If ID is dead, why are some obsessed with shutting it down?

_{Denyse O'Leary

May 27, 2020

Academic Freedom, Culture, Darwinism, Intelligent Design}

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Do scientists think more about sex or ID? That was an Enter Laughing question at Evolution News and Science Today but it prompts reflection on why some people in science seem driven around the bend by the idea of design in nature. And others alter their message to avoid confronting the questions:

First, if the critics are right to say ID is “dead,” why devote so much time to it? Evolution News reported in 2014 that an article in the journal Nature admitted that scientists self-censor criticisms of neo-Darwinism to avoid lending credence to ID. As Laland et al. (2014) conceded: “Perhaps haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front to those hostile to science.” In 2017 we observed how Laland followed his own advice, refusing to admit in a report published in Trends in Ecology and Evolution that the 2016 Royal Society meeting included strong critiques of the neo-Darwinian paradigm. Clearly, ID arguments are potent, and evolutionary biologists are aware of this — which is why they admit they don’t like to acknowledge problems in the evolutionary consensus.
Second, intelligent design’s supposed negative impact is hyped beyond reason. The notion that “financing of research” in the U.S. is being hurt by ID is laughable. ID research gets exactly zero dollars from the Federal Government. From other sources, the amount of money available to fund ID research, though not trivial, is minuscule compared to the amount of money available for evolutionary science. No evolutionary scientist has any right to complain.
Third, it’s a shame that “20 percent of their time and brain power” is going to ID because the trend in thought is now running toward government-backed censorship.
Evolution News, “Scientist Admits Biologists Are Obsessed with Intelligent Design” at Evolution News and Science Today

Ah yes. Mutterings about the need for censorship. When we don’t have a reasonable response to a troubling topic, first, we self-censor. Then we censor anyone who raises it. Sure, guys. That’ll work.

The questions are still there but only for those capable of addressing them.

