Saturday 2 September 2023
Yet more on why the origin of life = the origin of information.
Introducing the Unknome, Biology’s Black Box
"Ome” is not a mantra in science, but it is an increasingly common suffix in biochemistry, genetics, and molecular biology. We all know about the genome. Then there was the epigenome, followed by the proteome. Now there is the interactome, the metabolome, the transcriptome, and others. More “omes” seem to pop up in the literature from time to time. As in the genome representing the set of genes of an individual or species, the suffix -ome denotes a “body” or set of parts that can be described together: the proteome consists of all the proteins in a cell. The transcriptome is the set of DNA transcripts. The interactome is the set of all interacting parts in a process, and the metabolome is the full complement of metabolites in a cell, tissue, or organism at a particular state. A new one is the “unknome” — the set of all components we know nothing about. More on that later. The -ome suffix has also long been used on individual units like ribosome, cytochrome, cryptochrome, and chromosome. Poets should have an easy time writing verses about biochemistry.
The study of all omes can be called Omics, with family members like genomics, proteomics, and transcriptomics. Omics is not just a taxonomical exercise; it is an attempt to get a handle on the bewildering complexity facing cell biologists. And just when they think they’ve got all the members corralled in an ome, complications set in.
Your Genomes (Plural)
For example, the journal Science announced recently that “Your cells don’t have the genome you were born with.” Contrary to what most people were led to believe by 23andMe, none of us have “a” genome, except at conception. From then on, the genome changes cell by cell, tissue by tissue, throughout life. These can add up to tens of thousands of changes per somatic cell. Modifications to the genome by mutations or by developmental processes turn us into universes of genomes!
As a result, every person is actually a mosaic of genomes, varying across the body and often within the same organ or tissue. These DNA changes introduce a diversity to the body’s somatic, or nonreproductive, cells that may be as important to health as the more pervasive alterations inherited from parents. Now, the National Institutes of Health (NIH) has launched a 5-year, $140 million project to map this universe of genomic diversity — and probe why it matters.
Dan Landau calls this “a huge revolution in human genetics.” He is eager to see the results. “We are just at the beginning of this incredible adventure.”
Omics in 3-D
Another review article in Science announces “The Dawn of Spatial Omics.” The editor’s review says,
All of biology happens in space. In living organisms, cells must interact and assemble in three-dimensional tissues. The position of each cell is just as important as its intrinsic nature in determining how a tissue functions or malfunctions in a disease. Recently, many technologies have been invented to profile cells without removing them from their natural context, measuring gene expression and the regulatory landscape of a cell’s genome alongside its spatial location within a tissue. In a review, Bressan et al. describe the features of these methods, collectively named spatial omics, and discuss what is missing for them to unlock their full potential.
The authors, Bressan, Battistoni, and Hannon, begin with a fanfare: “Just as single-cell sequencing has revolutionized many fields of biology, spatial ‘omics,’ in which molecular parameters are measured in situ on intact tissue samples, is set to empower a new generation of scientific discoveries.”
Spatial molecular profiling at the tissue level (and sometimes at the cell level) with “multi-omic” technologies will allow researchers to study the genome, transcriptome, and proteome simultaneously in situ within an organ, tissue, or cell. This adds another layer of information that was hidden from earlier studies
One of the first steps along this journey was the emergence of single-cell “omics” technologies that operate on disaggregated tissues. These methods enabled the discovery of new cell types, cast new light on organismal development, and launched the process of creating comprehensive catalogs of human and mouse tissues. However, biological processes happen in a spatial context, and the three-dimensional (3D) arrangement of cells in a tissue has a profound effect on their functions…. Regardless of their undisputed power, measurements made on disaggregated cells or nuclei lack this layer of information. The need for such knowledge has driven the development of “spatial omics”: methods capable of measuring the molecular characteristics of cells in their native 3D context.
The authors say that “we are at the very beginning of the spatial omics revolution” and that “progress is happening at breakneck speed” that will undoubtedly give scientists “a much deeper understanding of biology in context.”
As an example of the profound effect of spatial and environmental influences on an organism, researchers at Harvard found that specific neurons become active when a mouse makes an error navigating a virtual reality maze.
The researchers found that when a mouse made and corrected a mistake while navigating, the subtype of neurons became active. This held true even when they guided the mouse to err, either by rotating the maze or changing the color cues. However, if the mouse didn’t make a mistake, or made a mistake but didn’t correct it, the neurons didn’t fire.
When the neurons became active, they did so in unison, prompting a follow-up experiment in which the researchers stimulated the cells with light. They found that the neurons are essentially hardwired to each other, meaning that the electrical current telling them to fire can flow directly from one cell to the next.
