Mystery at the heart of life

_{Denyse O'Leary

December 21, 2014

Cell biology, Intelligent Design, News}

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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.

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Comments

New insights in the clockwork mechanism regulating lineage specification DOI: 10.1002/dvdy.24228 Powerful transcription factors called fate determinants induce robust differentiation programs in multipotent cells and trigger lineage specification. These factors guarantee the differentiation of specific tissues/organs/cells at the right place and the right moment to form a fully functional organism. Fate determinants are activated by temporal, positional, epigenetic, and post-transcriptional cues, hence integrating complex and dynamic developmental networks. In turn, they activate specific transcriptional/epigenetic programs that secure novel molecular landscapes. In this review, we use the Drosophila Gcm glial determinant as a model to discuss the mechanisms that allow lineage specification in the nervous system. The dynamic regulation of Gcm via interlocked loops has recently emerged as a key event in the establishment of stable identity. Gcm induces gliogenesis while triggering its own extinction, thus preventing the appearance of metastable states and neoplastic processes. Using simple animal models that allow in vivo manipulations provides a key tool to disentangle the complex regulation of cell fate determinants. Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc. http://onlinelibrary.wiley.com/doi/10.1002/dvdy.24228/abstract
Dionisio_{December 30, 2014
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¡Feliz Año Nuevo! http://1.bp.blogspot.com/-gKHud3Kib0E/UhYvnhwz5XI/AAAAAAAAHyk/DdOVpjw-Xe4/s1600/quien+rie+ultimo+rie+mejor.jpgDionisio_{December 30, 2014
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#34 Seversky Hmm... Why did you answer my question posted @ 30 but did NOT answer my two questions posted @ 29 ? You don't have to answer any questions, but it is kind of ~~suspicious~~ interesting that you answered the post 30 but did not answer post 29 which was also addressed to you.Dionisio_{December 30, 2014
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Seversky @ 34 Why did you answer my question posted @ 30 but did NOT answer my two questions posted @ 29 ?Dionisio_{December 30, 2014
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Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation DOI: http://dx.doi.org/10.1016/j.cell.2013.06.052 Intron retention (IR) is widely recognized as a consequence of mis-splicing that leads to failed excision of intronic sequences from pre-messenger RNAs. Our bioinformatic analyses of transcriptomic and proteomic data of normal white blood cell differentiation reveal IR as a physiological mechanism of gene expression control. IR regulates the expression of 86 functionally related genes, including those that determine the nuclear shape that is unique to granulocytes. Retention of introns in specific genes is associated with downregulation of splicing factors and higher GC content. IR, conserved between human and mouse, led to reduced mRNA and protein levels by triggering the nonsense-mediated decay (NMD) pathway. In contrast to the prevalent view that NMD is limited to mRNAs encoding aberrant proteins, our data establish that IR coupled with NMD is a conserved mechanism in normal granulopoiesis. Physiological IR may provide an energetically favorable level of dynamic gene expression control prior to sustained gene translation. http://www.cell.com/cell/abstract/S0092-8674(13)00834-9Dionisio_{December 28, 2014
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The present study, originally designed to investigate cellular and signaling mechanisms underlying the regulatory role of GPER in vascular SMC proliferation using G-1, unexpectedly revealed off-target effects of G-1. DOI: 10.1002/jcp.24817 http://onlinelibrary.wiley.com/doi/10.1002/jcp.24817/abstract
unexpectedly revealed ? What did they expect to find?Dionisio_{December 27, 2014
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Keeping an eye on SOXC proteins DOI: 10.1002/dvdy.24235 The formation of a mature, functional eye requires a complex series of cell proliferation, migration, induction among different germinal layers, and cell differentiation. These processes are regulated by extracellular cues such as the Wnt/BMP/Hh/Fgf signaling pathways, as well as cell intrinsic transcription factors that specify cell fate. In this review article, we provide an overview of stages of embryonic eye morphogenesis, extrinsic and intrinsic factors that are required for each stage, and pediatric ocular diseases that are associated with defective eye development. In addition, we focus on recent findings about the roles of the SOXC proteins in regulating vertebrate ocular development and implicating SOXC mutations in human ocular malformations. Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc. http://onlinelibrary.wiley.com/doi/10.1002/dvdy.24235/abstract
