Michael J. Behe's Blog, page 188

Human cells write RNA sequences into DNA

Challenging, they say, a central principle in biology:

Cells contain machinery that duplicates DNA into a new set that goes into a newly formed cell. That same class of machines, called polymerases, also build RNA messages, which are like notes copied from the central DNA repository of recipes, so they can be read more efficiently into proteins. But polymerases were thought to only work in one direction DNA into DNA or RNA. This prevents RNA messages from being rewritten back into the master recipe book of genomic DNA. Now, Thomas Jefferson University researchers provide the first evidence that RNA segments can be written back into DNA, which potentially challenges the central dogma in biology and could have wide implications affecting many fields of biology…

In a series of elegant experiments, the researchers tested polymerase theta against the reverse transcriptase from HIV, which is one of the best studied of its kind. They showed that polymerase theta was capable of converting RNA messages into DNA, which it did as well as HIV reverse transcriptase, and that it actually did a better job than when duplicating DNA to DNA. Polymerase theta was more efficient and introduced fewer errors when using an RNA template to write new DNA messages, than when duplicating DNA into DNA, suggesting that this function could be its primary purpose in the cell.

Thomas Jefferson University, “New Discovery Shows Human Cells Can Write RNA Sequences Into DNA – Challenges Central Principle in Biology” at SciTech Daily (June 12, 2021)

The paper is open access.

Dogmas are bouncing off the wall all over these days… there were probably too many of them to begin with.

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Why is science reporting so bad?

Neurologist Steven Novella offers some suggestions:

In the science communication world, perhaps especially in the subset that we self-identify as “scientific skepticism”, there is a lot of criticism of bad science reporting. The media often gets a lot of this criticism, and much of that is deserved. But various studies over the last decade or so have shown that journalists, while all too eager to participate, are often not the source of misreporting of science news. Much of it can be traced back to the press release, and even to study authors themselves.

Steven Novella, “The Causes of Bad Science Reporting” at Science-Based Medicine (June 16, 2021)

He focuses on whether studies of Alzheimer disease make clear that mouse models were used. Why that matters? Because, we are told, only humans “go Alz” = get Alzheimer disease (AD), though animals do get plaques in the brain, which are considered a model for the plight of humans. The plaques are related to dementia in humans.

Whether all that turns out to be true or not, as stated, if it is a conventional assumption, properly described rodent studies might be useful. But are they properly described?

What the authors of the new study looked at, therefore, was AD research on mouse models and whether the fact that they involved mice was mentioned in the title of the paper itself. They report:

“To this end, we analyzed a sample of 623 open-access scientific papers indexed in PubMed in 2018 and 2019 that used mice either as models or as the biological source for experimental studies in AD research. We found a significant association (p < 0.01) between articles’ titles and news stories’ headlines, revealing that when authors omit the species in the paper’s title, writers of news stories tend to follow suit.”

Specifically, if the article title declared that the study involved mice, than 46.2% of news headlines did also. If the title did not mention mice, then only 10.4% did. This is a very large difference that traces directly back to the published science article itself. This is also an extremely easy fix – journals should require that animal research declare the focus of their research in the title. But also notice that these results do not let journalists off the hook – in less than half of the news reporting about AD research in mice, the headlines failed to disclose this. Of course, journalists often don’t write their headlines, so much of the blame is on the headline writers, but this is all part of the news reporting and the outlet has ultimate responsibility.

Steven Novella, “The Causes of Bad Science Reporting” at Science-Based Medicine (June 16, 2021) The paper is open access.

Fair enough. But, if anything, media tend to be too deferential to science sources and are most likely to just follow their lead, in time for the 6:00 am deadline. If you are in media, you must publish something, and soon.

A question remains: Is it true that no other life form gets Alzheimer? Wild animals would simply be eaten and tame ones would likely be euthanized. It’s only humans who find their way to care homes where the disease flourishes, largely uncontested. Let’s not be too hasty about assuming no other life form “gets” it.

Anyway, Novella’s general point is well taken.

Note: Neurosurgeon Michael Egnor, who writes at Mind Matters News, has often clashed with neurologist Steven Novella on many issues. See, for example,

Has neuroscience “proved” that the mind is just the brain? This is hardly the first time that bizarre claims have been made for minimal findings. In neuroscience, materialism is the answer only if you don’t understand the questions. Can a study of mice really prove that? I challenge materialist neuroscientist Steven Novella to disprove dualism rigorously!

and

Why the mind can’t just be the brain Thinking it through carefully, the idea doesn’t even make sense. It turns out that even a committed materialist like neuroscientist Steven Novella doesn’t really believe that.

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Can only math solve the mystery at the heart of the universe?

