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

@153: That recent paper shows that the plot thickens and the bad news for the Darwinian (macroevolutionary) ideas keep getting worse. :)
Fundamental issues regarding enhancer function, however, remain unclear. For example, the dominant model for how enhancers communicate with their cognate gene promoters, termed looping, involves direct interactions between factors bound to enhancers and factors bound near promoters. Evidence for such interactions, however, has provided little insight into how a distal enhancer finds a gene promoter, or how it distinguishes among potential promoters in gene-dense regions. Moreover, some evidence suggests that mechanisms of enhancer-promoter communication may be more varied
jawa_{September 14, 2020
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@152: Correction: TO and SW have been within the 1% range before, but have lately dropped to the 2% level recently. It could be temporary.jawa_{September 14, 2020
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Hyperacetylated chromatin domains mark cell type-specific genes and suggest distinct modes of enhancer function https://www.nature.com/articles/s41467-020-18303-0jawa_{September 14, 2020
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Alexa ranks (update): Top 0.1% AiG:....... 57,240 Top 1% CMI:....... 174,850 RTB:....... 231,021 ICR:....... 295,589 EN:....... 297,307 BL:....... 363,848 MM:....... 388,600 UD:....... 662,559 Top 2% TO:....... 1,060,561 SW:....... 1,663,253 PS:....... 1,947,079 Top 8% PT:....... 7,485,326 TSZ:....... [insignificant traffic] Why has PT lost so much traffic recently? Their server was down but has been restored. Any thoughts? The situation of TSZ is quite puzzling too. They lost so much traffic. PS has gone up significantly from the bottom of the ranks (at one point was off like TSZ is now). TO and SW have been within the 1% range but have lately sunk into the 2% level recently. It could be temporary. Note that the % refers to the top 100 million active websites.jawa_{September 11, 2020
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Truthfreedom, Interesting article.jawa_{September 11, 2020
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"Materialism" is dead. Say hello to hylemorphism. Materialism’s Failures: Hylemorphism’s Vindication. (Aristotle is back).Truthfreedom_{September 8, 2020
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A paradigm shift in medicine: A comprehensive review of network-based approaches https://www.sciencedirect.com/science/article/pii/S1874939919302500?via%3Dihub
Network medicine is a rapidly evolving new field of medical research, which combines principles and approaches of systems biology and network science, holding the promise to uncovering the causes and to revolutionize the diagnosis and treatments of human diseases. This new paradigm reflects the fact that human diseases are not caused by single molecular defects, but driven by complex interactions among a variety of molecular mediators. The complexity of these interactions embraces different types of information: from the cellular-molecular level of protein-protein interactions to correlational studies of gene expression and regulation, to metabolic and disease pathways up to drug-disease relationships. The analysis of these complex networks can reveal new disease genes and/or disease pathways and identify possible targets for new drug development, as well as new uses for existing drugs. In this review, we offer a comprehensive overview of network types and algorithms used in the framework of network medicine.