Comments

No objectors in this thread?jawa_{June 14, 2020
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@93: Undoubtedly ID
In conclusion we demonstrated preparation of ionic circuits that were inspired by systems in biology and electronics.
Any objector out there?jawa_{June 13, 2020
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@92:
In principle ionic amplification is observed in the classic biological example of spatially and chemically complex ion transport that occurs in the synaptic cleft, where signaling molecules, driven by a propagating action potential, are released from the presynaptic terminal, diffuse across the synaptic cleft, and are taken up by receptors on the postsynaptic terminal14. This process—selective release (e.g., from vesicle fusion at the presynaptic terminal), confined transport of ions in space (in the synaptic cleft), and selective uptake (e.g., a specific ion channel receptor in the postsynaptic cleft), provides an ultimate example of what can be realized with gated and selective transport of ions. While abiotic systems cannot presently approach this level of sophistication, we can provide simplified, layered designs to construct synaptic cleft inspired devices.
ID on steroidsjawa_{June 13, 2020
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ID is the only empirically known cause for this: Ionic amplifying circuits inspired by electronics and biology
Integrated circuits are present in all electronic devices, and enable signal amplification, modulation, and relay. Nature uses another type of circuits composed of channels in a cell membrane, which regulate and amplify transport of ions, not electrons and holes as is done in electronic systems. the physiological processes of living organisms rely on another type of circuit, which is entirely ionic and functions in an aqueous environment3,4. The key players in physiological processes are biological channels in a cell membrane that facilitate exchange of ions and molecules, for instance between the intracellular and extracellular spaces in cells and tissues. This transmembrane ionic transport is often the first step in a biological amplification process, which enables sensing external stimuli including light, sound, and odor. In the signal transduction of sound, for example, hair cells of the cochlea mechanically transduce sound waves into ion currents by opening cochlear ion channels to ionic transport; open channels allow millions of ions to pass through per second, which leads to signal generation (in the form of a change in transmembrane potential), and is ultimately detected and processed by the brain
jawa_{June 13, 2020
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No ID objectors here yet? Where did they all go? Did they run for the hills? :)jawa_{June 12, 2020
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@88:
The non-Gaussian folding statistics and global coupling between chromatin properties suggest that interphase DNA explores the great genomic landscape as a complex network rather than a simple polymer. The possibility of chromatin having tree data structures and universal folding principles opens an exciting new paradigm to understand genomic organization and presents many new questions, the answering of which would require collaborations between experimentalists and theorists from different fields. We hope that our insights in this paper could inspire future interdisciplinary efforts on this grand challenge of life science.
interphase DNA explores the great genomic landscape as a complex network rather than a simple polymer. opens an exciting new paradigm to understand genomic organization and presents many new questions grand challenge of life sciencejawa_{June 11, 2020
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@88:
The intimate connection between three-dimensional (3D) interphase DNA structure and gene expression in eukaryotic cells has made chromatin folding a rapidly developing field. In the past decade, previously well-accepted concepts have been continuously challenged by new experimental discoveries.
Haven’t we heard this before? “previously well-accepted concepts have been continuously challenged by new experimental discoveries”jawa_{June 11, 2020
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Another set of evidences supporting ID: Physical and data structure of 3D genome
With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topology of DNA double helix. These functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi–self-similar manner, as revealed by our electron and optical imaging. Our multiscale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.
https://advances.sciencemag.org/content/6/2/eaay4055?rss=1 Any objections?jawa_{June 11, 2020
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Here’s another evidence that supports ID: The 3D genome
The three-dimensional configuration of the genome is complex, dynamic and crucial for gene regulation. the organization of the genome is interconnected with nuclear architecture and can vary between cell types and during cell differentiation and development. genome organization and nuclear architecture regulate gene expression, cell fate and cell function
https://www.nature.com/collections/rsxlmsyslk Any objections?jawa_{June 11, 2020
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Here’s another evidence that supports ID:
Cell fate decisions are orchestrated in large part by the concerted actions of transcription factors (TFs) and chromatin remodeling proteins. Cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small populations of cells within developing embryos. comprehensive maps of the binding sites of TFs and chromatin regulators are necessary to understand how gene expression patterns are rewired during cell fate changes.
Profiling of Pluripotency Factors in Single Cells and Early Embryos https://www.cell.com/cell/fulltext/S0092-8674(19)30276-4 Anybody dares to object?jawa_{June 10, 2020
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More ID evidences: Gene network reverse engineering: The Next Generation Transcriptional Profiles and Regulatory Gene Networks Gene regulatory network inference resources: A practical overview Highlights • Gene Regulatory Networks (GRNs) control all aspects of cellular behavior. • Several approaches exist to infer GRNs. These can be broadly categorized based on the input data. • GRN inference can stem from: coexpression, sequence motifs, ChIP-Seq, orthology, literature and Protein-Protein Interaction. • We provide an extensive and commented list of >90 current GRN inference tools. • Best Practices and Examples of GRN inference using multiple methods are described.
Transcriptional regulation is a fundamental molecular mechanism involved in almost every aspect of life, from homeostasis to development, from metabolism to behavior, from reaction to stimuli to disease progression. In recent years, the concept of Gene Regulatory Networks (GRNs) has grown popular as an effective applied biology approach for describing the complex and highly dynamic set of transcriptional interactions, due to its easy-to-interpret features. Since cataloguing, predicting and understanding every GRN connection in all species and cellular contexts remains a great challenge for biology, researchers have developed numerous tools and methods to infer regulatory processes. In this review, we catalogue these methods in six major areas, based on the dominant underlying information leveraged to infer GRNs: Coexpression, Sequence Motifs, Chromatin Immunoprecipitation (ChIP), Orthology, Literature and Protein-Protein Interaction (PPI) specifically focused on transcriptional complexes. The methods described here cover a wide range of user-friendliness: from web tools that require no prior computational expertise to command line programs and algorithms for large scale GRN inferences. Each method for GRN inference described herein effectively illustrates a type of transcriptional relationship, with many methods being complementary to others. While a truly holistic approach for inferring and displaying GRNs remains one of the greatest challenges in the field of systems biology, we believe that the integration of multiple methods described herein provides an effective means with which experimental and computational biologists alike may obtain the most complete pictures of transcriptional relationships. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
Which came first, the transcriptional regulator or its target genes? An evolutionary perspective into the construction of eukaryotic regulons
Eukaryotic regulons are regulatory units formed by a set of genes under the control of the same transcription factor (TF). Despite the functional plasticity, TFs are highly conserved and recognize the same DNA sequences in different organisms. One of the main factors that confer regulatory specificity is the distribution of the binding sites of the TFs along the genome, allowing the configuration of different transcriptional regulatory networks (TRNs) from the same regulator. A similar scenario occurs between tissues of the same organism, where a TRN can be rewired by epigenetic factors, modulating the accessibility of the TF to its binding sites. In this article we discuss concepts that can help to formulate testable hypotheses about the construction of regulons, exploring the presence and absence of the elements that form a TRN throughout the evolution of an ancestral lineage.
This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony. Non-coding RNA regulatory networks Highlights • Transcriptional regulatory networks regulate cell physiology and may determine pathologies. • Network analyses could provide new insights on gene regulation and dysfunction mechanisms. • Several ncRNAs (miRNAs, lncRNAs and circRNAs) have been shown to be involved in regulation. • Integration of ncRNAs into regulatory networks is essential to identify molecular driver events.
It is well established that the vast majority of human RNA transcripts do not encode for proteins and that non-coding RNAs regulate cell physiology and shape cellular functions. A subset of them is involved in gene regulation at different levels, from epigenetic gene silencing to post-transcriptional regulation of mRNA stability. Notably, the aberrant expression of many non-coding RNAs has been associated with aggressive pathologies. Rapid advances in network biology indicates that the robustness of cellular processes is the result of specific properties of biological networks such as scale-free degree distribution and hierarchical modularity, suggesting that regulatory network analyses could provide new insights on gene regulation and dysfunction mechanisms. In this study we present an overview of public repositories where non-coding RNA-regulatory interactions are collected and annotated, we discuss unresolved questions for data integration and we recall existing resources to build and analyse networks.
OLV_{June 8, 2020
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Apparently this thread got so technically boring that it’s practically shutdown. :( As we know we’ll, the ID objectors shun scientific discussions. They seem allergic to serious science.jawa_{June 7, 2020
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KF @72: “The real onward issue is when the proud tower will crumble enough for its intimidation to lose power to suppress the manifest.” Spot on.jawa_{June 7, 2020
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More evidences supporting ID: Mitochondria as intracellular signaling platforms in health and disease
Mitochondria, long viewed solely in the context of bioenergetics, are increasingly emerging as critical hubs for intracellular signaling.