The issue is quantum field theory (QFT):

“This is [a] very embarrassing thing that we don’t have a single quantum field theory we can describe in four dimensions, nonperturbatively,” said Rejzner. “It’s a hard problem, and apparently it needs more than one or two generations of mathematicians and physicists to solve it.”

But that doesn’t stop mathematicians and physicists from eyeing it greedily. For mathematicians, QFT is as rich a type of object as they could hope for. Defining the characteristic properties shared by all quantum field theories will almost certainly require merging two of the pillars of mathematics: analysis, which explains how to control infinities, and geometry, which provides a language for talking about symmetry.

“It’s a fascinating problem just in math itself, because it combines two great ideas,” said Dijkgraaf.

If mathematicians can understand QFT, there’s no telling what mathematical discoveries await in its unlocking. Mathematicians defined the characteristic properties of other objects, like manifolds and groups, long ago, and those objects now permeate virtually every corner of mathematics. When they were first defined, it would have been impossible to anticipate all their mathematical ramifications. QFT holds at least as much promise for math.

Kevin Hartnett, “The Mystery at the Heart of Physics That Only Math Can Solve” at Quanta

Be warned: The quantum world is tricky and nothing is what it seems.

See also: In quantum physics, “reality” really is what we choose to observe. Physicist Bruce Gordon argues that idealist philosophy is the best way to make sense of the puzzling world of quantum physics.

and

Can a materialist consciousness theory survive quantum mechanics? Quantum mechanics requires that the observer be part of the measurement; thus quantum measurements must include consciousness.

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Misleading claims about a long running evolution experiment

Richard Lenski’s experiment is in the news again:

The LTEE required 33,000 generations and many years for the bacteria to acquire the supposedly new trait. In the video Lenski says that one of his lab’s researchers wanted to explore “why did it take so long to evolve this and why has only one population evolved that ability?” The implication is that this is a complex trait that required many slow mutations to arise. Lenski says it was a “difficult” trait to evolve because it required both a “rare mutation” and also a “series of events” where multiple mutations were needed before any advantage was conferred. Van Hofwegen realized there was something fishy about these claims. As he explained to IDTF:

“The only difference is that in the conditions of the [LTEE] experiment, they didn’t have a transporter. They [E. coli bacteria] didn’t have the ability to bring that citrate outside of their cells into the cells and actually use it for energy. And so when I looked at that experiment as a microbiologist I thought, all they have to do is turn that thing on. That’s really easy for bacteria to do. Why did it take them 33,000 generations to do that?”

Van Hofwegen draws a comparison to a light switch. Normal E. coli have the metabolic pathways to live off citrate, and they have the ability to transport it into their cells. But under the conditions of the experiment that “light switch” was turned off. The bacteria didn’t need to evolve a new metabolic pathway or a new transport feature to eat citrate. All they needed to do was turn on their transporter under the oxic conditions of the LTEE experiment. The organisms used the “light switch” to express their citrate transporter. So how did they do it?

A 2016 peer-reviewed study in the Journal of Bacteriology, “Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA,” co-authored by Van Hofwegen and biologists Scott Minnich and Carolyn Hovde, has the answer. In their research they witnessed the same trait, the ability to use this “lemony dessert,” arise in under 100 generations and 14 days. This result was repeatable 46 times. They found that the trait is not very genetically complicated — again, akin to flipping a switch — and that there is more to the story than is being been told. Indeed, their paper shows that no new genetic information arose during the evolution of this trait.

Casey Luskin, “Viral Video Overstates the Evidence About Bacterial Evolution” at Evolution News and Science Today

Hey. The Darwinians are marketing magic and it is really difficult to refute magic.

Here’s the vid making the claim:

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

An astonishing underwater world

We tend to think that life only got complex when it moved to land but look at this:

Note: The underwater world even has very intelligent life forms. For example, can octopuses really feel pain? The brainy cephalopods behaved about the same as lab rats under similar conditions, raising both neuroscience and ethical issues:

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Nature attempts to paper over a genuine and reasonable lack of trust in China over COVID-19

This matters to us because it bears on the fate of science in general, as China becomes a global superpower. Introducing “A special issue on COVID-era research collaboration highlights the benefits to science and society of working across borders, cultures and disciplines,” the editors of Nature tell us,

Analyses of bibliometric data reveal that international collaborations were less common on COVID-19-related papers in 2020 than they were for research on other coronaviruses in previous years. Moreover, as the pandemic has progressed, papers in which the authors are all in the same country have occupied a greater share of the COVID-19 literature. Looking at 2020 as a whole, the rate of international collaboration for COVID-19-related science was similar to that for all recorded research.

Indicators that some international collaboration is waning are evident when looking at data for China and the United States. The fraction of China’s international collaborations that involve US authors has been falling since 2017. Such trends are likely to continue if geopolitical tensions with the United States worsen.

That would be regrettable.