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New insights in the clockwork mechanism regulating lineage specification DOI: 10.1002/dvdy.24228 Powerful transcription factors called fate determinants induce robust differentiation programs in multipotent cells and trigger lineage specification. These factors guarantee the differentiation of specific tissues/organs/cells at the right place and the right moment to form a fully functional organism. Fate determinants are activated by temporal, positional, epigenetic, and post-transcriptional cues, hence integrating complex and dynamic developmental networks. In turn, they activate specific transcriptional/epigenetic programs that secure novel molecular landscapes. In this review, we use the Drosophila Gcm glial determinant as a model to discuss the mechanisms that allow lineage specification in the nervous system. The dynamic regulation of Gcm via interlocked loops has recently emerged as a key event in the establishment of stable identity. Gcm induces gliogenesis while triggering its own extinction, thus preventing the appearance of metastable states and neoplastic processes. Using simple animal models that allow in vivo manipulations provides a key tool to disentangle the complex regulation of cell fate determinants. Developmental Dynamics, 2014. © 2014 Wiley Periodicals, Inc. http://onlinelibrary.wiley.com/doi/10.1002/dvdy.24228/abstract
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Mitosis https://www.youtube.com/embed/DwAFZb8juMQDionisio_{December 25, 2014
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Microtubules and chromosome segregation https://www.youtube.com/embed/KV03282vHP4Dionisio_{December 25, 2014
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RNA interference https://www.youtube.com/embed/nRuefh6OO-E Provided by William Orfanos in: https://www.youtube.com/channel/UCbFS2uVI4xvFGg-MDq9WuXg/aboutDionisio_{December 25, 2014
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Chaperones for protein folding - unfolding and disassembling https://www.youtube.com/embed/7BfThtnXLY0Dionisio_{December 25, 2014
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Protein folding https://www.youtube.com/embed/zm-3kovWpNQDionisio_{December 24, 2014
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Protein folding and chaperones https://www.youtube.com/embed/jOhNyVjkChM https://www.youtube.com/embed/4GYOmosYerQDionisio_{December 24, 2014
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Any atheist who believes that life can come from non-life does so on pure blind faith in spite of a mountain of evidence against it EVER happening. Modern research has only further highlighted how impossible it is. The law of biogenesis, i.e. life comes only from life, remains as solid as ever!
The Theist holds the Intellectual High-Ground - March 2011 Excerpt: To get a range on the enormous challenges involved in bridging the gaping chasm between non-life and life, consider the following: “The difference between a mixture of simple chemicals and a bacterium, is much more profound than the gulf between a bacterium and an elephant.” (Dr. Robert Shapiro, Professor Emeritus of Chemistry, NYU) http://www.faithfulnews.com/contents/view_content2/49631/rabbi-moshe-averick-the-theist-holds-the-intellectual-high-ground-apologetics-christian-apologetics-defending-gospel Scientists Prove Again that Life is the Result of Intelligent Design - Rabbi Moshe Averick - August 2011 Excerpt: “To go from bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.” - Dr. Lynn Margulis http://www.algemeiner.com/2011/08/17/scientists-prove-again-that-life-is-the-result-of-intelligent-design/ The current status of origin-of-life chemistry. - Charles Garner - Dec. 2014 - video https://www.youtube.com/watch?v=RUmT6aY4gMY
as to:
"What’s a “nonmaterial event”?"
That would be anything that cannot be reduced to a material basis, such as mind and information!
“From the beginning of this book we have emphasized the enormous information content of even the simplest living systems. The information cannot in our view be generated by what are often called ‘natural’ processes, as for instance through meteorological and chemical processes occurring at the surface of a lifeless planet. As well as a suitable physical and chemical environment, a large initial store of information was also needed. We have argued that the requisite information came from an ‘intelligence’, - Sir Fred Hoyle, Chandra Wickramasinghe - A Theory of Cosmic Creationism - pg. 150
Verse and Music:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. Joy Williams - 2000 Decembers ago https://www.youtube.com/watch?v=4W8K3OhxVSw
bornagain77_{December 24, 2014
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bornagain77 @ 32
Seversky, besides people being paid by government funds to try to find the slightest hint that life might come from non-life, and dogmatic atheists/Neo-Darwinists, such as yourself who will deny even their very own mind before they will ever admit to any evidence for God, who exactly is this ‘we’ you are talking about?