mitochondria possess their own genome and carry unique lipid components that endow these organelles with specialized properties to help orchestrate multiple signaling cascades.

Mitochondrial signaling modulates diverse pathways ranging from metabolism to redox homeostasis to cell fate determination.

mitochondria serve as intracellular signaling platforms with a particular emphasis on lipid-mediated signaling, innate immune activation, and retrograde signaling.

these signaling properties might potentially be exploited to develop new therapeutic strategies for a range of age-related conditions.

Blending in and standing out, mitochondria are uniquely positioned to function as signaling hubs. Though expressed in hundreds of copies per cell, their unique composition and genome make them a complicated mix of the familiar and the distinct.

key questions remain unanswered
More research is needed... we look with much anticipation to reading future papers on new discoveries... it's exciting. OLV_{June 5, 2020
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@67: Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology
The steady-state morphology of the mitochondrial network is maintained by a balance of constitutive fission and fusion reactions. Disruption of this steady-state morphology results in either a fragmented or elongated network, both of which are associated with altered metabolic states and disease. How the processes of fission and fusion are balanced by the cell is unclear.

ER MCSs define the interface between polarized and depolarized segments of mitochondria and can rescue the membrane potential of damaged mitochondria by ER-associated fusion.

Mitochondrial morphology and dynamics are critical to normal cellular function. Mitochondrial morphology is maintained by a balance of constitutive fission and fusion reactions and by dynamic movements that occur along the cytoskeleton.

How fission and fusion machineries are coordinatedto produce mitochondria of appropriatesize is a fundamentalquestionthat is still unresolved.

the processes of fission and fusion are spatially coordinated and colocalized in a system of ER MCS nodes to regulate mitochondrial shape and health.

The major question that remains is how do ER MCSs contribute to both the fission and fusion of mitochondria?

