Michael J. Behe's Blog, page 155

At The Ness: Science is not Just Philosophy

Atheist neurologist blogger Steven Novella wants us to know:

So no – in general scientists and the institutions of science do not pretend that science is pristine or monolithic, nor that we have some magical insight into the ultimate nature of reality (another saying is that, there is no teacher’s edition to the universe so we cannot look up the answers in the back). Science is admittedly difficult, messy, always a work in progress, with conclusions that are tentative. It is also operationally a series of refined models for predicting observations or the results of experiments. But, from a practical point of view, those models can be very useful. We can put fuel in a metal tube and ignite it, and based upon our models send the payload on top of that tube across the solar system to take detailed pictures of a distant world. Our models are so precise it is as if scientists sunk a putt from across the country.

Steven Novella, “Science is not Just Philosophy” at The Ness (September 20, 2021)

Wait. If Novella is right, the science presenters in media must be speaking a different language from the rest of us. The impression that he says they don’t convey (“insight into the ultimate nature of reality”), they in fact do — by a variety of means. That’s okay, of course, until the whipped cream hits the fan.

There is no problem with this when science theorists are theorizing about dark energy. But it can be a big problem when they are discussing real-life issues today where the rest of us are involved. Like COVID lockdowns, to name one example.

Note: Novella’s comments are in support of getting the COVID-19 jab.

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At Quanta: Mathematical Analysis of Fruit Fly Wings Hints at Evolution’s Limits

Apparently, constraint is quite strict:

On one hand, despite dramatic mutations in individuals’ genes and diverse environments in which they grow, members of a species develop into strikingly similar creatures. This robustness ensures that almost all individuals are functional. On the other hand, for evolution to occur, members of a species need diverse traits that natural selection can act upon. Those two forces — robustness and evolvability — tug in opposite directions. One wants less variation, and one wants more.

Around 20 years ago, biologists expected genetics and environmental factors to produce substantial heterogeneity, giving natural selection plenty of choice, said Alex Lancaster, an evolutionary biologist at the Ronin Institute in New Jersey who wasn’t involved in the new study. But, he said, more recent observations have attested to unexpected similarity across populations…

The photos of fly wings offered no clues as to the mechanisms that restrict the possible morphologies that can develop. Rather, the results substantiated the extensive power of these guardrails. Natural selection must mostly act on the significant diversity exhibited in the small number of linked, variable traits, while robustness tightly constrains the rest. Elena Renken, “Mathematical Analysis of Fruit Fly Wings Hints at Evolution’s Limits” at Quanta

Evolution has LIMITS? Isn’t it supposed to account for everything? Put another way, consider the Darwinian claim:

It may be said that natural selection is daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, wherever and whenever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.

The claim is doubtful, given the huge constraints on the system.

The paper is open access.

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At Lancet: An appeal for an honest debate in science about the origin of COVID-19

Specifically, the origin of the virus that causes the disease, An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2 — lab or nature:

On July 5, 2021, a Correspondence was published in The Lancet called “Science, not speculation, is essential to determine how SARS-CoV-2 reached humans”.1 The letter recapitulates the arguments of an earlier letter (published in February, 2020) by the same authors,2 which claimed overwhelming support for the hypothesis that the novel coronavirus causing the COVID-19 pandemic originated in wildlife. The authors associated any alternative view with conspiracy theories by stating: “We stand together to strongly condemn conspiracy theories suggesting that COVID-19 does not have a natural origin”. The statement has imparted a silencing effect on the wider scientific debate, including among science journalists.3 The 2021 letter did not repeat the proposition that scientists open to alternative hypotheses were conspiracy theorists, but did state: “We believe the strongest clue from new, credible, and peer-reviewed evidence in the scientific literature is that the virus evolved in nature, while suggestions of a laboratory leak source of the pandemic remain without scientifically validated evidence that directly supports it in peer-reviewed scientific journals”. In fact, this argument could literally be reversed. As will be shown below, there is no direct support for the natural origin of SARS-CoV-2, and a laboratory-related accident is plausible.