See previous comment re "WE" As for government funding of origins of life research, who else is going to put money into it? Not private enterprise because they will only put money into research that offers the prospect of a good return on their investment. This means that the pharmaceutical industry will only conduct research into diseases that afflict enough people to provide a lucrative market for any theraprutic agent they might develop. People who suffer from rarer ailments generally have to go without - unless the government stumps up some research funding.
Suzan Mazur: Origin of life shifting to “nonmaterial events”? – December 15, 2013
What's a “nonmaterial event”?Seversky_{December 24, 2014
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Dionisio @ 30
Who is “the rest of us”?
Those of us who aren't "WE"Seversky_{December 24, 2014
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Tissue-Resident Memory T Cells DOI: http://dx.doi.org/10.1016/j.immuni.2014.12.007 Tissue-resident memory T (Trm) cells constitute a recently identified lymphocyte lineage that occupies tissues without recirculating. They provide a first response against infections reencountered at body surfaces, where they accelerate pathogen clearance. Because Trm cells are not present within peripheral blood, they have not yet been well characterized, but are transcriptionally, phenotypically, and functionally distinct from recirculating central and effector memory T cells. http://www.cell.com/immunity/abstract/S1074-7613(14)00449-XDionisio_{December 24, 2014
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Seversky, besides people being paid by government funds to try to find the slightest hint that life might come from non-life, and dogmatic atheists/Neo-Darwinists, such as yourself who will deny even their very own mind before they will ever admit to any evidence for God, who exactly is this 'we' you are talking about? Suzan Mazur: Origin of life shifting to “nonmaterial events”? - December 15, 2013 Excerpt: The first paradox is the tendency of organic matter to devolve and to give tar. If you can avoid that, you can start to try to assemble things that are not tarry, but then you encounter the water problem, which is related to the fact that every interesting bond that you want to make is unstable, thermodynamically, with respect to water. If you can solve that problem, you have the problem of entropy, that any of the building blocks are going to be present in a low concentration; therefore, to assemble a large number of those building blocks, you get a gene-like RNA — 100 nucleotides long — that fights entropy. And the fourth problem is that even if you can solve the entropy problem, you have a paradox that RNA enzymes, which are maybe catalytically active, are more likely to be active in the sense that destroys RNA rather than creates RNA. https://uncommondescent.com/origin-of-life/origin-of-life-shifting-to-nonmaterial-events/ Chemistry by Chance: A Formula for Non-Life by Charles McCombs, Ph.D. Excerpt: The following eight obstacles in chemistry ensure that life by chance is untenable. 1. The Problem of Unreactivity 2. The Problem of Ionization 3. The Problem of Mass Action 4. The Problem of Reactivity 5. The Problem of Selectivity 6. The Problem of Solubility 7. The Problem of Sugar 8. The Problem of Chirality The chemical control needed for the formation of a specific sequence in a polymer chain is just not possible through random chance. The synthesis of proteins and DNA/RNA in the laboratory requires the chemist to control the reaction conditions, to thoroughly understand the reactivity and selectivity of each component, and to carefully control the order of addition of the components as the chain is building in size. http://www.icr.org/article/chemistry-by-chance-formula-for-non-life/bornagain77_{December 23, 2014
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The many functions of the endoplasmic reticulum chaperones and folding enzymes DOI: 10.1002/iub.1272 Endoplasmic reticulum (ER) is an essential sub-cellular compartment of the eukaryotic cell performing many diverse functions essential for the cell and the whole organism. ER molecular chaperones and folding enzymes are multidomain proteins that are designed to support nascent proteins entering ER lumen to achieve their native conformation, mediate post-translational modification, prevent misfolded protein aggregation, and facilitate exit from the ER. Typically the role of ER chaperones expands beyond protein folding. Here, we illustrate the multifunctional nature of many ER associated molecular chaperones and folding enzymes and unique functional overlap of these proteins all designed to support the many functions of the ER membrane. © 2014 IUBMB Life, 66(5):318–326, 2014 http://onlinelibrary.wiley.com/doi/10.1002/iub.1272/abstract
designed? Was this paper peer-reviewed? How could they miss that politically incorrect term twice?Dionisio_{December 23, 2014
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#28 Seversky
The rest of us aren’t so sure.