Studying these neurons in isolation would not have revealed this concerted, dynamic activity
Interactome Sentries
Scientists at Leiden University in the Netherlands found that the “cytosolic interactome protects against protein unfolding” with a continuous process of “biological origami at the molecular level.” According to Phys.org, the
Group leader, Alireza Mashaghi, said, “When a cell experiences stress, a protein can unfold to a completely unfolded chain. Once that has happened, it’s very hard to reverse. But we noticed the cytoplasm puts a break on this process, not allowing the unfolding to go all the way. This protects the proteins and ensures a proper functionality, and also makes it easier for proteins to refold once the stress in resolved.”
Unknome: The Final Frontier
From the Public Library of Science comes word of “The ‘unknome’: the set of gene transcripts we know almost nothing about.” This black box consists of “thousands of understudied proteins encoded by genes in the human genome, whose existence is known but whose functions are mostly not.”
The sequencing of the human genome has made it clear that it encodes thousands of likely protein sequences whose identities and functions are still unknown. There are multiple reasons for this, including the tendency to focus scarce research dollars on already-known targets, and the lack of tools, including antibodies, to interrogate cells about the function of these proteins. But the risks of ignoring these proteins are significant, the authors argue, since it is likely that some, perhaps many, play important roles in critical cell processes, and may both provide insight and targets for therapeutic intervention.
Echoed by Phys.org, this news says that researchers in the UK are putting together a public database of these proteins that they trust will shrink over time. The Unknome [Unknown Genome] Project has started at http://www.unknome.org. The proteins are ranked by how little is known about them, stimulating researchers’ curiosity to find out what they do.
It’s clear that Omics is discovering additional layers of biological information in living systems. Antiquated 1960s-era concepts of genes and proteins, like the Central Dogma, are being overwhelmed by this new vista of multi-dimensional dynamic organization. If the earlier geneticists were looking at a 2-D flat map, the new generation is looking at a thriving city. Old dogmas about Darwinian evolution seem woefully inadequate to understand complexity at this level. Science in the 21st century will require a theoretical framework equipped to handle information flow in time and space. There is one. It’s known as intelligent design
Reviewing a "win" for Darwinism.
An Impressive Instance of Unguided Evolution? Not So Much
On a classic episode of ID the Future, host and biologist Ray Bohlin interviews biophysicist Cornelius Hunter, author of Darwin’s God, about an article in the journal Science concerning a virus invasion of E. coli bacteria. The article subtitle announces “Natural Selection Caught in the Act,” and suggests that an impressive instance of unguided evolution has been directly witnessed. Not so fast, Hunter says. The results were intelligently designed (by the lab scientists), he notes, and the changes are less impressive than they may appear at first glance. Hunter also explains protein-protein binding and counters evolutionist Dennis Venema to argue that the way the vertebrate immune system drives change is not at all analogous to the evolutionary process of random mutations and natural selection. Moreover, Hunter says, the mammalian immune system is itself an enormous challenge for evolutionary theory.
Unfortunately, it’s common for studies such as this one to be hyped up by the scientific community and the establishment media. “Evolutionists are driven by non-scientific factors, non-scientific influences,” says Hunter. “There is a desire for the theory to be true in spite of the science, not because of the science.” Download the podcast or listen to it here.
Ecosystems vs. Darwinism
Ecosystems — A Tribute to Intelligent Design, or to Chance and Adaptation?
Although intelligent design is evident in the biochemistry of the cell and the physiological systems of the body, living organisms are not independent but exist in a web of life, interdependent upon other living things in an ecosystem.
As we think about all the species of animals, birds, and fishes on Earth, it becomes apparent that each one requires a certain type of food, suitable for its anatomy. Domestic livestock, including cattle, horses, sheep, and goats, can be nourished through grazing on grasses and broadleaf weeds, although each has different preferences.1 Among the wild animals, carnivores have varying needs for prey that match their size and abilities. With the thousands of species of birds, the preferred menu selections stretch from sips of nectar to berries, insects, smaller animals, carrion, or fish.
Variety and Quantity
Considering that water covers 71 percent of the Earth’s surface, it’s not surprising that the variety and quantity of fish inhabiting oceanic and freshwater ecosystems is legion.
