Michael J. Behe's Blog, page 141

Microorganisms defy expectations, produce elemental carbon

The researchers wondered about the black specks forming within their bacterial cultures…

New research at Virginia Tech, the University of Bremen, and the Max Planck Institute for Marine Microbiology has revealed that two kinds of microorganisms – methanogens and anaerobic methanotrophs – are able to produce a form of elemental carbon known as amorphous carbon.

For researchers who study methanogens and anaerobic methanotrophs, the discovery defies all previous expectations of what microorganisms can do, and sheds scientific light on some very interesting questions.

Why and how are these microorganisms making amorphous carbon? Is amorphous carbon being produced in large enough quantities to affect the carbon cycle on Earth?

“We never thought that amorphous carbon could be produced by living organisms because of the normally extreme chemical reactions that are needed to form it,” said Robert White, an emeritus professor of biochemistry in the College of Agriculture and Life Sciences. “This is the first report of amorphous carbon being produced by any organism on Earth, and we are very interested in the possible implications it may have for the carbon cycle.”

Virginia Tech, “Researchers discover the first instance of living organisms producing elemental carbon” at Eurekalert (November 12, 2021)

Our expectations should take into account how little we even know about so many life forms on our own planet.

The paper is open access.

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Human (or any other) uniqueness: Does Captain Kirk die going through the transporter?

Sabine Hossenfelder admits that “The problem has kept her up at night for decades, she says, and it appears we are no closer to an answer”

Why so difficult?

Assume that all the information about a person is contained in the exact configuration in which it appears at one moment in time. Hossenfelder accepts that as the correct view. So the transporter converts you into a different medium, putting all your life processes on pause. But then what?

She notes that “strictly speaking, the only way to copy a system elsewhere would require you to also reproduce its entire past, which isn’t possible.”

News, “Physicist: Does Captain Kirk die going through the transporter?” at Mind Matters News

But there’s another reason you might not be able to read out the information of a person without annihilating them in that process, namely that quantum mechanics says that this isn’t possible. You just can’t copy an arbitrary quantum state exactly.

Sabine Hossenfelder, “Does Captain Kirk die when he goes through the transporter?” at BackRe(Action) (October 23, 2021)

In a multiverse, she notes, an infinite number of transporters may produce an infinite number of Captain Kirks, some of which may be exact replicas. If a multiverse exists. Otherwise,

More.

The sci-fi version:

Takehome: The key problem: The transporter might require us to abandon the idea that we have a continuous self to begin with. Many won’t go there. Alternatively, it will never happen.

You may also wish to read: Theoretical physicist: Colonizing Mars is a ridiculous idea! Making Mars habitable (terraforming) has been kicking around engineering circles for decades. What are the chances, given Moore’s Law-level increases in technology? Sabine Hossenfelder points out that the Mars’ biggest habitability problem is lack of a magnetic field and no plausible technology solution is in sight.

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William Lane Craig on Adam and Eve as less intelligent than us

From Casey Luskin’s review of William Lane Craig’s In Quest of the Historical Adam, with a glance at his article in First Things:

In First Things Craig then proposes that Adam and Eve were not as cognitively advanced as modern humans, and postulates that humanity experienced standard evolutionary changes after Adam and Eve including some that would “emerge slowly through environmental niche construction and gene-cultural coevolution” to evolve the more advanced brains we have today.2 What this suggests is that not only does Craig seem to propose or allow that many (if not all) of humanity’s intellectual abilities evolved via natural mechanisms, but he effectively believes we evolved upward after Adam and Eve — a model which contrasts sharply with the traditional Christian view that humanity has fallen from Adam and Eve’s initial state.