Who is "the rest of us"?Dionisio_{December 23, 2014
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#28 Seversky
Then you’ll be happy to know that there are a few so-called science teachers who are failing in their duty to their students by teaching them in the science classroom that the theory of evolution is wrong and Christian creationism is right, the world was created by God out of nothing in six days flat.
Can you provide the source of that information? BTW, how do you know I'll be happy to know that?Dionisio_{December 23, 2014
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bornagain77 @ 4
But WE are very decided that unguided processes were not involved! :)
YOU may be. The rest of us aren't so sure. Dionisio @ 7
Well, there are some folks out there who have decided for everybody else to tell our kids in public school textbooks that it’s a known fact that it all happened by the power of the magic formula RV+NS+T=E!
Then you'll be happy to know that there are a few so-called science teachers who are failing in their duty to their students by teaching them in the science classroom that the theory of evolution is wrong and Christian creationism is right, the world was created by God out of nothing in six days flat. Which is the more magical? And what happened to the Christian duty not to bear false witness?Seversky_{December 23, 2014
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Getting Folded: Chaperone Proteins in Muscle Development, Maintenance and Disease DOI: 10.1002/ar.22980 http://onlinelibrary.wiley.com/doi/10.1002/ar.22980/abstractDionisio_{December 23, 2014
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Chaperone machines for protein folding, unfolding and disaggregation doi:10.1038/nrm3658 http://www.nature.com/nrm/journal/v14/n10/full/nrm3658.htmlDionisio_{December 23, 2014
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YidC protein, a molecular chaperone for LacY protein folding via the SecYEG protein machinery. doi: 10.1074/jbc.M113.491613. http://www.ncbi.nlm.nih.gov/pubmed/23928306Dionisio_{December 23, 2014
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A dynamic study of protein secretion and aggregation in the secretory pathway doi: 10.1371/journal.pone.0108496 Precise coordination of protein biogenesis, traffic and homeostasis within the early secretory compartment (ESC) is key for cell physiology. http://www.ncbi.nlm.nih.gov/pubmed/25279560Dionisio_{December 23, 2014
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Endoplasmic reticulum chaperones and oxidoreductases doi: 10.3389/fonc.2014.00291. Endoplasmic reticulum (ER) chaperones and oxidoreductases are abundant enzymes that mediate the production of fully folded secretory and transmembrane proteins. http://www.ncbi.nlm.nih.gov/pubmed/25386408Dionisio_{December 23, 2014
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Orchestration of secretory protein folding by ER chaperones. doi: 10.1016/j.bbamcr.2013.03.007 The endoplasmic reticulum is a major compartment of protein biogenesis in the cell, dedicated to production of secretory, membrane and organelle proteins. The secretome has distinct structural and post-translational characteristics, since folding in the ER occurs in an environment that is distinct in terms of its ionic composition, dynamics and requirements for quality control. The folding machinery in the ER therefore includes chaperones and folding enzymes that introduce, monitor and react to disulfide bonds, glycans, and fluctuations of luminal calcium. We describe the major chaperone networks in the lumen and discuss how they have distinct modes of operation that enable cells to accomplish highly efficient production of the secretome. This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum. http://www.ncbi.nlm.nih.gov/pubmed/23507200Dionisio_{December 23, 2014
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GroEL/ES Chaperonin Modulates the Mechanism and Accelerates the Rate of TIM-Barrel Domain Folding DOI: http://dx.doi.org/10.1016/j.cell.2014.03.038 The GroEL/ES chaperonin system functions as a protein folding cage. Many obligate substrates of GroEL share the (??)8 TIM-barrel fold, but how the chaperonin promotes folding of these proteins is not known. http://www.cell.com/cell/abstract/S0092-8674(14)00413-9Dionisio_{December 23, 2014
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