There is so far no scientifically validated evidence that directly supports a natural origin. Among the references cited in the two letters by Calisher and colleagues,1, 2 all but one simply show that SARS-CoV-2 is phylogenetically related to other betacoronaviruses. The fact that the causative agent of COVID-19 descends from a natural virus is widely accepted, but this does not explain how it came to infect humans. The question of the proximal origin of SARS-CoV-2—ie, the final virus and host before passage to humans—was expressly addressed in only one highly cited opinion piece, which supports the natural origin hypothesis,4 but suffers from a logical fallacy:5 it opposes two hypotheses—laboratory engineering versus zoonosis—wrongly implying that there are no other possible scenarios. The article then provides arguments against the laboratory engineering hypothesis, which are not conclusive for the following reasons. First, it assumes that the optimisation of the receptor binding domain for human ACE2 requires prior knowledge of the adaptive mutations, whereas selection in cell culture or animal models would lead to the same effect. Second, the absence of traces of reverse-engineering systems does not preclude genome editing, which is performed with so-called seamless techniques.6, 7 Finally, the absence of a previously known backbone is not a proof, since researchers can work for several years on viruses before publishing their full genome (this was the case for RaTG13, the closest known virus, which was collected in 2013 and published in 2020).8 Based on these indirect and questionable arguments, the authors conclude in favour of a natural proximal origin. In the last part of the article, they briefly evoke selection during passage (ie, experiments aiming to test the capacity of a virus to infect cell cultures or model animals) and acknowledge the documented cases of laboratory escapes of SARS-CoV, but they dismiss this scenario, based on the argument that the strong similarity between receptor binding domains of SARS-CoV-2 and pangolins provides a more parsimonious explanation of the specific mutations. However, the pangolin hypothesis has since been abandoned,9, 10, 11, 12 so the whole reasoning should be re-evaluated.

Jacques van Helden et al., “An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2” at Lancet (September 17, 2021)

We wish Jacques van Helden and his co-authors good luck getting an honest discussion going. It’s not like China is going to become transparent anytime soon. In any event, few virus researchers would want to be told bluntly that, because gain-of-function research in viruses can go badly wrong, they now face controls. Some nations wouldn’t heed the controls. And nature never responds – on her own – to calls for clarification. Most likely, whatever happened with COVID will need to happen again a few more times until a pattern develops. Then we’ll see.

It doesn’t help that Lancet itself became politicized in recent years. See: “A Woke medical journal’s war on having kids” and “Why has a historic medical publication gone weird?” They’ll regret going Woke if they now need to be taken seriously about something important.

Note also from the current letter to Lancet:

Contrary to the first letter published in The Lancet by Calisher and colleagues,2 we do not think that scientists should promote “unity” (“We support the call from the Director-General of WHO to promote scientific evidence and unity over misinformation and conjecture”). As shown above, research-related hypotheses are not misinformation and conjecture. More importantly, science embraces alternative hypotheses, contradictory arguments, verification, refutability, and controversy. Departing from this principle risks establishing dogmas, abandoning the essence of science, and, even worse, paving the way for conspiracy theories. Instead, the scientific community should bring this debate to a place where it belongs: the columns of scientific journals.31, 32

Jacques van Helden et al., “An appeal for an objective, open, and transparent scientific debate about the origin of SARS-CoV-2” at Lancet (September 17, 2021)

In the context, “unity” could mean, in some cases, “in league with people who could not give a good account of themselves.” There are definitely principles more important than mere unity.

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At Mind Matters News: Life is so wonderfully finely tuned that it’s frightening

A mathematician who uses statistical methods to model the fine tuning of molecular machines and systems in cells reflects…

Ola Hössjer: It turns out that [only] a very small fraction of amino acids sequences give us a functioning protein. That is the first definition of fine tuning. It’s complex. It is unlikely to happen by chance, to get a functioning protein. The second part: We should have an independent specification. In this case, the specification is that the protein works. For that reason, a protein is an example of a fine tuned structure in biology.