In his book it’s never quite clear if Craig thinks that the specific mutations he discusses occurred via standard evolutionary mechanisms, God’s direct intervention, or some kind of hybrid of the two…

At most, the data he cites simply shows that humans, Neanderthals, and Denisovans share certain similar genes and genetic traits which are involved in our brain development and linguistic abilities — genes and genetic traits not found in living apes. This is not at all surprising since Neanderthals and Denisovans were highly similar to us, are thought to have had advanced cognitive abilities, and may even belong within our own species Homo sapiens. The evidence he recounts is not evidence of evolution. Rather, it simply identifies human-specific genetic features that probably help endow us with our advanced cognitive abilities. Merely identifying important genetic traits does not necessarily tell us that they arose by blind evolutionary mechanisms. After all, these traits could have been intelligently designed or even specially created by God in the creation of Adam and Eve.

But Craig’s arguments typically seem to treat these mutations no differently from blind evolutionary events, which suddenly produced humanlike intelligence in some early hominid. Those of us who have been around the debate over evolution for a while have heard these kinds of miracle mutation stories before, and we have multiple reasons to be skeptical.

Casey Luskin, “Missed Opportunity: Passing over Scientific Problems with Human Evolution” at Evolution News and Science Today (November 10, 2021)

Whatever else Craig’s view is, as Luskin notes, it is a far cry from the Scriptural traditional assumption that the unfallen Adam and Eve were our betters and that we have all deteriorated as a result of sin. Adopting Craig’s view is bound to have worldview consequences.

You may also wish to read: Evangelical scientists getting it wrong… Casey Luskin: Craig continues to rely upon BioLogos arguments that pseudogenes are “broken” and non-functional junk DNA that we share with apes, thereby demonstrating our common ancestry. Those arguments are increasingly contradicted by evidence presented in highly authoritative scientific papers which find that pseudogenes are commonly functional, and they ought not be assumed to be genetic “junk.”

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Big Bang theory is too big to fail, philosophers of science complain

In their view, it supports the entire discipline of cosmology in the sense that cosmologists are reputationally dependent on it:

Because cosmology as a professional discipline really only came about with the invention of the Big Bang Theory in the mid-20th century it has effectively been the only major operative hypothesis for astronomical research. Therefore it has become the only model that cosmologists can get funded to research. The observational evidence it produces and accumulates is usually interpreted in its favour. This gives it the appearance of solidity while giving cosmologists a false sense of security.

Note: Ekeberg is the author of Metaphysical Experiments: Physics and the Invention of the Universe (2019)

However, it would take a lot of scientists, funding and time to be able to produce a reasonable alternative theory that could account for almost nine decades of observations using the Big Bang framework. As a result, cosmology seems locked into a ‘zombie state’ – path dependent and stuck – and too big to fail.

As astrophysicist Stacy McGaugh says in the context of dark matter theory, “like a fifty year mortgage, we are still basically stuck with this decision we made in the 1980s… we’re stuck still pounding these ideas into the heads of innocent students, creating a closed ecosystem of stagnant ideas self-perpetuated by the echo chamber effect.”

McGaugh and Hossenfelder are among a growing group of scientists concerned about the ‘dark stuff’ who are making progress in questioning some of the most critical theories in cosmology.

Their effort may help the new generation of cosmologists realize that if these decade-old theories can be overturned, there is hope in solving cosmology’s deeper problems by re-examining the core principles of cosmology.

– Bjørn Ekeberg and Louis Marmet, “Escaping cosmology’s failing paradigm” at iai news (November 4, 2021)

Recent months have seen a number of opinion pieces against the Big Bang. Some think that’s related to Steve Meyer’s The Return of the God Hypothesis. Nah. Can’t be.

At any rate, you may also wish to read: Experimental physicist Rob Sheldon on CNN’s “problem” with the Big Bang Theory. The story is really about the fact that inflation theory — way Cooler than the Big Bang — was not especially confirmed.

One thing focusing attacks on the Big Bang theory does is, it takes the attention off theories with far less support from the evidence. Some may yet sneak through to acceptance because no one is putting them down…

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Springer Nature retracts 44 “utter nonsense” papers

Gizmodo is unsparing: “Unadulterated gibberish snuck into Springer Nature’s Arabian Journal of Geosciences, and not for the first time.”

The publisher Springer Nature was forced to retract over 40 papers from its Arabian Journal of Geosciences after realizing they were nothing more than garbled jargon. This is just the latest in a series of shoddy research papers getting past the publisher.

First reported by research journal watchdog Retraction Watch, the slew of retractions comes on the heels of other issues at the publisher, where hundreds of papers were previously flagged with “expressions of concern” for research integrity breaches…

They read a bit like a college student throwing around big words to cover up a lack of understanding. Though purportedly written by humans, the content of each paper definitely reads as if it were put together by a computer that doesn’t quite grasp speech patterns or grammar. The papers are filled with redundancies and generally lack logic.

Isaac Schultz, “Science Publisher Retracts 44 Papers for Being Utter Nonsense” at Gizmodo (November 5, 2021)

The editor of the journal has suggested that the autobabble papers got into the journal via hacking. Retraction Watch says that that does happen, giving an example.

Here’s the Retraction Watch piece on the current spout of nonsense.

As we’ve noted earlier, it’s getting to the point where “Trust the science!” is sounding more ridiculous all the time. It’s like saying “Trust the mountains” or “Trust milk.” It’s not a rational response to a lot of what we face just now.

You may also wish to read: Neil deGrasse Tyson vs. SteakUmm on the philosophy of science The thing is, the saucy social media team at Steak-Umm has a point: What does it mean to say that science is “true”? Was all the contradictory nonsense barked at us during the COVID pandemic “true”? That isn’t even possible. Yet all the barkers will insist that whatever stuff they said was “science” and we will, it seems have to believe them on that one. But with what outcome… we shall see.

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Rob Sheldon on lowering the standard for detecting gravitational waves

Recently, an article in Nature advised that:

Gravitational-wave observatories have released their latest catalogue of cosmic collisions, bringing their total number of detections to 90. The new crop of 35 events includes one featuring the lightest neutron star ever seen, as well as two clashes involving surprisingly large black holes…

Gravitational waves are ripples in the fabric of space-time that are produced when large masses accelerate. Like the detections previously reported by LIGO–Virgo, the latest ones are all attributed to pairs of dense stellar remnants spiralling into each other and merging. The vast majority, including LIGO’s first historic detection in 2015, have involved pairs of black holes, but in a few cases one or both of the objects were neutron stars.

The collaboration initially released data on only high-confidence detections, but the latest catalogue — as well as the previous one, released in October 2020 — includes any detections that have better-than-even chances of being genuine gravitational waves. The team estimates that around 10–15% of the latest candidates in the catalogue are false alarms, “caused by instrumental noise fluctuations”.

Davide Castelvecchi, “Astrophysicists unveil glut of gravitational-wave detections” at Nature (09 November 2021)

Experimental physicist Rob Sheldon comments,

We are several years into the LIGO experiment, now we have VIRGO in Italy online and soon KAGRA in Japan. The [open access] paper mentioned above has some 1570 authors. It takes 10 pages to list the authors.

In the early days of LIGO, they announced that they would provide public alerts of a merger event, so that astronomers could point their telescopes and see the afterglow. It was expected that any event energetic enough to make gravity waves would make intense lightshow as well. Much data has been collected from the afterglows associated with Gammaray Bursts (GRBs) and it was thought the same would be true of gravity mergers. For that purpose, LIGO was point to a patch in the sky and say “That’s where this gravity wave came from, look there.”

Again, in the early days, LIGO gave really big patches of sky and apologized that with only two detectors they could not localize the direction too well, but as soon as they had a third detector, as soon as VIRGO came online, we would have pinpoint accuracy for the astronomers.

Five years have gone by, what do 1570 scientists have to say?

“These public alerts enable the astronomy community to search for multimessenger counterparts to potential GW signals. There were 39 low-latency candidates reported during O3b. Of these, 18 … survive our detailed analyses to be included as potential CBC signals in GWTC-3. Additionally, GWTC-3 includes 17 candidates with p astro > 0.5 that have not been previously presented. No confident multimessenger counterparts have currently been reported from the O3b candidates.”

Surely you must be joking. Nothing? What about localizing those patches in the sky?

“the observing time includes periods when at least two detectors were observing, and the Euclidean sensitive volume is the volume of a sphere with a radius equal to the BNS inspiral range of the second most sensitive detector in the network.”

What they just said, was they don’t do localization, they do magnitude only. Large signals happened in close, weak ones further out. And they do it with single detectors, occasionally dual, but never three. Why?

Because they don’t have triple coincidences.

And that should end the whole program right there.

Individually, the detectors have a 10,000:1 Noise to Signal Ratio. They use “matched filters” to discover waves, a method invented by the radar community who say that when the noise is twice greater than the signal the method doesn’t work. But physicists say “Bosh! we can find signals so small your radar could see a candy wrapper 10,000 miles away. You engineers are just not as creative as physicists.”

Well how do you know its real? After all, the radar guys make their own signal, but you can’t, so how do you know its not something else?

“We use coincidences. We reject a signal unless both Hanford and Louisiana see something at the same time. “

How do you know some event isn’t correlating the noise at both locations?

“We’ll use a third coincidence, we’ll use VIRGO. With three coincidences, the noise just vanishes.”

Well, VIRGO has been online for at least 2 years, show me your triple coincidences.

“Harrum. They aren’t there. But that’s okay–we can get the same results by using magnitudes and, well, we really didn’t need arrival locations anyway, the astronomers can use all-sky cameras. Clumsier, but workable.”

Why aren’t they there? I thought you said the whole secret to getting 10,000:1 noise removed was coincidences?

We don’t know, but we have the Nobel Prize and now we’re getting almost two hits a week. The data set is growing, and lots of papers are getting written, and 1570 scientists are putting these publications on their resume. We can’t let a little thing like missing triple coincidences stop us. We’ll model it as if they were there, that allows us to proceed with our analysis. And someday we’ll solve that mystery, but we really haven’t the time to stop and solve every problem right now.

Oh, and we’ll stop mentioning direction of gravity waves in our announcements. We’ll pretend the magnitude is all we have.”

So to summarize, the absence of triple coincidences is being withheld from the paper, when in fact, it delegitimizes the entire data analysis pipeline. Now we have 4 Gravity wave detectors, and soon one in space. At what point does the lack of a triple coincidence become fatal? What observation can they make that would disprove the existence of gravity waves?

Maybe they can’t stop until they have potted together evidence for a multiverse.

Note: In media work, we say: It takes three to make a trend.

Rob Sheldon is the author of Genesis: The Long Ascent and The Long Ascent, Volume II .

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Tim Standish on those five new alternate genetic codes in bacteria: It’s way more complicated than they are making out.

Readers may recall that a couple of days ago, we noted the surprising find that even more species of bacteria do not use the traditional universal genetic code they were thought to have inherited from the First Cell or whatever. From a researcher: “Changing the genetic code requires changing ancient, important molecules like tRNAs that are so fundamental to how biology works.”

Tim Standish

Tim Standish at the Geoscience Research Institute offers some thoughts on the situation — and the spin put on it:

The spin inherent in the headline for this article is fascinating: Screen of 250,000 Species Reveals Tweaks to Genetic Code.

Changing codon meaning isn’t merely a tweak. As one of the authors notes, “It’s just mind-boggling that an organism could survive that.” But he is dead wrong when he says, “Stop codon shifts are considerably less ‘dramatic’”. Changing a stop codon seems significantly more challenging than changing any other codon meaning because the mechanism for stop codon recognition is totally different and involves more than RNA-RNA interactions.

It’s also a mindbender that on average having 1/3 of genes read through after a regular stop codon, producing who knows what random AA sequence until another still functioning stop codon is encountered, could be survived. Even if either kind of change was survivable, the idea that there might be some incremental increase in fitness at each necessary step along the way makes about as much sense as hitting one’s big toe with a hammer and expecting this will make you a faster runner.

As is so common with these things, some functional explanation for why the different genetic codes in these new examples are somehow better than the “universal” code is treated as sufficient to explain these impossible changes that must be achieved in an incremental and unguided way. This implies that some need on the part of an organism is miraculously capable of producing an outcome that resolves the need. If only life was really like that, because I need a few million dollars to buy a home on the shore of Sydney Harbour and a private jet to get there.

I’m not sure that they are listing all known genetic codes in this article as there are variations in the genetic codes used in mitochondria, and these show an interesting pattern of distribution that requires the same changes in multiple taxa. In addition, using a different genetic code than the nucleus makes moving genes from mtDNA to chromosomal DNA and expecting a good outcome incredibly optimistic.

Good luck with the private jet and Sydney Harbour, Tim. That mind of magic only works with Darwinian theory. Not with life.

You may also wish to read: Five more species of bacteria use alternate genetic codes At The Scientist: “The genetic code has been set in stone for 3 billion years,” study coauthor Yekaterina Shulgina, a Harvard University graduate student in systems biology, tells The Scientist. “The fact that some organisms have found a way to change it is really fascinating to me. Changing the genetic code requires changing ancient, important molecules like tRNAs that are so fundamental to how biology works.”

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James Tour on the practical side of intelligent design

At COSM 2021, scientists like James Tour and entrepreneurs like Matt Scholz offer a window into how we are learning to manipulate the building blocks of life, applying intelligent design to biology:

Yesterday COSM 2021, philosopher of science Stephen Meyer, synthetic organic chemist James Tour, and biotech entrepreneur Matthew Scholz looked at how nanotechnology (working directly with very small things, like molecules) will advance biology and medicine.

“Oscar Wilde said nature imitates art,” Meyer opened by saying. And today we’re going to see that “technology is now able to imitate and even in some ways, improve upon nature.”

He noted that since the 1960s we’ve been ;learning that living cells function because of the actions performed by molecular machines—those molecular machines are built using information.

Casey Luskin, “Manipulating molecules: Combining info + nano for better medicine” at Mind Matters News (November 12, 2021)

Tour explained to the audience that his nanodrills can be programmed to target the so-called “super bacteria” that have become resistant to drugs by drilling holes through their cell walls. Drilling either kills the bacterial cells or weakens them so that antibiotics work again against them!

Nanodrills are a valuable new tool because bacteria cannot simply develop resistance to them, as he noted:

This is not a chemical interaction. This is a mechanical interaction that is happening at the molecular scale. And because it’s a mechanical interaction, it’s very hard for a cell to deal with this.

It would be like developing resistance to a scalpel.

It gets better: When the nanodrills punch holes in the cell walls and cytoplasmic membranes of bacteria, the cells burst and their contents are dumped out into the body of the host. Then we can “couple this with immunotherapy,” he explained, so that an organism’s natural immune system can recognize the contents of bacteria and be activated to target those bacteria.

Adding information to our cells’ systems is key here: These nanodrills don’t just kill cells at random. They can be programmed so as to target only certain types of dangerous bacterial cells. They can even be programmed to recognize, target, and destroy cancerous cells in a host’s body where most cells aren’t cancerous.

Tour hopes that his nanodrills will find a place in future therapies to treat problems like antibiotic resistance and tumors. At the core of his research is using our own intelligence to create therapies that outsmart antibiotic resistance—in other words, to beat evolution with intelligent design.

More.

Takehome: Designed information is the basis of biology so if you want to fix medical problems at the root, designing better information is the way to go.

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Reflections on Harvard astronomer’s intelligent design without God

He drags in Darwinism, of course:

What if, as the Harvard scientist (not a late-night radio host) suggests, our universe was “created in a laboratory of an advanced technological civilization … Since our universe has a flat geometry with a zero net energy, an advanced civilization could have developed a technology that created a baby universe out of nothing through quantum tunneling.” Such an idea, he concludes, “unifies the religious notion of a creator with the secular notion of quantum gravity.”

Loeb doesn’t speculate on the identity of our universe’s engineer(s), or the location of the “laboratory” where it came to be. But if his proposal sounds familiar, it’s because it is. Specifically, he’s proposing a form of intelligent design, only one with an infinite number of extra steps.

John Stonestreet & G.S. Morris, “Intelligent Design Without God?” at The Stream (November 6, 2021)

Is that how it works? Stonestreet and Morris go on to ask:

If the universe were cooked up through quantum tunneling in a cosmic laboratory by alien scientists, who made the alien scientists who created the universe?

Loeb certainly tries to answer that question by suggesting that there may be countless baby universes, all engineered by “advanced civilizations,” which in turn create more life-sustaining universes, but which are not self-existing or eternal. The process, he writes, may proceed along Darwinian lines, ensuring a selection advantage for life-sustaining universes since they can, in a manner of speaking, “reproduce.”

John Stonestreet & G.S. Morris, “Intelligent Design Without God?” at The Stream (November 6, 2021)

Somebody fetch Occam’s Razor quick:

Hat tip: Ken Francis, co-author with Theodore Dalrymple of The Terror of Existence: From Ecclesiastes to Theatre of the Absurd

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At Mind Matters News: Historian supports new anti-Cancel Culture university

Niall Ferguson hopes that the new University of Austin will unite traditional wisdom with new technology in a spirit of free enquiry:

At COSM 2021 yesterday, prominent historian Niall Ferguson talked about his decision to sign up with the new University of Austin, founded in explicit opposition to rampant political correctness and censorship on university campuses, which is beginning to affect quality scholarship.

In response to a question from the floor, Ferguson, author of Doom: The politics of catastrophe (2021), outlined the seriousness of the problem.

News, “Historian supports new anti-Cancel Culture university” at Mind Matters News (November 11, 2021)

Well, it’s just been announced this week that we’re trying to create a new university, University of Austin, committed to the fundamental principles of, of academic freedom of free inquiry. And the reason we have to do this is that we see so many limitations on, on free inquiry and academic freedom at the established universities.

The growing illiberalism on campuses is being documented in survey research:

Not only do 66 percent of students say it is acceptable to shout down a speaker to prevent them from speaking on campus, that result is up four percentage points from last year.

Another key finding is that nearly one in four students say it’s acceptable to use violence to stop a campus speech — up 5 percent over last year’s survey — with some elite colleges bringing that figure to as high as one in three students accepting of such violence.

Katelynn Richardson – UNLV, “Overwhelming majority of college students say shouting down a speaker is acceptable: survey” at The College Fix (September 23, 2021)

The problem may have worsened during the COVID lockdown, which was Ferguson’s slated topic.

He has few illusions about the difficulty he and a disparate group of Cancelled or embattled professors, media figures, and university presidents who have expressed a degree of commitment to the idea face. These figures include Bari Weiss, Panos Kanelos, Arthur Brooks, Sohrab Ahmari, Andrew Sullivan, Heather Heying, Geoffrey Stone, Peter Boghossian, Kathleen Stock, Joe Lonsdale, and Ayaan Hirsi Ali. Ferguson told COSM 2021 …

More.

Takehome: At COSM 2021, he noted that proposed faculty had spent the last 48 hours dealing with a tidal wave of Twitter hate. So, he said, they are over the target…

Note: The University of Austin would, of course, still face the hurdle of accreditation in a hostile environment and, quite possibly, refusal to public academic research by anyone associated with it. That could prove more significant than the hatestorms on Twitter.

You may also wish to read: In Big Tech World: the journalist as censor, hit man, and snitch. Glenn Greenwald looks at a disturbing trend in media toward misrepresentation as well as censorship.

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