Future studies will investigate whether the forward and reverse rates could be determined at the ER MCS by the relative recruitment and/or posttranslational modifications of fission and fusion machineries, by small signaling molecules like Ca2+, or by the recruitment of activators or inhibitors of these machineries.
235OLV_{June 5, 2020
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Darwin’s Desperation? https://evolutionnews.org/2020/06/darwins-desperation/jawa_{June 5, 2020
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Hello! Any ID objector out there? Are they afraid of scientific discussions? Can they invite an academic objector to come and lecture us? :)jawa_{June 4, 2020
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A ubiquitin-based mechanism for the oligogenic inheritance of heterotaxy and heart defects https://www.biorxiv.org/content/10.1101/2020.05.25.113944v1.full developmental patterning events can be tightly regulated by mechanisms in target cells that function to precisely tune sensitivity to extracellular morphogens. left-right patterning (and cardiac and limb development) depend on a just-right “goldilocks” level of Hh signal amplitude or duration. The ubiquitination of receptors by membrane-tethered E3 ligases represents an attractive post-transcriptional mechanism to control the sensitivity of tissues to signaling ligands during development or tissue renewal. the MGRN1 family of RING E3 ligases can associate more generally across eukaryotes with single-pass TM proteins with conserved cytoplasmic motifs, each of which function as a substrate adaptor to target the ubiquitination of specific receptors or transportersjawa_{June 4, 2020
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The transcription factor E2A drives neural differentiation in pluripotent cells https://dev.biologists.org/content/early/2020/05/29/dev.184093 The intrinsic mechanisms that link extracellular signalling to the onset of neural differentiation are not well understood. Our results suggest a crucial role for E2A in establishing neural lineage commitment in pluripotent cells.jawa_{June 4, 2020
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What would make the ID objectors engage in a discussion in this thread? What is keeping them away? Is it the fact that recent research papers have been cited as evidence that supports ID? Don’t they have any argument against that affirmation?jawa_{June 4, 2020
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Sonic Hedgehog is not a limb morphogen but acts as a trigger to specify all digits https://www.biorxiv.org/content/10.1101/2020.05.28.122119v1.full Limb patterning by Sonic hedgehog (Shh) is among the most highly touted and studied models of “morphogen” function1. Yet how Shh instructs distinct digit types (index to little finger) remains controversial.jawa_{June 4, 2020
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KF, “even if they were to start from LA or from Singapore it would make no difference.” Good point. Agree 100%. However, if that were the case, then the pop-sci journals would gladly display large puffed up headlines affirming that they’re almost there! :)jawa_{June 4, 2020
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KF: “The observed cosmos does not have enough search resources to plausibly discover FSCO/I beyond 1000 bits by blind forces.” Exactly. And yet some folks out there still believe that “somewhere, out there...” some evidences could be found that would support their wishful thinking. Who’s really worshiping some fictional gods of the gaps? The table has turned around. The first verse of the first chapter of the first book of the Christian Bible doesn’t say that in the beginning God created the things that are unknown. The first few verses of the first chapter of the fourth book in the NT confirm that Logos is God, who made the whole enchilada and the whole nine yards and their cousins. Everything. We worship the God of the entire show. God reveals His creation through the things that are known. The better we understand things, more of God’s work is revealed. Undoubtedly most scientific discoveries, specially in biology, increasingly point to our amazing Creator. Perhaps that’s a reason why most ID objectors refrain from engaging in any discussion that deals with recent biology research papers? Dunno.jawa_{June 4, 2020
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Jawa, even if they were to start from LA or from Singapore it would make no difference. The truth is, the debate over the design inference as best current and prospective explanation was decided once it became clear that Science was not fettered to a priori ideological evolutionary materialistic scientism AND -- logic operator -- we realised that there is complex, coded algorithmic alphanumeric information in the heart of the cell's operations. There is just one serious explanation for such and once the ideological blinkers are removed, question begging is removed. Design is well warranted. The real onward issue is when the proud tower will crumble enough for its intimidation to lose power to suppress the manifest. Beyond, lies how can we reverse engineer as part of industrial civ 2.0. KF PS: The observed cosmos does not have enough search resources to plausibly discover FSCO/I beyond 1000 bits by blind forces.kairosfocus_{June 4, 2020
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@70, But many could argue that we don’t understand, because it’s not about one swimmer, but a huge number of them attempting the same trick. And moreover, the experiment is repeated gazillion times. And the swimmers have to their disposition all the time they can use. That makes a difference, doesn’t it? Yeah, right. In their dreams.jawa_{June 4, 2020