The total number of living fish species — about 32,000 — is greater than the total of all other vertebrate species (amphibians, reptiles, birds, and mammals) combined.2
Fish species include herbivores and carnivores (smaller fish get eaten by bigger fish). The largest marine species include baleen whales that are uniquely outfitted to obtain their nourishment from the smallest organisms:
[Baleen whales] are the largest animals on Earth, yet they live off some of the smallest. They can grow to lengths of 30 meters (90 feet), but it is the microscopic zooplankton, krill and small fish that sustains them.3
The main point here is not a lesson on what different creatures eat, but that the multiplied billions of creatures on Earth all need to be fed according to their specific dietary needs and their physiological and anatomical specifications. Anyone who has taken care of animals knows that concern over providing sufficient food of the right type never takes a vacation. Not many of us have pet hummingbirds, but if we did, we might lose weight just making sure they didn’t:
Hummingbirds have a very high metabolism and must eat all day long just to survive. They consume about half their body weight in bugs and nectar, feeding every 10-15 minutes and visiting 1,000-2,000 flowers throughout the day.4
Caring for more prosaic animals is also demanding
Cows are natural grazers, preferring to eat 5 to 9 meals a day, plus drinking. For this reason, cows have free access to fresh food and water throughout the day….So just how much does a cow eat? While each cow is different, a typical milk-producing dairy cow, weighing around 600kg, eats around 29kg [64 pounds] of feed each day and may drink about 100L of water (about a bathtub’s worth).
Apart from domesticated animals, wildlife depends upon an ecosystem in which the lives of multiple species are interconnected. We can observe how many species of living things thrive in a given ecosystem, but to take for granted the finely tuned balance within these life-nourishing habitats is to overlook layered evidence for design.
Let’s Look at a Few Specific Examples
In the wild, an apex predator such as a lion is equipped to hunt prey, but of course an abundance of suitable prey must exist within its territory. The prey, typically herbivores, need sufficient grassland to graze upon and water to drink. Seasonal weather changes must be moderate, so that vegetation and surface water are available year-round. The perspective of naturalism takes it for granted that these requirements are simply adaptations that occurred in time and location without any thought or foresight.
Consider another example. A raptor such as a red-tailed hawk is equipped with the ability of flight, sight and talons to hunt and capture small creatures. Rather than ascribing the sophisticated, finely tuned characteristics of such a bird of prey and its ecosystem to unguided evolutionary adaptations, purposeful design provides an explanation more consistent with the specific, interdependent functionality in this and other examples.
Design or Adaptation?
Surviving a cold winter that can last four to six months or longer, when no plant growth occurs and insects vanish, would seem impossible for many types of birds. However, several species of songbirds manage just fine, even when the average temperature falls well below freezing, eating seeds, nuts, and berries. Is this evidence for design, or is it just natural adaptation?
If the ability of birds to thrive across the Earth is just a matter of adaptation, the process works unbelievably well with the thousands of species of birds. “New research estimates there are between 50 billion and 430 billion birds on Earth.”5 The sheer number and variety of birds thriving in multiple environments on every continent argues that something far more than luck and unguided nature is behind it all.
Our increased understanding of the biochemical complexity within any living organism, coupled with a growing awareness of the delicately balanced ecosystems sustaining life on Earth, suggest ingenious foresight, planning, and design with every type of life we observe.6
Fish far outnumber birds on our planet, with estimates of 3.5 trillion fish inhabiting the oceans,7 and each one of these trillions of creatures needs a regular supply of food accessible to it in a suitable form and quantity. Let’s imagine an experiment: given a planet with oceans empty of life, how much intelligence would it take to design an interdependent ecosystem capable of supporting thousands of species of fish over a time frame stretching across hundreds of millions of years?
From Molecules to Gills
Oh, and if you, as a designer substitute, think of a type of fish to introduce into the pond, you’ll have to design everything about it, from molecules to gills. “Trial and error will save the day!” you say? “Once life gets going as a single-cell organism, chance and natural selection will succeed where human intelligence falls short.” Ah, yes. That makes sense.
Notes
“Understanding Working Rangelands — Cattle, Sheep, Goats, and Horses: What’s the Difference for Working Rangelands?” Univ. of California, Agriculture and Natural Resources, publ. 8524 (July, 2015).
https://www.nationalgeographic.com/animals/fish .
Jon Lapidese, “Baleen Whales — The Gentle Giants of the Ocean,” https://oceanwide-expeditions.com/blog/baleen-whales-the-gentle-giants-of-the-ocean
https://www.adirondackcouncil.org/page/blog-139/news/10-facts-about-hummingbirds–and-other-interesting-tidbits-1101.html .
How many birds are there in the world? | National Geographic .
Marcos Eberlin, Foresight: How the Chemistry of Life Reveals Planning and Purpose, https://www.discovery.org/store/product/foresight/ .
“How Many Fish Live in the Ocean?” WorldAtlas.
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