When did design in nature stop being a swear word?

_{Denyse O'Leary

June 12, 2016

Intelligent Design, News}

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Did we miss it? From 2015:

Does the universe embody beautiful ideas?

Artists as well as scientists throughout human history have pondered this “beautiful question.” With Nobel laureate Frank Wilczek as your guide, embark on a voyage of related discoveries, from Plato and Pythagoras up to the present. Wilczek’s groundbreaking work in quantum physics was inspired by his intuition to look for a deeper order of beauty in nature. In fact, every major advance in his career came from this intuition: to assume that the universe embodies beautiful forms, forms whose hallmarks are symmetry—harmony, balance, proportion—and economy. There are other meanings of “beauty,” but this is the deep logic of the universe—and it is no accident that it is also at the heart of what we find aesthetically pleasing and inspiring.

Wilczek is hardly alone among great scientists in charting his course using beauty as his compass. As he reveals in A Beautiful Question, this has been the heart of scientific pursuit from Pythagoras, the ancient Greek who was the first to argue that “all things are number,” to Galileo, Newton, Maxwell, Einstein, and into the deep waters of twentieth century physics. Though the ancients weren’t right about everything, their ardent belief in the music of the spheres has proved true down to the quantum level. Indeed, Wilczek explores just how intertwined our ideas about beauty and art are with our scientific understanding of the cosmos. More.

Really, there needs to be a respectful discussion:

1. Could human beings in fact know if the universe shows evidence of design? Or are our brains shaped for fitness, not truth? Does everyone who says they believe that want to follow it through to its logical implications?

2. If evidence matters, what counts as evidence, what doesn’t? Or should we move in the direction of non-evidence-based science? We could quite easily confirm the pop science view of reality instead, and a great many people would be happy and prosperous. And still dim.

See also: Second layer of information in DNA?

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Comments

The pace of modern science is staggering. The quantities of data now flowing from DNA sequencers, fluorescence and electron microscopes, mass spectrometers, and other mind-blowing instruments leave us faced with information overload. This explosion in data has brought on its heels a concomitant need for efforts at the kinds of synthesis and unification we see in theoretical physics. [...] to learn about the philosophy of science, one should not listen to what scientists say, but rather watch what they do. It is an important time to reexamine the role of theory in biology. The explosion of data in the life sciences has created a deep tension between fact and concept. [...] the exercise of converting our ‘pathetic’ thinking into mathematical form and then exploring the consequences of the assumptions behind that thinking [...] [...] people use the word surprise if they find a particular fact to be novel. One of the most intriguing aspects of genomes is action at a distance, referring to the fact that binding of proteins on one part of the genome can affect what happens elsewhere on the genome. Living organisms exhibit beautiful and surprising phenomena at every turn. [...] there is no one approach that guarantees success in uncovering the secrets of the living world. [...] theoretical descriptions of biological phenomena couched in the language of mathematics have the capacity of revealing insights that would otherwise remain hidden.
Theory in Biology: Figure 1 or Figure 7? Rob Phillips DOI: http://dx.doi.org/10.1016/j.tcb.2015.10.007

