Author Archives: petrushka

Origins of Life: The Protein Folding Problem all over again

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https://www.pnas.org/doi/full/10.1073/pnas.2315000121

How did specific useful protein sequences arise from simpler molecules at the origin of life? This seemingly needle-in-a-haystack problem has remarkably close resemblance to the old Protein Folding Problem, for which the solution is now known from statistical physics. Based on the logic that Origins must have come only after there was an operative evolution mechanism—which selects on phenotype, not genotype—we give a perspective that proteins and their folding processes are likely to have been the primary driver of the early stages of the origin of life.

Assembly theory explains and quantifies selection and evolution

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Abstract
Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics. These laws underpin life’s origin, evolution and the development of human culture and technology, yet they do not predict the emergence of these phenomena.

Evolutionary theory explains why some things exist and others do not through the lens of selection. To comprehend how diverse, open-ended forms can emerge from physics without an inherent design blueprint, a new approach to understanding and quantifying selection is necessary3,4,5.

We present assembly theory (AT) as a framework that does not alter the laws of physics, but redefines the concept of an ‘object’ on which these laws act. AT conceptualizes objects not as point particles, but as entities defined by their possible formation histories. This allows objects to show evidence of selection, within well-defined boundaries of individuals or selected units.

We introduce a measure called assembly (A), capturing the degree of causation required to produce a given ensemble of objects. This approach enables us to incorporate novelty generation and selection into the physics of complex objects. It explains how these objects can be characterized through a forward dynamical process considering their assembly.

By reimagining the concept of matter within assembly spaces, AT provides a powerful interface between physics and biology. It discloses a new aspect of physics emerging at the chemical scale, whereby history and causal contingency influence what exists.

Link

Maximum mutational robustness in genotype–phenotype maps follows a self-similar blancmange-like curve

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Abstract

Phenotype robustness, defined as the average mutational robustness of all the genotypes that map to a given phenotype, plays a key role in facilitating neutral exploration of novel phenotypic variation by an evolving population. By applying results from coding theory, we prove that the maximum phenotype robustness occurs when genotypes are organized as bricklayer’s graphs, so-called because they resemble the way in which a bricklayer would fill in a Hamming graph. The value of the maximal robustness is given by a fractal continuous everywhere but differentiable nowhere sums-of-digits function from number theory. Interestingly, genotype–phenotype maps for RNA secondary structure and the hydrophobic-polar (HP) model for protein folding can exhibit phenotype robustness that exactly attains this upper bound. By exploiting properties of the sums-of-digits function, we prove a lower bound on the deviation of the maximum robustness of phenotypes with multiple neutral components from the bricklayer’s graph bound, and show that RNA secondary structure phenotypes obey this bound. Finally, we show how robustness changes when phenotypes are coarse-grained and derive a formula and associated bounds for the transition probabilities between such phenotypes.

Source

Lysenko Returns

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The Soviet Era’s Deadliest Scientist Is Regaining Popularity in Russia
Trofim Lysenko’s spurious research prolonged famines that killed millions. So why is a fringe movement praising his legacy?

Wheat, rye, potatoes, beets—most everything grown according to Lysenko’s methods died or rotted, says Hungry Ghosts. Stalin still deserves the bulk of the blame for the famines, which killed at least 7 million people, but Lysenko’s practices prolonged and exacerbated the food shortages. (Deaths from the famines peaked around 1932 to 1933, but four years later, after a 163-fold increase in farmland cultivated using Lysenko’s methods, food production was actually lower than before.) The Soviet Union’s allies suffered under Lysenkoism, too. Communist China adopted his methods in the late 1950s and endured even bigger famines. Peasants were reduced to eating tree bark and bird droppings and the occasional family member. At least 30 million died of starvation.

Lysenko’s grip on power began to weaken after Stalin died in 1953. By 1964, he’d been deposed as the dictator of Soviet biology, and he died in 1976 without regaining any influence. His portrait did continue to hang in some institutes through the Gorbachev years, but by the 1990s, the country had finally put the horror and shame of Lysenkoism behind it.

Until recently. As the new Current Biology article explains, Lysenko has enjoyed a renaissance in Russia over the past few years. Several books and papers praising his legacy have appeared, bolstered by what the article calls “a quirky coalition of Russian right-wingers, Stalinists, a few qualified scientists, and even the Orthodox Church.”

There are several reasons for this renewal. For one, the hot new field of epigenetics has made Lysenko-like ideas fashionable. Most living things have thousands of genes, but not all those genes are active at once. Some get turned on or off inside cells, or have their volumes turned up or down. The study of these changes in “gene expression” is called epigenetics. And it just so happens that environmental cues are often what turn genes on or off. In certain cases, these environmentally driven changes can even pass from parent to child—just like Lysenko claimed.

https://www.theatlantic.com/science/archive/2017/12/trofim-lysenko-soviet-union-russia/548786/

A recipe for irreproducible results

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Abstract.Recent studies have shown that many results published in peer-reviewed scientific journals are not reproducible. This raises the following question: why is it so easy to fool myself into believing that a result is reliable when in fact it is not? Using Brownian motion as a toy model, we show how this can happen if ergodicity is assumed where it is unwarranted. A measured value can appear stable when judged over time,although it is not stable across the ensemble: a different result will be obtained each time the experiment is run.

just for fun.

https://arxiv.org/pdf/1706.07773.pdf

Why Is Science Unreasonably Effective?