Another confirmation of IDjawa_{September 8, 2020
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Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3337-9 I thought you could reverse-engineer what has been engineered first. Where did I get this wrong? Did I miss something?jawa_{September 8, 2020
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The sequence of nucleotides in DNA could serve as a code for amino acids (used later at the tRNA-aaRS/ribosome level) or a code for regulatory ncRNA or a code for pre-mRNA (before post-transcriptional modifications) or a code for transcriptional regulation (TF binding sites, promoter, enhancer and the whole nine yards). Then apart we have the epigenetic marks, including the ones associated with the nucleosomes, and so on and so forth. Then we have the splicing code. Then the post-translational modification code. What else? But the most important thing is that all of the above came to be as result of undirected processes. How?jawa_{September 8, 2020
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@145: Forgot the link to the paper: https://www.biorxiv.org/content/10.1101/777532v2.fulljawa_{September 7, 2020
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ID on steroids: Chromatin information content landscapes inform transcription factor and DNA interactions
Interactions between transcription factors (TFs) and chromatin are fundamental to genome organization and regulation and, ultimately, cell state. variations in the information content of chromatin architecture reflect functional biological variation, with implications for cell state dynamics and memory. application of information theory methods to chromatin profiles captures a dynamic landscape of TF-chromatin interactions, with implications for cell state memory and gene regulation. local chromatin architecture encodes rich signatures of TF interactions TF-chromatin interaction patterns are driven by TF residence time, resulting in distinct CIE signatures. directional binding is an intrinsic property of TF-chromatin interactions. the landscape of TF-chromatin interactions varies across tissues and reflects protein domain-level TF properties. high f-VICE TFs are more likely to mediate genetic effects on gene expression, but not their magnitude. TFs with potential pioneer-like properties bookmark regions of the genome to allow binding of other migrant-like TFs
Obviously, all that functional information was the result of unguided processes, random variations and natural selection.jawa_{September 7, 2020
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ID all over :) Clock-controlled rhythmic transcription: is the clock enough and how does it work?
Circadian clocks regulate the rhythmic expression of thousands of genes underlying the daily oscillations of biological functions. Here, we discuss recent findings showing that circadian clock rhythmic transcriptional outputs rely on additional mechanisms than just clock gene DNA binding, which may ultimately contribute to the plasticity of circadian transcriptional programs.
https://www.tandfonline.com/doi/full/10.1080/21541264.2019.1673636jawa_{August 24, 2020
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@141: Apparently PT sank so deep after having server problems that kept them off for a long time. They’re back on and their Alexa stats could improve soon.jawa_{August 21, 2020
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After noticing that TSZ hasn’t been ranked by Alexa, I looked into it and found that they haven’t had a new article posted for over 1.5 month. Why?jawa_{August 21, 2020
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Alexa ranks: AiG:....... 54,612 CMI:....... 152,722 RTB:....... 243,699 ICR:....... 246,139 EN:....... 318,123 BL:....... 388,769 MM:....... 474,500 UD:....... 823,033 TO:....... 1,085,205 SW:....... 1,677,682 PS:....... 1,729,263 IGH:....... 2,284,628 PT:....... 3,227,929jawa_{August 21, 2020
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KF, Yes, that seems to be the case.jawa_{August 20, 2020
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Jawa there are a few big Creationist orgs. which antedate the web. They built their own platforms, and their web engagement is really secondary. KFkairosfocus_{July 28, 2020
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An old paper that shows abundant evidences for ID: Alternative pre-mRNA splicing: the logic of combinatorial control (published 20 years ago)
Alternative splicing of mRNA precursors is a versatile mechanism of gene expression regulation that accounts for a considerable proportion of proteomic complexity in higher eukaryotes. Its modulation is achieved through the combinatorial interplay of positive and negative regulatory signals present in the RNA, which are recognized by complexes composed of members of the hnRNP and SR protein families.
OLV_{July 28, 2020
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Alexa Internet ranks AIG:……. 52,021 CMI:……. 152,656 ICR:……. 226,008 RTB:……. 271,555 EN:……. 306,383 BL:……. 356,068 MM:……. 480,673 TO:……. 842,175 UD:……. 902,119 SW:……. 1,404,957 PS:……. 1,684,357 IGH:……. 1,885,604 PT:……. 2,084,078 TSZ…….[internet traffic dropped too low – off the radar] Updated list of acronyms: AIG: Answers in Genesis BL: Biologos CMI: Creation Ministries International EN: Evolution News ICR: Institute for Creation Research IGH: Is Genesis History? MM: Mind Matters PS: Peaceful Science PT: Panda’s Thumb RTB: Reasons to Believe SW: Sandwalk (Dr Larry Moran) TO: Talk Origins TSZ: The Skeptical Zone UD: Uncommon Descent Note: it’s interesting to see Answer in Genesis, and other creationist websites (CMI, ICR) having relatively much higher volume of internet engagement than anti-ID websites like TO, SW, PT, despite the censoring impact of biased search engine algorithms. Also, it’s interesting to see how those numbers fluctuate so often in all directions. Perhaps this confirms what KF wrote @130 about the censoring impact of biased search engine algorithms, but could there be other factors involved here too? Lastly, it’s interesting to see TSZ having so little traffic that it’s out of Alexa’s radar. Not long ago PS was in that situation, but it has gone up quite rapidly lately. Here's a interesting observation about a website that perhaps does not exactly qualify to be in the above list, but shows that their internet traffic increased substantially around the time their founder passed away. Over two months after that event, the traffic hasn't decreased. https://www.alexa.com/siteinfo/rzim.orgjawa_{July 28, 2020
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Obvious ID on display here: BMP Signaling Gradient Scaling in the Zebrafish Pectoral Fin
Secreted growth factors can act as morphogens that form spatial concentration gradients in developing organs, thereby controlling growth and patterning. For some morphogens, adaptation of the gradients to tissue size allows morphological patterns to remain proportioned as the organs grow. In the zebrafish pectoral fin, we found that BMP signaling forms a two-dimensional gradient. The length of the gradient scales with tissue length and its amplitude increases with fin size according to a power-law. Gradient scaling and amplitude power-laws are signatures of growth control by time derivatives of morphogenetic signaling: cell division correlates with the fold change over time of the cellular signaling levels. We show that Smoc1 regulates BMP gradient scaling and growth in the fin. Smoc1 scales the gradient by means of a feedback loop: Smoc1 is a BMP agonist and BMP signaling represses Smoc1 expression. Our work uncovers a layer of morphogen regulation during vertebrate appendage development.

Taken together, our data suggest a scenario where the fin contains a proximal BMP source that generates a single gradient deployed along the proximo-distal axis, while signaling, as revealed by the BRE reporter, is only seen in the ROI. This is consistent with the presence of BMP signaling antagonists in the endoskeletal disc (Bauer et al., 1998, Fürthauer et al., 1999), which could decrease the signaling levels in the center of the endoskeletal disc. This could generate an effective scenario where two signaling gradients are deployed in the fin.

Further exploration into the specific properties of a fold change detection system during the embryonic growth of the pectoral fin will provide a general framework to understand growth and patterning of vertebrate appendages.
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Reverse engineering biological processes? Huh? :) Engineering in Development and Aging
Chemical Engineering plays a role in how we understand and modify human development and aging. This session will cover the applications of biological and chemical engineering principles to reverse engineer the biological processes associated with development and aging, including but not limited to cell signaling, biomechanics, patterning and organogenesis. Also relevant is the application of systems and synthetic biology approaches toward engineering multicellular systems.
OLV_{July 28, 2020
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.......OLV_{July 28, 2020
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More ID displayed here: Evaluation of BMP-mediated patterning in a 3D mathematical model of the zebrafish blastula embryo
Bone Morphogenetic Proteins (BMPs) play an important role in dorsal–ventral (DV) patterning of the early zebrafish embryo. BMP signaling is regulated by a network of extracellular and intracellular factors that impact the range and signaling of BMP ligands. Recent advances in understanding the mechanism of pattern formation support a source-sink mechanism, however it is not clear how the source-sink mechanism shapes patterns in 3D, nor how sensitive the pattern is to biophysical rates and boundary conditions along both the anteroposterior (AP) and DV axes of the embryo. We propose a new three-dimensional growing Partial Differential Equation (PDE)-based model to simulate the BMP patterning process during the blastula stage. This model provides a starting point to elucidate how different mechanisms and components work together in 3D to create and maintain the BMP gradient in the embryo. We also show how the 3D model fits the BMP signaling gradient data at multiple time points along both axes. Furthermore, sensitivity analysis of the model suggests that the spatiotemporal patterns of Chordin and BMP ligand gene expression are dominant drivers of shape in 3D and more work is needed to quantify the spatiotemporal profiles of gene and protein expression to further refine the models.