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KF, “they don’t even realise how generous the assumptions are.” Excessively generous. Imagine a person having to swim from Odessa (Ukraine) to any beach in Hawaii. No auxiliary boat going next to the swimmer. What Dr Cronin, Dr Szostak and other distinguished OOL scientists are trying to achieve seems like finding a way to getting a pair of fins, a mask and snorkel for the swimmer. The alternative models they present sound like determining whether the swim should start from Jaffa (Israel) instead. Quite a major improvement. Other discussions try to determine whether the swimmer should go (model a) through the Gibraltar strait to the Atlantic Ocean and the Panama Canal out to the Pacific Ocean or (model b) through the Suez Canal out to the Indian Ocean. In the model “a”, the ultimate breakthrough would be to find a way for the swimmer to start from Heraklion (Crete). In the model “b” the ultimate breakthrough would be to find a way for the swimmer to start from Ismailia (Egypt). They may have the swimmer wear a necklace with a shark tooth as a talisman. That’s it. Good luck. Cross your fingers. Knock on wood. Whatever. What are the odds? Low? Very low? Extremely low? Total nonsense. :)jawa_{June 4, 2020
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JC, yup, and they don't even realise how generous the assumptions are. Start with, thermodynamics of highly endothermic molecules with bonds in a vulnerable energy range. Ask yourself how a viable abiotic soup could reasonably come about and be sustained, then how right molecules of right geometry -- chirality! -- would be assembled and protected. Notice, ATP and the enzyme that synthesises it, the one with the rotary mechanism. As a beginning. KFkairosfocus_{June 4, 2020
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KF @ 61: And this is with the generous assumption that it's a nothing more than a matter of probability, i.e. we actually have states and sequences of states that map to the whole of the necessary set of gene sequences and could actually produce them with sufficient recombination; or, similarly, that physical processes will necessarily exhaustively search the genomic space rather than falling into some cyclic and/or deterministic output whose range likely excludes large portions of the genome. The need for evolution to appeal to undefined/undefinable distributions, magical "randomness", is rather damning for anything that would be called a "theory"; after all, a theory is not a statement of truth; its value lies purely in its ability to make predictions.JClark_{June 3, 2020
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More discoveries supporting ID: Fission and fusion machineries converge at ER contact sites to regulate mitochondrial morphology
The steady-state morphology of the mitochondrial network is maintained by a balance of constitutive fission and fusion reactions. Disruption of this steady-state morphology results in either a fragmented or elongated network, both of which are associated with altered metabolic states and disease. How the processes of fission and fusion are balanced by the cell is unclear.
OLV_{June 3, 2020
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More ID-supporting evidences: Crosstalk between Mitochondria and Cytoskeleton in Cardiac Cells
Elucidation of the mitochondrial regulatory mechanisms for the understanding of muscle bioenergetics and the role of mitochondria is a fundamental problem in cellular physiology and pathophysiology. The cytoskeleton (microtubules, intermediate filaments, microfilaments) plays a central role in the maintenance of mitochondrial shape, location, and motility. In addition, numerous interactions between cytoskeletal proteins and mitochondria can actively participate in the regulation of mitochondrial respiration and oxidative phosphorylation. In cardiac and skeletal muscles, mitochondrial positions are tightly fixed, providing their regular arrangement and numerous interactions with other cellular structures such as sarcoplasmic reticulum and cytoskeleton. This can involve association of cytoskeletal proteins with voltage-dependent anion channel (VDAC), thereby, governing the permeability of the outer mitochondrial membrane (OMM) to metabolites, and regulating cell energy metabolism. Cardiomyocytes and myocardial fibers demonstrate regular arrangement of tubulin beta-II isoform entirely co-localized with mitochondria, in contrast to other isoforms of tubulin. This observation suggests the participation of tubulin beta-II in the regulation of OMM permeability through interaction with VDAC. The OMM permeability is also regulated by the specific isoform of cytolinker protein plectin. This review summarizes and discusses previous studies on the role of cytoskeletal proteins in the regulation of energy metabolism and mitochondrial function, adenosine triphosphate (ATP) production, and energy transfer.

Cells are highly organized units with multifaceted functional and structural interactions between various subcellular systems. A large number of studies provides strong evidence that elucidating individual organelles alone is not sufficient, and only systemic approaches must be applied for understanding intracellular signaling pathways and crosstalk between subcellular organelles. This may involve a “systems biology” approach and combinations of several most modern technologies such as genetic manipulations, live cell imaging, mathematical modelling, etc.

Many structural and functional interactions were found to be involved in the integration of mitochondria with other cellular systems like the SR and cytoskeleton, connecting mitochondrial function, dynamics, and regulation with the entire cell physiology, in particular in the most energy consuming organ, the heart.

The detailed characterization of molecular mechanisms implicated in mitochondrial–cytoskeleton interactions under normal and pathological conditions can be helpful for the development of new therapeutic approaches.

many structural and functional aspects of mitochondria–cytoskeletal proteins interactions, as well as detailed molecular mechanisms of their formation, are not yet known, and the interactions of tubulin beta-II or plectin 1b with mitochondria (mitochondrial VDAC) have to be shown more directly, using the most modern methodologies
OLV_{June 2, 2020
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