Then we could get up to the next hierarchical level and look at complexes of proteins, like molecular machines. The ribosome that manufactures proteins in the cell is itself a molecular machine that consists of many proteins that have to be arranged in a certain structure in order to work.

Another example is mitochondria in the cell plasma. These are the power stations of the cell that generate ATP. This is also an example of a molecular machine where all parts have to be structured in a certain way. One could say — we talked about this during the first episode — a specific case or a special case of fine tuning are irreducibly complex systems: It consists of many small parts, and all parts must function in order for the whole system to work.

Robert J. Marks: So if you remove one of the parts in the process you’re talking about, the whole thing breaks down. Let me give you a guess as an example, on the macroscopic level. Our lungs, for example, have a bunch of individual cells, and one of these cells has no idea what the other cells are doing but they all work together to allow us to breathe and put oxygen in our blood and other things. Would that be a big example of what you’re talking about?

Ola Hössjer: Yes. And another, you could view the whole cell as a cellular city. It has a network of roads, or factories and power stations.

Robert J. Marks: These are things which display irreducible complexity. You take away one piece, the whole thing falls apart. News, “Life is so wonderfully finely tuned that it’s frightening” at Mind Matters News

Takehome:
Every single cell is like a city that cannot function without a complex network of services that must all work together to maintain life.

You may also wish to read:

Ours is a finely tuned — and No Free Lunch — universe. Mathematician Ola Hössjer and biostatistician Daniel Andrés Díaz-Pachón explain to Walter Bradley Center director Robert J. Marks why nature works so seamlessly. A “life-permitting interval” makes it all possible — but is that really an accident?

and

Fine-tuning? How Bayesian statistics could help break a deadlock Bayesian statistics are used, for example, in spam filter technology, identifying probable spam by examining vast masses of previous messages. The frequentist approach assesses the probability of future events but the Bayesian approach assesses the probability of events that have already occurred.

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Granville Sewell on the first “self-replicating” cardboard box

Which, of course, tests claims about “the first simple self-replicator” in nature:

I do not believe scientists actually have any clue as to how the first living things evolved into intelligent, conscious human beings (see my video “Why Evolution Is Different“). However, to appreciate that the first step is not a small problem you only have to realize that with all our advanced technology we are still not close to designing any type of self-replicating machine. That is still pure science fiction. So how could we imagine that such a machine could have arisen by pure chance?

A Self-Replicating Box

To understand why human-engineered self-replicating machines are so far beyond current human technology, let’s imagine trying to design something as “simple” as a self-replicating cardboard box. Let’s place an empty cardboard box (A) on the floor, and to the right of it let’s construct a box (B) with a box-building factory inside it. I’m not sure exactly what the new box would need to build an empty box, but I assume it would at least have to have some metal parts to cut and fold the cardboard and a motor with a battery to power these parts. In reality, to be really self-replicating like living things, it would have to go get its own cardboard, so maybe it would need wheels and an axe to cut down trees and a small sawmill to make cardboard out of wood. But let’s be generous and assume humans are still around to supply the cardboard. Well, of course box B is not a self-replicating machine, because it only produces an empty box A.

So, to the right of this box, let’s build another box C which contains a fully automated factory that can produce box B’s. This is a much more complicated box…

Granville Sewell, “The First “Simple” Self-Replicator?” at Evolution News and Science Today (September 13, 2021)

But then people wouldn’t dare say anything as silly about the origin of boxes as they feel free to say about the origin of life forms …

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New vid from the John 10:10 Project: God is in the details

There’s an old proverb that says, “God is in the details.” The truth of those words has never been more obvious. Every day, 21st century technology opens extraordinary windows on biological systems once too small to see with our unaided eyes. In this fascinating video, superb microscopic photography reveals some of the hidden wonders that enable butterflies to thrive on earth, while filling our eyes with unforgettable evidence of intelligent design in the living world.

