Science & TechnologyS


Beaker

Designer organelles bring new functionalities into cells


Science Daily
Thu, 28 Mar 2019 10:43 UTC
organelle city
© Gemma Estrada GironaThe authors see the newly developed synthetic host as a city. On the one hand, typical cellular processes -- seen as encapsulated, isolated, and made up of non-interchangeable elements -- are represented as repetitive structures: squared, isolated blocks which are always fenced, just like membranous organelles. On the other hand, the image highlights the making of a new organelle -- a new building that is not fenced -- which is accessible to the rest of the city while having its own identity, a building which is more dynamic and flexible.
For the first time, scientists have engineered the complex biological process of translation into a designer organelle in a living mammalian cell. Research by the Lemke group at the European Molecular Biology Laboratory (EMBL) -- in collaboration with JGU Mainz and IMB Mainz -- used this technique to create a membraneless organelle that can build proteins from natural and synthetic amino acids carrying new functionality. Their results -- published in Science on 29 March -- allow scientist to study, tailor, and control cellular function in more detail.

During evolution, the development of new organelles allows cells and organisms to become more complex, due to the ability to sort cellular processes into specific hotspots. "Our tool can be used to engineer translation, but potentially also other cellular processes like transcription and post-translational modifications. This might even allow us to engineer new types of organelles that extend the functional repertoire of natural complex living systems," explains Christopher Reinkemeier, PhD student at EMBL and JGU Mainz and co-first author of the paper. "We could for example incorporate fluorescent building blocks that allow a glimpse inside the cell using imaging methods."

"The organelle can make proteins by using synthetic non-canonical amino acids. Currently we know of more than 300 different non-canonical amino acids -- compared to 20 which are naturally occurring. We are no longer restricted to the latter ones," says co-first author Gemma Estrada Girona. "The novelty we introduce is the ability to use these in a confined space, the organelle,, which minimises the effects on the host."

Comment: Imagine the amount of effort and trouble went into designing such a component, yet a Darwinist approach expects us to believe this happened by random processes. See also:

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Microscope 2

Quantum machine appears to defy the push to disorder - remembers its ordered state

Marcus Woo
Quanta
Wed, 20 Mar 2019 18:27 UTC
quantum lab
© Mikhail LukinA view of the lab where researchers built the 51-qubit quantum simulator.
Given enough time, even a tidy room will get messy. Clothes, books and papers will leave their ordered state and scatter across the floor. Annoyingly, this tendency toward untidiness reflects a law of nature: Disorder tends to grow.

If, for example, you cut open a pressurized scuba tank, the air molecules inside will spew out and spread throughout the room. Place an ice cube in hot water and the water molecules frozen in the ordered, crystalline lattice will break their bonds and disperse. In mixing and spreading, a system strives toward equilibrium with its environment, a process called thermalization.

It's common and intuitive, and precisely what a team of physicists expected to see when they lined up 51 rubidium atoms in a row, holding them in place with lasers. The atoms started in an orderly pattern, alternating between the lowest-energy "ground" state and an excited energy state. The researchers assumed the system would quickly thermalize: The pattern of ground and excited states would settle almost immediately into a jumbled sequence.

And at first, the pattern did jumble. But then, shockingly, it reverted to the original alternating sequence. After some more mixing, it returned yet again to that initial configuration. Back and forth it went, oscillating a few times in under a microsecond - long after it should have thermalized.

It was as if you dropped an ice cube in hot water and it didn't just melt away, said Mikhail Lukin, a physicist at Harvard University and a leader of the group. "What you see is the ice melts and crystallizes, melts and crystallizes," he said. "It's something really unusual."

Physicists have dubbed this bizarre behavior "quantum many-body scarring." As if scarred, the atoms seem to bear an imprint of the past that draws them back to their original configuration over and over again.


Comment: That sounds a lot like memory. But how can atoms have memory? How are they able to bear such an 'imprint'? As the scientists quoted below make clear, no one knows. Perhaps it has to do with something most scientists don't let into their theorizing. Maybe the mysterious scarring is the physical trace of a fundamental form of memory in the most basic kinds of matter? But in order to think that, you would have to consider panpsychism as a real possibility.

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Info

Bio-engineered blood vessels that are self-sustaining

Andrew Masterson
Cosmos Magazine
Wed, 27 Mar 2019 19:37 UTC
Bio-engineered blood vessel
© Kirkton et alA bio-engineered blood vessel (left) and the different cell structures that soon come to inhabit it.
Researchers have bio-engineered blood vessels that when implanted into a patient are quickly colonised by native cells and become self-sustaining.

A team led by Robert Kirkton of US-based regenerative medical tech company Humacyte Inc created biodegradable scaffolds in the form of blood vessels and then seeded them human vascular cells before incubating them in a bioreactor for eight weeks.

After the incubation, Kirkton and his colleagues removed all the cellular material, leaving behind what they term human acellular vessels (HAVs).

In a four year phase II clinical trial, the HAVs were implanted into 60 patients with end-stage kidney failure, where they served as entry ports for hemodialysis treatments - an approach which requires access to healthy blood vessels.
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Magnify

Michael Behe responds to his Lehigh colleagues: Molecular machines really are machines

Michael Behe
Evolution News
Tue, 26 Mar 2019 17:53 UTC
Lehigh University campus
© Joseph Giansante ’76 / Wikimedia CommonsLehigh University campus
Recently two of my Lehigh University Department of Biological Sciences colleagues published a seven-page critical review of Darwin Devolves in the journal Evolution. As I'll show below, it pretty much completely misses the mark. Nonetheless, it is a good illustration of how sincere-yet-perplexed professional evolutionary biologists view the data, as well as how they see opposition to their views, and so it is a possible opening to mutual understanding. This is the third of a three-part reply. It continues directly from Part 2. See here for Part 1.

Of Course Proteins Are Machines

A basic difference between the views of Greg Lang and Amber Rice and my own concerns the nature of the molecular foundation of life. They object that I consider many biochemical systems to be actual machines. They quote a line from Darwin Devolves stating that protein systems are "literal machines - molecular trucks, pumps, scanners, and more." They write disapprovingly that the book claims "rod cells are fiber optic cables ... The planthopper's hind legs are a 'large, in your face, interacting gear system.'" They do concede that I didn't make up those claims about the machine-like nature of the systems out of whole cloth: "Most of the analogies in Darwin Devolves are not Behe's creation - he has done well to scour press coverage and the scientific literature for relatable metaphors; and he is generous with their use." Nonetheless, they say, "reality remains: proteins are not machines, a flagellum is not an outboard motor."

On this point they are simply wrong. "Molecular machine" is no metaphor; it is an accurate description. Unless Lang and Rice are arguing obliquely for some sort of vitalism - where the matter of life is somehow different from nonliving matter - then of course proteins and systems such as the bacterial flagellum are machinery. What else could they be? Although they aren't made of metal or plastic like our everyday tools, protein systems consist of atoms of carbon, oxygen, nitrogen, and so on - the same kinds of atoms as are found in inorganic matter, nothing special.

Comment: See the previous two parts here:

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2 + 2 = 4

Michael Behe responds to his Lehigh colleagues on the true likelihood of degradative mutation

Michael Behe
Evolution News
Mon, 25 Mar 2019 18:20 UTC
Lehigh University campus
© IR393DEME / Wikimedia CommonsLehigh University campus
Recently two of my Lehigh University Department of Biological Sciences colleagues published a seven-page critical review of Darwin Devolves in the journal Evolution. As I'll show below, it pretty much completely misses the mark. Nonetheless, it is a good illustration of how sincere-yet-perplexed professional evolutionary biologists view the data, as well as how they see opposition to their views, and so it is a possible opening to mutual understanding. This is the second of a three-part reply. It continues directly from Part 1.