Editorial, “Research collaborations bring big rewards: the world needs more” at Nature (June 16, 2021)

No, it wouldn’t be “regrettable.” Not so long as China cannot be trusted.

The article goes on to identify comparatively piffling examples of co-operation where nothing much was at stake. Nothing like the need for an honest account of the origin of the global COVID-19 pandemic.

These people are not serious. It is reasonable to assume that this is a factor:

“Nature and The Lancet played important roles in enabling, encouraging, and enforcing the false narrative that science evidence indicates Sars-CoV-2 had a natural-spillover origin points and the false narrative that this was the scientific consensus”.

Or as another well-placed observer put it: “The game seems to be for Nature and The Lancet to rush non-peer revised correspondences to set the tone and then delay critical papers and responses.” But why would they do this? This is where things become even murkier. Allegations swirl that it was not down to editorial misjudgement, but something more sinister: a desire to appease China for commercial reasons. The Financial Times revealed four years ago that debt-laden Springer Nature, the German group that publishes Nature, was blocking access in China to hundreds of academic articles mentioning subjects deemed sensitive by Beijing such as Hong Kong, Taiwan or Tibet. China is also spending lavishly around the world to win supremacy in science — which includes becoming the biggest national sponsor of open access journals published by both Springer Nature and Elsevier, owner of The Lancet.

One source estimated that 49 sponsorship agreements between Springer Nature and Chinese institutions were worth at least $10m last year. These deals cover the publishing fees authors would normally pay in such journals, so they smooth the path for Chinese authors while creating a dependency culture. They have worked well for both sides: they offer the publishers access to the surging Chinese market and its well-resourced universities, while offering international recognition and status in return. But we know President Xi Jinping demands compliance with his world view, even from foreign-owned companies — and especially on an issue as sensitive as his nation’s possible role in unleashing a global catastrophe.

Ian Birrell, “Beijing’s useful idiots” at Unherd

By all means, read Birrell’s article, if only to take in his chronicle of the politically inspired nonsense about pangolins, aimed, perhaps, at misdirection:

More re pangolin:

See also:

Why trust in “science” is becoming unwise. In case you wondered: “China is also spending lavishly around the world to win supremacy in science — which includes becoming the biggest national sponsor of open access journals published by both Springer Nature and Elsevier, owner of The Lancet.”

and

That time they invented scientists as well as research papers…

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Why science is losing prestige…

When it behaves like Hollywood, it deserves to

David Coppedge cites various instances of untrustworthiness, including:

What’s not in the news headlines or titles of Alzheimer disease articles? #InMice (PLoS Biology). Mouse models are routinely used to test treatments on humans, but researchers often fail to reveal the fact. These authors feel that humans and mice are too different to transfer findings from mouse models. Look what can happen when the media fails to disclose that fact:

Around 200 rodent models have been developed to study AD [Alzheimer’s Disease], even though AD is an exclusively human condition that does not occur naturally in other species and appears impervious to reproduction in artificial animal models, an information not always disclosed…. We found a significant association (p < 0.01) between articles’ titles and news stories’ headlines, revealing that when authors omit the species in the paper’s title, writers of news stories tend to follow suit. We also found that papers not mentioning mice in their titles are more newsworthy and significantly more tweeted than papers that do. Our study shows that science reporting may affect media reporting and asks for changes in the way we report about findings obtained with animal models used to study human diseases.

David Coppedge, “Science Prestige Crumbles ” at Creation–Evolution Headlines (June 19, 2021)

Question: Do we really know that animals do not get Alzheimer? Maybe, whereas humans get care homes, animals get eaten. So how would we know?

See also: That time they invented scientists as well as research papers…

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Child burial from 80,000 years ago shows the existence of abstract ideas

The lovingly prepared site on the Kenyan coast held the remains of a 2–3 year-old child:

A child’s grave, found recently in Kenya, pushes clear evidence of abstract thinking back to 80,000 years ago, the Middle Stone Age. The child, nicknamed “Mtoto” (child in Swahili) by the archaeologists, was 2½ – 3 years old; whether a boy or a girl is as yet unclear…

“In a tour de force of discovery, recovery, and analysis, an interdisciplinary research team has uncovered the earliest known human burial in Africa. The grave, found less than 10 miles inland from southeast Kenya’s lush ocean beaches, contained the remains of a two- to three-year-old child buried with extraordinary care by a community of early Homo sapiens some 78,000 years ago. While some human burials in the Middle East and Europe are older, the find in Africa provides one of the earliest unequivocal examples anywhere of a body interred in a pit prepared for that purpose and covered with earth.” JAMIE SHREVE, “CHILD’S GRAVE IS THE OLDEST HUMAN BURIAL FOUND IN AFRICA” AT NATIONAL GEOGRAPHIC (MAY 6, 2021) …

Death, as applied to ourselves, is an abstraction as well as a reality. When we say that the dead do not come back to life or that everyone dies or wonder what happens to our minds after death, we are dealing in abstractions. The rituals around death that help us grieve embody these abstractions. Items buried with the deceased (grave goods) may be merely fond remembrances but they may also be things that mourners think the deceased might need in another life — stone tools, for example. Jewelry may just be jewelry but it may also be good luck charms or amulets, to ward off evil. Perhaps the snail shell with the excisions gave an identity to “Mtoto” — a message to another world, perhaps, about who the child was.