Hat tip: Philip Cunningham

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Policy analyst: More funding is not going to solve current science problems

Funding has increased but so have systemic problems:

With some notable exceptions, current proposals to stimulate American science and innovation focus almost exclusively on the need for more federal money. Yet, there are several other problems that beset the U.S. R&D system besides inadequate federal funding. Foremost among them are the unequal distribution of federal science funding; mounting concerns about the integrity of scientific research, and the increasing bureaucratization of the scientific enterprise. Increasing federal funding will not solve these problems, and could even make them worse. But if left unresolved, these problems could undermine the express purpose of calls to increase federal R&D funding.

It has long been the case that federal R&D funding is highly concentrated, being clustered around a handful of geographic regions and their prominent institutions, such as Harvard University, Duke University, and Johns Hopkins University on the East Coast and Stanford University, the University of California San Diego, and the University of Washington on the West Coast.6 Meanwhile, worries about scientific integrity have been growing over the past decade in light of the so-called “replication crisis,” exacerbated by high-profile incidents of scientific misconduct. As for bureaucratization: Scientists have been complaining for years about an increasing number of federal rules and regulations that hamper research productivity, requiring scientists to spend nearly as much time on paperwork as they do research. Unfortunately, current proposals to increase R&D spending do little, if anything, to address these problems.

M. Anthony Mills, “Fix Science, Don’t Just Fund It” at Innovation Frontier Project (September 16, 2021)

Two thoughts: Unclear what Dr. Mills means by a “so-called” “replication crisis.” There IS a replication crisis. They can call it an ice cream cone if they want.

Second, more funding, under the circumstances, not only “could” make the problems worse; they almost certainly WILL do so. If systemic issues are not addressed, more funding helps magnify the problem.

It’s like giving a gambling addict more money.

You may also wish to read: When people claim that “the science” says this or that… Discussing the recent essay by medical statistician John Ioannidis on the was politicization and shoddy research around COVID-19 are corrupting science, philosopher Edward Feser focuses on a couple of his points, including this one, “the deleterious role that social media have played”

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At Mind Matters News: Researchers: The universe simulated itself into existence

A recent physics journal paper proposes self-simulation as the origin of the universe, using a quantum gravity model:

A new hypothesis says the universe self-simulates itself in a “strange loop”. A paper from the Quantum Gravity Research institute proposes there is an underlying panconsciousness. The work looks to unify insight from quantum mechanics with a non-materialistic perspective.

How real are you? What if everything you are, everything you know, all the people in your life as well as all the events were not physically there but just a very elaborate simulation? Philosopher Nick Bostrom famously considered this in his seminal paper “Are you living in a computer simulation?,” where he proposed that all of our existence may be just a product of very sophisticated computer simulations ran by advanced beings whose real nature we may never be able to know. Now a new theory has come along that takes it a step further – what if there are no advanced beings either and everything in “reality” is a self-simulation that generates itself from pure thought?

Paul Ratner, “New hypothesis argues the universe simulates itself into existence” at Big Think (April 26, 2020) (A podcast is available.)

The paper, which appeared in Entropy in 2020, is open access.

The most significant element of this new theory is surely that it is explicitly a theory of “panconsciousness” and non-materialism.

For that reason, it bears comparison with newer theories of consciousness, which are explicitly panpsychist. Remarkably, the science world is growing comfortable with non-materialist theories of consciousness. Whether that it because materialist theories of consciousness are not providing much insight and end in absurdities or due to other causes would be hard to say at present.

(Continues at Mind Matters News.)

Takehome: It will be significant if physics journals continue to accept panpsychist and non-materialist models of the universe that recognize the reality of the mind.

You may also wish to read: When a simulated world begins to fall apart. In “Untitled Earth Sim 64,” Marie has reason to expect trouble when the simulator who explains reality to her cannot get her name right… If Marie has found God amid strange events, as her friend thinks, the God she has found is highly disorganized one.

