Michael J. Behe's Blog, page 419

October 15, 2019

How do liquid organelles coexist without merging?

New research may help to explain an intriguing phenomenon inside human cells: how wall-less liquid organelles are able to coexist as separate entities instead of just merging together.

The results — published on Aug. 22 in the Journal of the American Chemical Society — point to the chemical structure of protein and RNA molecules within the droplets as one key factor that may prevent MLOs from mixing.

The team found that certain types of RNA and proteins are “stickier” than others, enabling them to form gelatinous droplets that don’t fuse easily with other droplets in the same viscoelastic state. Specifically, droplets are more likely to be gel-like when they contain RNA molecules rich in a building block called purine, and proteins rich in an amino acid called arginine.
Paper. (open access) – Ibraheem Alshareedah, Taranpreet Kaur, Jason Ngo, Hannah Seppala, Liz-Audrey Djomnang Kounatse, Wei Wang, Mahdi Muhammad Moosa, Priya R. Banerjee. Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein–RNA Complexes. Journal of the American Chemical Society, 2019; 141 (37): 14593 DOI: 10.1021/jacs.9b03689 More.

They know what they are without a membrane, just by being gelatinous.

See also: Only some cells have “licences to kill” Let’s look at what that means

and

In nature, cells have “secret conversations”

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Published on October 15, 2019 14:54

Giant molecules show quantum effects: Appear in two places at once

Quantum mechanics demonstrates that it is possible but only recently could it be shown to be true in a molecule with 2000 atoms:

But it’s one thing to create an interference pattern with electrons. Doing it with giant molecules is a lot trickier. Bigger molecules have less-easily detected waves, because more massive objects have shorter wavelengths that can lead to barely-perceptible interference patterns. And these 2,000-atom particles have wavelengths smaller than the diameter of a single hydrogen atom, so their interference pattern is much less dramatic.
Rafi Letzter, “Giant Molecules Exist in Two Places at Once in Unprecedented Quantum Experiment” at Scientific American

Paper. (open access)

We’re told, no, it’s not Star Trek because people would be killed going through the interferometer.

—

See also: Sean Carroll: Physicists Don’t Even Want To Understand Quantum Mechanics

and

Theoretical Physicist: Recent Claim About Big Quantum Mechanics Find Is “Silly”

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Published on October 15, 2019 14:13

The war on math targets the equals sign

The plus and minus signs better look out too:

The equal sign is the bedrock of mathematics. It seems to make an entirely fundamental and uncontroversial statement: These things are exactly the same.
But there is a growing community of mathematicians who regard the equal sign as math’s original error. They see it as a veneer that hides important complexities in the way quantities are related—complexities that could unlock solutions to an enormous number of problems. They want to reformulate mathematics in the looser language of equivalence.
(Original story reprinted with permission from Quanta Magazine, an editorially independent publication of the Simons Foundation whose mission is to enhance public understanding of science by covering research develop-ments and trends in mathe-matics and the physical and life sciences.)
“We came up with this notion of equality,” said Jonathan Campbell of Duke University. “It should have been equivalence all along.”
The most prominent figure in this community is Jacob Lurie. In July, Lurie, 41, left his tenured post at Harvard University for a faculty position at the Institute for Advanced Study in Princeton, New Jersey, home to many of the most revered mathematicians in the world.
Lurie’s ideas are sweeping on a scale rarely seen in any field.
Kevin Hartnett, “Is the Equal Sign Overrated? Mathematicians Hash It Out” at Wired

Lurie has moved beyond the equals sign.

But he is not nearly so innovative as Hartnett makes out. Woke math teachers have moved well beyond right and wrong answers. But they will be heartened by this support in the face of fierce criticism elsewhere.

See also: The progressive war on science takes dead aim at math

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Published on October 15, 2019 13:18

October 14, 2019

US AG Barr on the importance of religious liberty

Here:

Money clip:

The imperative of protecting religious freedom was not just a nod in the direction of piety. It reflects the framers’ belief that religion was indispensable to sustaining our free system of government . . . ”

Food for thought. END

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Published on October 14, 2019 16:46

“Junk DNA” as a cause of cancer

Useless is not the same as harmful, unfortunately. From ScienceDaily:

An Ontario-led research group has discovered a novel cancer-driving mutation in the vast non-coding regions of the human cancer genome, also known as the “dark matter” of human cancer DNA.

The mutation, as described in two related studies published in Nature on October 9, 2019, represents a new potential therapeutic target for several types of cancer including brain, liver and blood cancer. This target could be used to develop novel treatments for patients with these difficult-to-treat diseases.

“Non-coding DNA, which makes up 98 per cent of the genome, is notoriously difficult to study and is often overlooked since it does not code for proteins,” says Dr. Lincoln Stein, co-lead of the studies and Head of Adaptive Oncology at the Ontario Institute for Cancer Research (OICR). “By carefully analyzing these regions, we have discovered a change in one letter of the DNA code that can drive multiple types of cancer. In turn, we’ve found a new cancer mechanism that we can target to tackle the disease.”

The research group discovered that the mutation, termed the U1-snRNA mutation, could disrupt normal RNA splicing and thereby alter the transcription of cancer-driving genes. These molecular mechanisms represent new ways to treat cancers carrying the mutation. One of the potential treatment approaches includes repurposing existing drugs, which, by bypassing early drug development stages, could be brought into the clinic at an accelerated rate.

“Our unexpected discovery uncovered an entirely new way to target these cancers that are tremendously difficult to treat and have high mortality rates,” says Dr. Michael Taylor, Paediatric Neurosurgeon, Senior Scientist in Developmental and Stem Cell Biology and Garron Family Chair in Childhood Cancer Research at The Hospital for Sick Children (SickKids) and co-lead of the studies. “We’ve found that with one ‘typo’ in the DNA code, the resultant cancers have hundreds of mutant proteins that we might be able to target using currently available immunotherapies.” Paper 1 and Paper 2 paywalls – Hiromichi Suzuki et al., Recurrent non-coding U1-snRNA mutations drive cryptic splicing in Shh medulloblastoma. Nature, 2019; DOI: 10.1038/s41586-019-1650-0; Shimin Shua et al., The U1 spliceosomal RNA is recurrently mutated in multiple cancers. Nature, 2019; DOI: 10.1038/s41586-019-1651-z More.

But, if things turn out as the researchers say, they now know what to target.

See also: Remember Junk RNA? Cell Division Requires A Balanced Level Of It

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Published on October 14, 2019 14:31

Our enterprising ancestors’ version of canned soup, 400 kya

From ScienceDaily:

Tel Aviv University researchers, in collaboration with scholars from Spain, have uncovered evidence of the storage and delayed consumption of animal bone marrow at Qesem Cave near Tel Aviv, the site of many major discoveries from the late Lower Paleolithic period some 400,000 years ago.

The research provides direct evidence that early Paleolithic people saved animal bones for up to nine weeks before feasting on them inside Qesem Cave…

“Bone marrow constitutes a significant source of nutrition and as such was long featured in the prehistoric diet,” explains Prof. Barkai. “Until now, evidence has pointed to immediate consumption of marrow following the procurement and removal of soft tissues. In our paper, we present evidence of storage and delayed consumption of bone marrow at Qesem Cave.”

“This is the earliest evidence of such behavior and offers insight into the socioeconomics of the humans who lived at Qesem,” adds Dr. Blasco. “It also marks a threshold for new modes of Paleolithic human adaptation.”

“Prehistoric humans brought to the cave selected body parts of the hunted animal carcasses,” explains Prof. Rosell. “The most common prey was fallow deer, and limbs and skulls were brought to the cave while the rest of the carcass was stripped of meat and fat at the hunting scene and left there. We found that the deer leg bones, specifically the metapodials, exhibited unique chopping marks on the shafts, which are not characteristic of the marks left from stripping fresh skin to fracture the bone and extract the marrow.”

The researchers contend that the deer metapodials were kept at the cave covered in skin to facilitate the preservation of marrow for consumption in time of need.

What’s really interesting about this study is that the researchers tried it themselves:

“We discovered that preserving the bone along with the skin, for a period that could last for many weeks, enabled early humans to break the bone when necessary and eat the still nutritious bone marrow,” adds Dr. Blasco.

“The bones were used as ‘cans’ that preserved the bone marrow for a long period until it was time to take off the dry skin, shatter the bone and eat the marrow,” Prof. Barkai emphasizes.

They don’t explicitly say that they actually ate the stuff themselves but then maybe this is just a really good time to be a vegan. They do say, however,

Until recently, it was believed that the Paleolithic people were hunter gatherers who lived hand-to-mouth (the Stone Age version of farm-to-table), consuming whatever they caught that day and enduring long periods of hunger when food sources were scarce.

“We show for the first time in our study that 420,000 to 200,000 years ago, prehistoric humans at Qesem Cave were sophisticated enough, intelligent enough and talented enough to know that it was possible to preserve particular bones of animals under specific conditions, and, when necessary, remove the skin, crack the bone and eat the bone marrow,” Prof. Gopher explains. Paper. (open access) – R. Blasco, J. Rosell, M. Arilla, A. Margalida, D. Villalba, A. Gopher, R. Barkai. Bone marrow storage and delayed consumption at Middle Pleistocene Qesem Cave, Israel (420 to 200 ka). Science Advances, 2019; 5 (10): eaav9822 DOI: 10.1126/sciadv.aav9822 More.

It puts one in mind of the researchers who went to the trouble of flint knapping Neanderthal tools themselves. They discovered that the tools were not clumsier; they were just designed for bigger hands. And where is that subhuman when we need him?

See also: Do racial assumptions prevent recognizing Homo erectus as fully human?

In any Darwinian scheme, someone must be the subhuman. Otherwise, there is no beginning to human history.

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Published on October 14, 2019 11:44

Bacteria thrive via non-Darwinian “survival of the friendliest”

But it makes a lot of sense if you think about it:

New microbial research at the Department of Biology reveals that bacteria would rather unite against external threats, such as antibiotics, rather than fight against each other. The report has just been published in the scientific publication ISME Journal. For a number of years the researchers have studied how combinations of bacteria behave together when in a confined area. After investigating many thousands of combinations it has become clear that bacteria cooperate to survive and that these results contradict what Darwin said in his theories of evolution.
“In the classic Darwinian mindset, competition is the name of the game. The best suited survive and outcompete those less well suited. However, when it comes to microorganisms like bacteria, our findings reveal the most cooperative ones survive,” explains Department of Biology microbiologist, Professor Søren Johannes Sørensen.
Faculty of Science, “Friendly bacteria collaborate to survive” at University of Copenhagen

Of course, in the real world, “survival of the friendliest” makes a great deal more sense than a Darwinian war of all against all because most life forms are best off to minimize energy-draining hostilities wherever possible.

By isolating bacteria from a small corn husk (where they were forced to “fight” for space) the scientists were able to investigate the degree to which bacteria compete or cooperate to survive. The bacterial strains were selected based upon their ability to grow together. Researchers measured bacterial biofilm, a slimy protective layer that shields bacteria against external threats such as antibiotics or predators. When bacteria are healthy, they produce more biofilm and become stronger and more resilient.

Time after time, the researchers observed the same result: Instead of the strongest outcompeting the others in biofilm production, space was allowed to the weakest, allowing the weak to grow much better than they would have on their own. At the same time the researchers could see that the bacteria split up laborious tasks by shutting down unnecessary mechanisms and sharing them with their neighbors.

“It may well be that Henry Ford thought that he had found something brilliant when he introduced the assembly line and worker specialization, but bacteria have been taking advantage of this strategy for a billion years,” says Søren Johannes Sørensen referring to the oldest known bacterial fossils with biofilm. He adds:

“Our new study demonstrates that bacteria organize themselves in a structured way, distribute work and even to help each other. This means that we can find out which bacteria cooperate, and possibly, which ones depend on each another, by looking at who sits next to who.”
Faculty of Science, “Friendly bacteria collaborate to survive” at University of Copenhagen

Don’t be too surprised if many pathogens get a lot of co-operation from “harmless” bacteria too, complicating the picture. But then who said life was simple?

Paper. (open access)

See also: What the fossils told us in their own words

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Published on October 14, 2019 10:09

October 13, 2019

Is Mathematics falling under the sway of a computerised, AI-driven celebrity-authority culture?

Two recent remarks in VICE (a telling label, BTW) raise some significant concerns. First, Kevin Buzzard — no, this is not Babylon Bee [itself a sign when it is harder and harder to tell reality from satire] — Sept 26th:

Number Theorist Fears All Published Math Is Wrong

“I think there is a non-zero chance that some of our great castles are built on sand,” he said, arguing that we must begin to rely on AI to verify proofs.

[ . . . ]

Kevin Buzzard, a number theorist and professor of pure mathematics at Imperial College London, believes that it is time to create a new area of mathematics dedicated to the computerization of proofs. The greatest proofs have become so complex that practically no human on earth can understand all of their details, let alone verify them. He fears that many proofs widely considered to be true are wrong. Help is needed.

What is a proof? A proof is a demonstration of the truth of a mathematical statement. By proving things and learning new techniques of proof, people gain an understanding of math, which then filters out into other fields.
To create a proof, begin with some definitions. For example, define a set of numbers such as the integers, all the whole numbers from minus infinity to positive infinity. Write this set as: … , -2, -1, 0, 1, 2, … Next, state a theorem, for example, that there is no largest integer. The proof then consists in the logical reasoning that shows the theorem to be true or false, in this case, true. The logical steps in the proof rely on other, prior truths, which have already been accepted and proven. For example, that the number 1 is less than 2.
New proofs by professional mathematicians tend to rely on a whole host of prior results that have already been published and understood. But Buzzard says there are many cases where the prior proofs used to build new proofs are clearly not understood. For example, there are notable papers that openly cite unpublished work. This worries Buzzard.
“I’m suddenly concerned that all of published math is wrong because mathematicians are not checking the details, and I’ve seen them wrong before,” Buzzard told Motherboard while he was attending the 10th Interactive Theorem Proving conference in Portland, Oregon, where he gave the opening talk.

