell has to do is "minimize variational free energy" in order to construct an organism? Seriously?
At this point, it will express the appropriate signals and fulfil the predictions of all other cells; thereby, maximizing the evidence for its model of the ensemble (and minimizing the free energy of the ensemble). This behaviour can be seen as autonomous, self-constructing or ‘autopoietic’ in the sense of Maturana & Varela [45].
Okay. Well this bottom-up attempt by Karl Friston et al requires an enormous amount of information. IOW this is no problem whatsoever for ID. Another matter is if it constitutes a realistic concept for "selforganization".
Box_{June 21, 2015
June
06
Jun
21
21
2015
06:02 AM
6
06
02
AM
PDT}

#592 follow up The paper is so juicy, that it could be highlighted almost completely.Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
04:30 AM
4
04
30
AM
PDT}

Box @593 Thank you for paying attention, with a discerning eye, to what's written in that and other papers. Many people (including myself) don't read things so carefully. Well done! BTW, did you notice the 'm' word used @587 & @588? Also, you may want to check the reference @592 too:
Knowing one's place: a free-energy approach to pattern regulation Karl Friston, Michael Levin, Biswa Sengupta, Giovanni Pezzulo DOI: 10.1098/rsif.2014.1383 http://rsif.royalsocietypublishing.org/content/12/105/20141383 Understanding how organisms establish their form during embryogenesis and regeneration represents a major knowledge gap in biological pattern formation. It has been recently suggested that morphogenesis could be understood in terms of cellular information processing and the ability of cell groups to model shape.
"major knowledge gap" seems like an understatement, doesn't it? cellular information processing? the ability of cell groups to model shape? Is this serious? Do cells process information? Do they have the ability to model shape? I thought computers did that kind of stuff. Where are the 'procedures' to guide all that processing and modeling (as per gpuccio's terminology)? Did I read the abstract correctly? Is this a peer-reviewed paper? What about the rest of this open access article?Dionisio_{June 21, 2015
June
06
Jun
21
21
2015
03:41 AM
3
03
41
AM
PDT}

//follow up #593// Stephen Meyer on electromagnetic fields; "Darwin's Doubt", ch.14, 'Epigenetic Revolution', 'Beyond Genes', 'Ion Channels and Electromagnetic Fields'.
Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism. In particular, some experiments have shown that the targeted disturbance of these electric fields disrupts normal development in ways that suggest the fields are controlling morphogenesis.22 Artificially applied electric fields can induce and guide cell migration. There is also evidence that direct current can affect gene expression, meaning internally generated electric fields can provide spatial coordinates that guide embryogenesis.23 Although the ion channels that generate the fields consist of proteins that may be encoded by DNA (just as microtubules consist of subunits encoded by DNA), their pattern in the membrane is not. Thus, in addition to the information in DNA that encodes morphogenetic proteins, the spatial arrangement and distribution of these ion channels influences the development of the animal. [My emphasis]
Box_{June 21, 2015
June
06
Jun
21
21
2015
02:54 AM
2
02
54
AM
PDT}

A definite game changer, which should be headlined at UD! Dionisio #591, Thank you very much for pointing to this extremely interesting article by Richard H. W. Funk. Excerpt:
Each cell (not only neural cells!) produces a membrane potential that is specific for its type and tissue and which is also specific for its degree of differentiation. The electric nature of these membrane potentials producing endogenous electric fields (…), comes from the segregation of charges by molecular machines like pumps, transporters and ion channels that are mostly situated in the plasma membrane. All these factors carry information for a single cell but also for the neighboring cells. Thus, an extreme complex picture emerges, “drawn” by cell- and molecular biological methods, which gathered a tremendous amount of new data in the recent decade. Taken together, the membrane potential—generated EF is possibly the first and most subtle hitherto detectable general biological information system, at least with recent technologies. (…) they can be observed with modern in vivo dyes directly in cell- and even in sub-cellular dimensions (see also the reviews mentioned above). And since the last decade it is possible to link these EFs directly to “hard—core” molecular biology of the cell. Later on these fields spread over the early embryo. Such EFs are in general the first information cues that determine domains like anterior/posterior or left/right in the very early embryo (…).EF and ion flows are tightly involved in developmental differentiation control. Gap junctions connect nearly all cell types, and interestingly connect also cells which are not residing in close proximity, by extended processes that often also possess gap junctions (Wang et al., 2012) Regarding migration there is mounting evidence that EF are driving factors in cell migration that often override other cues in a multi–cue environment. Thus, from the early embryonic development on, many steps in further cell differentiation and cell migration should be revisited in the light of these new findings.
N.B. any bottom-up explanation for EF coherence is lacking.Box_{June 21, 2015
June
06
Jun
21
21
2015
02:14 AM
2
02
14
AM
PDT}

Knowing one's place: a free-energy approach to pattern regulation Karl Friston, Michael Levin, Biswa Sengupta, Giovanni Pezzulo 2015. DOI: 10.1098/rsif.2014.1383 http://rsif.royalsocietypublishing.org/content/12/105/20141383
Dionisio_{June 20, 2015
June
06
Jun
20
20
2015
08:59 PM
8
08
59
PM
PDT}

Endogenous electric fields as guiding cue for cell migration Front. Physiol., 13 http://dx.doi.org/10.3389/fphys.2015.00143 Richard H. W. Funk http://journal.frontiersin.org/article/10.3389/fphys.2015.00143/full
Very interesting article.Dionisio_{June 20, 2015
June
06
Jun
20
20
2015
08:53 PM
8
08
53
PM
PDT}

Prev 1 … 95 96 97 98 99 … 117 Next

You must be logged in to post a comment.

Leave a Reply