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Do any of the skeptics of skepticism think there is an alternative to science in medicine or engineering?

When confronted with unexplained mysteries, is incredulity a better stance than parsimony?

Is the invisible hand that constructs complex systems Adam Smith’s, or the hand of a deity?

Is nature regular or subject to caprice?

ID In A Nutshell

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ID is like the old locked room mysteries.

Scenario: Mr Body is found in a locked room with two bullet wounds in the back of his head. Lethal weapon found in his hand.

All the people known to profit from his death have airtight alibis. Security cameras show no one entering the room after Mr Body enters.

Only Mr Body’s fingerprints are found on the gun.

1. Suicide?
2. Magic or Divine Intervention?
3. Space Aliens having unknown technology?
4. Something else?

Interestingly, number one has actually been put forward in at least one actual, recent case.
If we substitute biogenesis for Mr Body’s death, ID proponents assume number two or number three.
If we substitute evolution for Mr Body’s Death, then Michael Behe and Mendel’s Accountant proponents assume number two or number three.

What do you guys think? What assumption do you think is most reasonable? I’m not asking what really happened. I’m asking what is the first working hypothesis that comes to mind?

Paul Nelson, Evolution, or Design ?

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Source link

Paul Nelson, Evolution, or design ? I transcribed it for who is too lazy to see the video, but its worth to watch, a great speech:

Thanks to another reader, I have gotten a copy of McDonald’s actual paper. Reading it, I wonder how many of the Discovery Institute authors have actually read it. How many have just taken what one of their fellows said previously and done what most 10th grade students do for research papers (i.e. change a few words in an attempt to avoid plagiarism).

By adding their own interpretation of the prior authors work (using secondary sources instead of primary sources), quite a bit of error has crept in. I’m sure it’s just a bit of error, we all know that no creationist would say something that wasn’t true, especially if he is quoting an actual scientist’s paper.
No, I can’t do it, that level of sarcasm is too much for me. These people are liars. Either they are directly lying in order to make someone appear to say something that they actually didn’t or they are the worst researchers ever and shouldn’t be allowed to write non-fiction. Which is it creationists?

Darwin Day

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Even on his birthday, don’t say Darwin unless you mean it

How Darwin’s name is taken in vain, with mini-reviews of some of the worst offenders

Don’t say Darwin unless you mean it. Above all, don’t say “Darwin” when you mean “evolution”. It’s like saying “Dalton” when you mean atoms. Our understanding of atoms has moved on enormously since Dalton’s time, and our understanding of evolution has moved on similarly since Darwin’s. Neither of them knew, or could have known, the first thing regarding what they were talking about, and both would be delighted at how thoroughly their own work has been superseded. (Dalton of course deserves further discussion in his own right, which I will be providing in a few weeks time.)

DaltonsAtoms

From John Dalton’s A New System of Chemical Philosophy (1808)

Imagine if a lot of people decided that atomic theory was against their religion. We would see a parallel world of sacred science, in which molecules were “intelligently constructed”, and real chemistry would be referred to as Daltonism, or possibly, these days, neo-Daltonism. The scientific dissidents from Daltonism would invoke Dalton’s name on every possible occasion, and draw attention to the many inadequacies of atomic theory as he presented it in 1808.

Excilience and Contextomy

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consilience. : the linking together of principles from different disciplines especially when forming a comprehensive theory.

contextomy. : an informal fallacy and a type of false attribution in which a passage is removed from its surrounding matter in such a way as to distort its intended meaning. Quote mining.

excilience. : the linking together of Contextomies from different disciplines especially when forming a comprehensive theory. Thought mining.

The Quote Mine Project provides excellent examples of contextomy. Uncommondescent provides excellent examples of excilience.

The practices lend themselves to all kinds of humorous incongruities. Among them are:

1. free will vs predestination
2. deism vs interventionism (Michael Denton vs Michael Behe)
3. front loading vs twiddling (Mike Gene vs gpuccio, etc.)
4. ascentism vs degenerationism (Chardin vs Sanford)
5. old earth vs young earth
6. realism vs last thursdayism
7. biblical literalism vs inspirationism

There are probably a lot more, but these come up frequently. The humor comes from observing that the armies of ID clash by night, without ever mentioning or discussing their differences and their contradictory assumptions and conclusions.

Food for discussion.

Let the Game Begin

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A working version of FMM’s design detection game is available.

Download and install the applicable version of “Processing”.

https://processing.org/download/?processing

Get the fifthmonarchyman progam code from here, and paste it into the Processing script area.

http://pastebin.com/ZqGRxcjt

Sample data here

http://pastebin.com/raw/MjV8RmvW

You need two files in the same folder as the Processing executable.

real.txt and fake.txt

The testing and such starts here Continue reading →