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More ID on display here: The acquisition of positional information in the developing cochlea
The sensory epithelium of the mammalian murine auditory organ, the organ of Corti, is an exquisite example of how specialized asymmetry dictates auditory function. Across the radial axis, the organ consists of three rows of outer hair cells to one row of inner hair cells, which are innervated by efferent and afferent neurons. The mechanosensory inner hair cells that reside in the neural compartment detect sound whereas the outer hair cells in the abneural compartment modulate sound levels. A complex combination of spatiotemporal signaling inputs across the radial axis endows cells with positional information to take on specific cell fates. The Wnt and Bmp pathways are two potential signaling mechanisms that influence this radial asymmetry in an opposing manner. We analyzed the requirement of the Bmp pathway for setting up cochlear patterning. Smad4 cKOs showed a loss of the abneural compartment. Prolonged Bmp inhibition decreased the formation of the abneural compartment and outer hair cells. Bmp was required for determining the abneural boundary of the sensory domain. Immediately after hair cell differentiation, Bmp signaling was no longer required. Bmp is necessary, but not sufficient for patterning the entire epithelium. Activation of the Wnt pathway leads to a selective expansion of the neural compartment and inner hair cells. This selective neural expansion was also conserved in the chicken cochlea. Signaling crosstalk of these pathways in a spatiotemporal manner is necessary for proper patterning of the organ of Corti.
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KF, I see your point. It makes sense. Still it's interesting to see Answer in Genesis, and other creationist websites (CMI, ICR) having relatively much higher volume of internet engagement than anti-ID websites like TO, SW, PT, despite the he censoring impact of biased search engine algorithms. Also, it's interesting to see how those numbers fluctuate so often in all directions. Perhaps this confirms what you wrote about the censoring impact of biased search engine algorithms. Lastly, it's interesting to see TSZ having so little traffic that it's out of Alexa's radar. Not long ago PS was in that situation, but it has gone up quite rapidly lately.jawa_{July 28, 2020
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Jawa, such results are doubtless heavily biased by the censoring impact of biased search engine algorithms. We have a major war being waged by ideologues against truth. KFkairosfocus_{July 12, 2020
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Alexa Internet ranks AIG:……. 48,115 CMI:……. 157,759 ICR:……. 204,627 RTB:……. 285,515 EN:……. 318,883 BL:……. 346,506 MM:……. 521,238 UD:……. 716,976 TO:……. 919,958 PS:……. 1,406,582 IGH:……. 1,457,809 SW:……. 1,459,858 PT:……. 1,517,080 TSZ.......[internet traffic dropped too low - off the radar]jawa_{July 12, 2020
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Alexa Internet ranks AIG:.......47,336 CMI:.......157,446 ICR:.......207,705 RTB:.......289,060 EN:.......319,159 BL:.......333,297 MM:.......534,166 UD:.......714,898 TO:.......890,997 IGH:.......1,203,371 PS:.......1,402,140 SW:.......1,454,927 PT:.......1,512,057jawa_{July 9, 2020
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Updated list of acronyms: AIG: Answers in Genesis BL: Biologos CMI: Creation Ministries International EN: Evolution News ICR: Institute for Creation Research IGH: Is Genesis History? MM: Mind Matters PS: Peaceful Science PT: Panda’s Thumb RTB: Reasons to Believe SW: Sandwalk (Dr Larry Moran) TO: Talk Origins TSZ: The Skeptical Zone UD: Uncommon Descentjawa_{July 8, 2020
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For the first time PS has ranked higher than SW and PT! Dr Swamidass is getting more online traffic in his website. But TSZ sank so deep that got off Alexa radar - what happened? AIG:....... 46,947 RTB:....... 292,858 EN:....... 309,663 MM:....... 532,604 UD:....... 707,799 TO:....... 825,582 PS:....... 1,397,637 SW:....... 1,450,061 PT:...... 1,506,678jawa_{July 8, 2020
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