A Limited Accounting of Degradation

Greg Lang and Amber Rice cite a number of articles to show that loss-of-function mutations are just a small minority of those found in studies of organisms.
However, the truth is that loss of function mutations account for only a small fraction of natural genetic variation. In humans only ∼3.5% of exonic and splice site variants (57,137 out of 1,639,223) are putatively loss of function, and a survey of 42 yeast strains found that only 242 of the nearly 6000 genes contain putative loss of function variants. Compared to the vast majority of natural genetic variants, loss of function variants have a much lower allele frequency distribution.
Yet those three studies they cite all search only for mutations that are pretty much guaranteed to totally kill a gene or protein. For example, one paper says:
We adopted a definition for LoF variants expected to correlate with complete loss of function of the affected transcripts: stop codon-introducing (nonsense) or splice site-disrupting single-nucleotide variants (SNVs), insertion/deletion (indel) variants predicted to disrupt a transcript's reading frame, or larger deletions ...
That's akin to counting only burnt-out shells of wrecked cars as examples of accidents that degrade an auto, while ignoring fender benders, flat tires, and so on. There are many more mutations that would not be picked up by the researchers' methods that nonetheless would be expected to seriously degrade or even destroy the function of a protein. Since the rates leading to the kinds of mutations in the cited papers are likely to be at least ten-fold lower than general point mutations in the gene (which, again, the study passed over) there may be many more genes - perhaps five- to ten-fold more (about a quarter to a half of mutated genes) - that have been degraded or even functionally destroyed. Further research is needed to say for sure. (I know which way I'll bet.) The remaining fraction of mutated genes in the population is likely to consist mostly of selectively neutral changes, neither helping nor hurting the organism, and not contributing anything in themselves to the fitness of the species.

Comment: See the first part of Behe's response here: Michael Behe responds to his Lehigh colleagues' inability to grasp the first rule of adaptive evolution

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Radar

Like mountaineers, nerves need expert guidance to find their way


Salk
Fri, 22 Mar 2019 11:09 UTC
Motor neurons
© Salk InstituteLeft: Motor neurons (green) exit the spinal cord (red) and enter the periphery of the body to connect with muscles. Right: Motor neurons (white arrow) without the guidance of p190 are trapped within the spinal cord.
Similar to the dozens of Sherpas that guide hikers up treacherous Himalayan mountains to reach a summit, the nervous system relies on elaborate timing and location of guidance cues for neuronal axons-threadlike projections-to successfully reach their destinations in the body. Now, Salk Institute researchers discover how neurons navigate a tricky cellular environment by listening for directions, while simultaneously filtering out inappropriate instructions to avoid getting lost. The findings appeared in Neuron on March 19, 2019.

"There are 100 trillion connections in the nervous system governed by 20,000 genes, of which roughly 10 gene families are known to be involved in controlling axon guidance. We wanted to understand the clever genetic systems nature has employed to wire the most complicated biological machine in the universe," says Salk Professor Samuel Pfaff, senior author and a Howard Hughes Medical Institute investigator. "Thus, we set out to examine how motor neurons find their connections with muscles in the body, which is critical for our brain to relay information to our muscles to allow for movement."

The brain controls hundreds of different muscles to allow for precise movement. During development, motor neurons in the spinal cord extend their axons outside of the central nervous system to connect with muscle cells in the body. Every motor neuron relies on a set of genes to ensure the axon grows correctly to the muscle.

Comment: See also:

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Brain

Scientists 'clear' Alzheimer's plaque from mice using only light and sound

Mike McRae
Science Alert
Fri, 15 Mar 2019 00:01 UTC
mouse brains alzheimer's plaques
© Gabrielle DrummondMouse brain with (left) and without (right) treatment.
Clumps of harmful proteins that interfere with brain functions have been partially cleared in mice using nothing but light and sound.

Research led by MIT has found strobe lights and a low pitched buzz can be used to recreate brain waves lost in the disease, which in turn remove plaque and improve cognitive function in mice engineered to display Alzheimer's-like behaviour.