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“Understanding the protein circuits that perform computations within the cell is a central problem in biology.” Uri Alon Lab – Design Principles in Biology. http://www.weizmann.ac.il/mcb/UriAlon/homepage 2014 Systems Biology course by Uri Alon Lecture 1: Basic concepts https://www.youtube.com/embed/pyqBvxeVtG4 [Please, note the time marks given here are grossly approximate] @7:30 Goal: Central idea of the class – it gives unity to the discussed topic. Complex biological systems can be understood using design principles which can unify different systems in a mathematical framework. @8:30 it’s up to him to be clear and up to the students to tell him when he’s not. @14:30 Suggested textbook: An introduction to Systems Biology: design principles of biological systems. Here’s a very interesting part of professor Alon’s first lecture in the referenced course: Very early in his first lecture, at the time mark 2:30, he introduces himself to his students. He said he has been a professor at that institute 14 years (the lecture seems to be from 2014). He worked for a PhD in Physics, hence he was used to systems obeying very precise mathematical laws. Then a friend gave him a biology textbook and it was like a shock for him. He said it was like reading a thriller, because he saw this matter that was behaving completely different than what he was used to: [it was] dancing, amazing structures created and then destroyed almost magically, working very precisely under very strong thermodynamic noise and I had to find out how this works. That personal event changed his academic and scientific career radically. Apparently he did a post-doc in biology at Princeton University? At the time mark 43:20 professor Alon apparently said that everything in biology is an invitation to a question. [whatever that means] Systems biology course (2014) by Professor Uri Alon – lecture 2 @time mark 20:45 the professor says “evolution designed…” https://www.youtube.com/embed/xo-7m0YnN8o Systems biology course (2014) by Professor Uri Alon – lecture 4: Absolute robustness @time mark 8:50 he writes on the board: Robustness: Biological circuits are designed then he paused to clarify that by “designed” in this case he meant that evolution did it (or something like that) – a quick disclaimer for damage control? Here’s a link to the video of that lecture: https://www.youtube.com/embed/_dHaZdr0M24Dionisio_{June 15, 2016
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Perspectives on theory at the interface of physics and biology
Jeff Chen Gore https://jgore.org/2016/01/01/perspectives-on-theory-at-the-interface-of-physics-and-biology/
Biology is more theoretical than physics
[...] why do we confess the primary role of the system in our private day-to-day work while, at the same time, publicly insisting that reductionism works? When we do not know how to reason, we do not. We also like a quiet life. We prefer private schizophrenia to public outrage. There is so much we can do now, so much data to be gathered, so many reductionist models to be built, why spoil the party with explosive philosophical distractions? Expediency seems the best option, with freaks like frq being marginalized. But the loose end remains; the fuse continues to smolder. Eventually, we will need a new kind of mathematical theory to reconcile component and system. Theory's greatest contribution to biology may yet lie in the future. Jeremy Gunawardena doi: 10.1091/mbc.E12-03-0227 Mol. Biol. Cell vol. 24 no. 12 1827-1829 http://www.molbiolcell.org/content/24/12/1827.full
Models in biology: ‘accurate descriptions of our pathetic thinking’
A mathematical model is a logical machine for converting assumptions into conclusions. If the model is correct and we believe its assumptions then we must, as a matter of logic, believe its conclusions. This logical guarantee allows a modeler, in principle, to navigate with confidence far from the assumptions, perhaps much further than intuition might allow, no matter how insightful, and reach surprising conclusions. But, and this is the essential point, the certainty is always relative to the assumptions. Do we believe our assumptions? [...] we should not fool ourselves that our models are objective and predictive, in the sense of fundamental physics. They are, in James Black’s resonant phrase, ‘accurate descriptions of our pathetic thinking’. Building models for the sake of doing so might keep mathematicians happy but it is a poor way to do biology. Asking a question guides the choice of assumptions and the flavor of model and provides a criterion by which success can be judged. If the model cannot be falsified, it is not telling you anything. Fitting is the bane of modeling. It deludes us into believing that we have predicted what we have fitted when all we have done is to select the model so that it fits. So, do not fit what you want to explain; stick the model’s neck out after it is fitted and try to falsify it. Jeremy Gunawardena BMC Biology201412:29 DOI: 10.1186/1741-7007-12-29 http://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-12-29
Theory in Biology: Figure 1 or Figure 7? Rob Phillips DOI: http://dx.doi.org/10.1016/j.tcb.2015.10.007Dionisio_{June 15, 2016
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Isn't "design in nature" a relatively recent swear word? A meme that has stunted scientific understanding. Good to see science getting back on the right track. Physics leading the way as they try hard to break their "standard model". Biology holding back as they try to defend their standard model. Much of biology seems to be cargo cult science doesn't it?ppolish_{June 12, 2016
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