New theory of mind offers more information, less materialism
First, let’s begin by noting a remarkable fact: Panpsychism seems to have triumphed in the area of theories of consciousness. Are there materialist theories of consciousness out there any more? Yes. But it is unclear how many of them are taken seriously. Except in pop science mags.

and

The final materialist quest: A war on the reality of the mind Going to war with the very concept is an approach even George Orwell did not think up. When George Orwell wrote 1984, he addressed destroying minds, not denying their possibility and changing the language associated with them.

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At Quanta: “The molecular signaling systems of complex cells are nothing like simple electronic circuits.”

We are told, “The logic governing their operation is riotously complex — but it has advantages”:

Recently, by looking closely at the protein interactions within one key developmental pathway that shapes the embryos of humans and other complex animals, Elowitz and his co-workers have caught a glimpse of what the logic of complex life is really like. This pathway is a riot of molecular promiscuity that would make a libertine blush, where the component molecules can unite in many different combinations. It might seem futile to hope that this chaotic dance could convey any coherent signal to direct the fate of a cell. Yet this sort of helter-skelter coupling among biomolecules may be the norm, not some weird exception. In fact, it may be why multicellular life works at all.

“Biological cell-cell communication circuits, with their families of promiscuously interacting ligands and receptors, look like a mess and use an architecture that is the opposite of what we synthetic biologists might have designed,” Elowitz said.

Yet this apparent chaos of interacting components is really a sophisticated signal-processing system that can extract information reliably and efficiently from complicated cocktails of signaling molecules. “Understanding cells’ natural combinatorial language could allow us to control [them] with much greater specificity than we have now,” he said.

Philip Ball, “Biologists Rethink the Logic Behind Cells’ Molecular Signals” at Quanta (September 16, 2021)

Actually, the best way to understand the systems would be that they are somewhat like a great novel. To someone with no understanding of the language, it might seem like a “riot” or “mess” of meaningless characters. To someone who does understand the language and has a mature appreciation of literature and life, it seems like “a sophisticated signal-processing system that can extract information reliably and efficiently from complicated cocktails of” life.

But if we understand “molecular signaling systems of complex cells” (correctly) that way, we must assume that they are designed. Or, alternatively, that novels write themselves.

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At least, the “science of obesity” is now a legitimate topic of discussion

Much of what’s going wrong in science today is too much enforcement, too little reasoned argument.

Recently, we ran a note about a dissident science writer, Gary Taubes, and some dissident scientists arguing for a different approach to the causes of obesity. Another well-known science writer, Ross Pomeroy, says he’s wrong:

Taubes isn’t entirely off with his widely-read musings on low-carbohydrate diets. There certainly exists evidence that different nutrients and compounds in the foods we eat alter our metabolisms, but the effects are simply not large enough to drive significant weight loss or weight gain. What fuels weight gain is eating more calories than your body uses. What leads to weight loss is eating fewer calories. That’s what decades-worth of evidence demonstrates.

Taubes argues that if this is true, Americans – who hear the “eat less and move more” messaging constantly – should be getting thinner over time, not fatter. But there’s a simpler explanation: Americans have yet to put this advice into widespread action. Part of the reason might be that they would rather try fad diets like the one that Taubes and many others keep writing so much about.

Ross Pomeroy, “Gary Taubes Can’t Accept He’s Wrong About the Science of Obesity” at RealClearScience (September 17, 2021)

Fair comment. And it is a good thing we get to hear both sides of the argument. That is not happening often enough. People who complain about popular doubt or denial of science are too often among the first to demand that only their side of the argument be published — thus fueling the very thing they complain about.

Obesity is a serious business because — thanks to a successful war on hunger — it is becoming a worldwide problem. Jenny Craig probably doesn’t have the answer.

You may also wish to read: At Stat News: Science has got obesity all wrong A science writer reflects on the way paradigms work. If he’s right, a popular paradigm it was dangerous to doubt will come under fire.

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