It's a little like using light and sound to trigger their own brain waves to help fight the disease.

Comment: See also:

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Laptop

Microsoft using manufactured DNA-based data storage

Matthew Humphries
PC Mag
Fri, 22 Mar 2019 12:32 UTC
DNA Data storage
© PC Mag
Existing data storage methods can't keep up with the amount of data we need to store, so Microsoft is creating a fully automated data-to-DNA storage system as a solution.

Microsoft says we're soon going to be faced with a bit of a data storage crisis. We are producing so much data that we're going to reach a point where there's more data than storage available. To solve this impending problem, Microsoft is turning to DNA.

According to Seagate, in 2018 we created 33 zettabytes of data, but by 2025 that will have grown to 175 zettabytes. Hard drives continue to grow in capacity, but even if they did manage to keep up with demand they require a lot of physical storage space and cooling, meaning datacenters will need to expand. DNA, on the other hand, can store data "in a space that's orders of magnitude smaller than datacenters," but we need to figure out how to automate the data-to-DNA process and to do so cheaply.

A team of researchers at Microsoft working with the University of Washington believe they have taken the first step towards doing just that. A proof-of-concept test successfully demonstrated "the first fully automated system to store and retrieve data in manufactured DNA."
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Info

New, massive storms forming on Neptune

Korey Haynes
Discover Magazine
Mon, 25 Mar 2019 16:01 UTC
Storm on Neptune
© NASA/ESA/GSFC/JPLNeptune’s dark storms were first captured by Voyager 2 in 1989 (left). In 2018, Hubble spied an entirely new storm system.
Neptune has a new storm, in the form of a large dark spot that appeared in late 2018. By analyzing Hubble images dating back to 2015, astronomers have discovered high-altitude clouds that formed years ahead of the visible storm, indicating it was already forming there, swirling beneath the clouds and haze. The telltale clouds are teaching astronomers more about how such storms form and evolve on all the giant outer planets.

Birth of a Storm

Neptune, like all the outer solar system planets, forms large and durable storms. While Jupiter's Great Red Spot is infamous, Neptune's dark blue spots were unknown until Voyager 2 flew past in 1989, sending back pictures of two large storms on its surface. Jupiter's Great Red Spot has been visible for at least 190 years, and possibly since the 1600s. But when Hubble peered at Neptune in 1994, its storms had already vanished.

Since then, Hubble has spotted dark storms appearing and disappearing on Neptune, lasting only two years or so - though maybe up to six years - before dissipating again. Like hurricanes on steroids, Neptune's storms are dark vortexes of clouds racing at high speeds, each roughly the size of planet Earth. But Earth storms rarely last more than a few weeks, and form around low-pressure areas. On the giant planets, they instead form around regions of high-pressure.

"That makes them more stable to start," says Simon. "And there are no land masses. That's what breaks storms up on Earth." On Jupiter, the planet's jet streams lock its massive storm in place near the equator, where it has safely churned for centuries. On Neptune, wind patterns push the storms north or south where they get shredded by opposing wind currents within a few years.
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Microscope 2

Ben Shapiro interviews Stephen Meyer about intelligent design

David Klinghoffer
Evolution News
Mon, 25 Mar 2019 18:03 UTC
Ben Shapiro
Ben Shapiro
Ben Shapiro's Sunday Special interview with Stephen Meyer is up and viewable now at YouTube. This might be the best interview with Meyer that I've ever seen. Check it out:


Why might it be the best? Partly because of the long video format - a full hour (with a provocative final question for Steve that you need to subscribe to The Daily Wire to see), and very well produced. Partly because Shapiro has done his homework. He knows the common challenges to intelligent design and poses them very articulately, and he's obviously absorbed Meyer's books, especially Darwin's Doubt and Signature in the Cell, as well other material on ID. That is more than you can say for some scientists and journalists I'm thinking of right now.
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