“I think there is a non-zero chance that some of our great castles are built on sand,” Buzzard wrote in a slide presentation. “But I think it’s small.”

The talk:

Now, let us cross-multiply by another report, on Oct 10, on how a software glitch has created a problem in Chemistry (and potentially medicine):

A Code Glitch May Have Caused Errors In More Than 100 Published Studies
The discovery is a reminder that science is collaborative and ideally self-correcting, but that nothing can be taken for granted.

[ . . . ]

Scientists in Hawaiʻi have uncovered a glitch in a piece of code that could have yielded incorrect results in over 100 published studies that cited the original paper.

The glitch caused results of a common chemistry computation to vary depending on the operating system used, causing discrepancies among Mac, Windows, and Linux systems. The researchers published the revelation and a debugged version of the script, which amounts to roughly 1,000 lines of code, on Tuesday in the journal Organic Letters.

“This simple glitch in the original script calls into question the conclusions of a significant number of papers on a wide range of topics in a way that cannot be easily resolved from published information because the operating system is rarely mentioned,” the new paper reads. “Authors who used these scripts should certainly double-check their results and any relevant conclusions using the modified scripts in the [supplementary information].”

Yuheng Luo, a graduate student at the University of Hawaiʻi at Mānoa, discovered the glitch this summer when he was verifying the results of research conducted by chemistry professor Philip Williams on cyanobacteria. The aim of the project was to “try to find compounds that are effective against cancer,” Williams said . . . . Luo’s results did not match up with the NMR values that Williams’ group had previously calculated, and according to Sun, when his students ran the code on their computers, they realized that different operating systems were producing different results. Sun then adjusted the code to fix the glitch, which had to do with how different operating systems sort files.

GIGO, anyone?

Garbage in, garbage out — or perhaps, garbage in, [presumed] gospel out.

So system of reasoning is better than its inputs [including controlling assumptions or assertions] and structure.

As in, what about brains as computational substrates, too.

Food for thought as we ponder where an AI age takes us, especially when many hope to use AI systems to p[rove correctness of software.

What could go wrong . . . ? END

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Published on October 13, 2019 23:53

Nathan Lents in USA Today: Evolution is Certain

In a recent USA Today opinion piece evolutionist Nathan Lents states that the human race has “evolved through a long line of ancestry that connects with all other living things going back nearly 4 billion years.” And if there was any doubt … read more

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Published on October 13, 2019 23:09

Has the universe really stopped making sense?

This image represents the evolution of the Universe, starting with the Big Bang. The red arrow marks the flow of time.

Big Bang/NASA

Are we really “getting something wrong” about it?

It’s possible that the CMB model is just wrong in some way, and that’s leading to some sort of systematic error in how physicists are understanding the universe.

“Everyone would love that. Physicists love to break their models,” Wechsler said. “But this model works pretty well so far, so my prior is that there has to be pretty strong evidence to convince me.”

The study does show that it would be difficult to match the Cepheid measurement from the local universe with all the others by introducing just one new piece of physics, Mack said.

It’s possible, Mack said, that the supernovas-Cepheid calculation is just wrong. Maybe physicists are measuring distances in our local universe wrong, and that’s leading to a miscalculation. It’s hard to imagine what that miscalculation would be, though, she said. Lots of astrophysicists have measured local distances from scratch and have come up with similar results. One possibility the authors raised is just that we live in a weird chunk of the universe where there are fewer galaxies and less gravity, so our neighborhood is expanding faster than the universe as a whole.

The answer to the problem, she said, could be just around the corner. But more likely it’s years or decades away.
Rafi Letzter, “How the Universe Stopped Making Sense” at LiveScience

It doesn’t sound like that big a problem, actually. Let’s save the “universe doesn’t make sense” for existentialist plays. What the universe is doing makes sense, in a physical way.

With, for example, the Big Bang and fine-tuning, it’s not at all that the universe doesn’t make sense but that it isn’t telling people what they want to hear.

See also: The Big Bang: Put simply,the facts are wrong.

and

What becomes of science when the evidence does not matter?

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Published on October 13, 2019 11:23