News, “Death: Child grave from 80,000 years ago shows abstract thinking” at Mind Matters News

Takehome: As more burials are found, we will start to get more answers. For example, if a number of such graves feature shells or similar objects with excisions, we can infer a symbolic intention.

You may also wish to read:

Do people suddenly gain clarity about life just before dying? A small number of cognitively challenged or dementia patients become lucid — for the first time in years — just before dying

and

Do animals truly grieve when other animals die? Yes, but “death” is, in some ways, an abstraction so there are only some things they can understand about it

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Off topic: The Cancel Culture ragtag volunteer army of censors

Only off topic if you are happy with a mob controlling what you read.

The new censorship is different from traditional “banned” or “challenged” lists because a younger, much more active crowd is behind it:

Most victims [of Cancel Culture] were targeted by race, ethnicity, sexuality, and gender activists, usually over matters that would surprise most readers. Some accept oblivion; others rewrite their books. Science fiction has been hit by “Woke zombies” too: “They inhibit free extrapolation and free speech through aggressive gatekeeping and social and professional ostracism, inspiring fearful writers to self-censor,” writes one author. Dissecting the controversies over books attacked in 2019, Krishdee Dismon captures a torrent of steaming resentment, much of it from people who have not read the books.

News, “Books: Cancel Culture as an invisible army of censors ” at Mind Matters News

Some demand that Random House Cancel best-selling atheist Richard Dawkins’s books. Even ideas as fashionable as Darwinism are not safe.

But some are fighting back: Many writers and artists are beginning to speak out and take action, recognizing that sharing the cost of speaking up reduces its burden:

The first step in fighting the Cancel Culture that is infesting the book industry, veterans say, is to refuse to issue, demand, or listen to groveling apologies. The recent exposure of social media Cancel Culture bully Chrissy Teigen may start a trend. If what Teigen did exposes her to legal action, other social media trolls will be duly warned. Whether she is sorry for what she did is her own business, not the public’s…

● Best-selling science fiction author Jon Del Arroz forced WorldCon 76 (a huge science fiction convention) to pay compensation, not just issue an apology, for banning him and tarring him as a racist with no real evidence: “The ban came about when Del Arroz asked Worldcon for security measures because he feared for his safety due to the mob-like attacks on him and his family from industry insiders.” (June 5, 2021) He had been targeted by social justice warriors for some time due to Incorrect views.

● A University of Washington AI notable, Pedro Domingos, was threatened with Cancelation when he questioned “ideological litmus tests” in his discipline. He not only sidelined the well-known industry bully who was targeting him and his university but he published a list of Fifteen Strategic Principles for beating back Cancel Culture.

News, “Books: The first step in fighting Cancel Culture ” at Mind Matters News

Malicious envy was always out there but before social media it could rarely assemble so large a mob. But that’s a challenge, not a prophecy.

We ID types can help fend them off. We are used to fighting Cancel Culture.

You may also wish to read: Comedy: An endangered art form in the Age of Rage

and

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.

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Michael Behe on the “purposeful arrangement of parts”

Although Michael Behe, is associated with the concept of irreducible complexity, he now says he prefers to explain ID as “purposeful arrangement of parts”:

A correspondent asked about “specified complexity” and the intelligent design of the eye. I explained why I much prefer the phrase “purposeful arrangement of parts” as a criterion for design — versus irreducible complexity, specified complexity, specified small probability, information, complex specified information, or other phrases.

The critical difference between ID and Darwinian evolution (and all other proposals for unintelligent evolutionary processes) is the involvement of a mind in ID. The philosopher Lydia McGrew once wrote that the basic question of ID boils down to the question of “other minds.” One of Alvin Plantinga’s claims to fame is that he argued fifty years ago in God and Other Minds that (I paraphrase) the perception of the existence of God is the same sort of problem as the perception of the existence of other minds.

Michael Behe, “Recognizing Design by a “Purposeful Arrangement of Parts”” at Evolution News and Science Today (June 10, 2021)

“Purposeful arrangement of parts” is actually much easier for the average person to understand.

Biochemist Michael Behe is the author of Darwin’s Black Box and (1996), The Edge of Evolution, and Darwin Devolves.

Copyright © 2021 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana