Yellow Tomato Mystery Solved [Romans 8:22]

 As Paul says: For we know that the whole creation groaneth and travaileth in pain together until now. Romans 8:22

Even tomato coloring which impacts nutritional value. Interesting how interconnected all these genetic pathways and mechanisms are....like a DESIGNED system breaking down, as if it "groaneth".

The Yellow ones are still nutritional....just not as much as the red ones.

"Researchers have discovered that a single genetic change in the YFT3 gene disrupts a vital enzyme involved in producing carotenoids, the pigments responsible for tomato coloration. The gene encodes the isopentenyl diphosphate isomerase enzyme, which maintains the delicate balance between IPP and DMAPP, two

essential C5 molecules in isoprenoid synthesis.

When one amino acid (Serine) is replaced by another (Arginine) at position 126, this balance is thrown off, weakening enzyme performance, hindering chromoplast formation, and drastically reducing lycopene, the red pigment that gives tomatoes their color. The findings uncover a key molecular mechanism behind tomato pigmentation and pinpoint Ser126 as a critical site for enzyme function, suggesting new possibilities for enhancing fruit quality through genetic approaches.

The color of a tomato depends heavily on the buildup of carotenoids, natural pigments that support both 

--plant reproduction 

--and human health. 

These pigments form through the isoprenoid pathway, which relies on the precise conversion between two molecular building blocks, isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). This conversion is carried out by the enzyme IDI1, ensuring a steady flow of metabolites for pigment production.

When this process is disrupted, it can alter chromoplast development and pigment levels, changing both 

--the fruit’s color 

--and its nutritional value. 

Although scientists have made great progress in decoding carotenoid biosynthesis, the specific amino acids that govern IDI1’s activity have been difficult to identify, prompting a closer look at how YFT3 contributes to this essential pathway.

Identification of the YFT3 Mutation

A research team from Shanghai Jiao Tong University has identified a

single-point mutation in the YFT3 gene responsible for yellow fruit coloration in tomatoes. Their findings, published in the journal Horticulture Research, reveal that the mutation disrupts a critical enzyme in the isoprenoid pathway, impairing carotenoid accumulation. 

Through map-based cloning, molecular assays, and in vivo functional analyses, the team demonstrated that a Ser126Arg substitution in YFT3 undermines its enzymatic activity, providing new insight into the molecular control of fruit pigmentation.

The researchers discovered that the yellow-fruited tomato mutant (yft3) carries a recessive allele of YFT3, encoding a mutated version of SlIDI1, a plastid-localized isomerase responsible for converting IPP to DMAPP. 

The mutation—an A→C transversion at nucleotide 2117—leads to a Ser126Arg substitution. 

Despite unchanged protein levels and plastid localization, enzymatic activity was drastically reduced.

Functional complementation restored red color, while knockout lines mimicked the yellow phenotype, confirming YFT3’s essential role.

Molecular and Structural Insights

Detailed expression analyses showed upregulation of carotenoid

pathway genes (DXS, DXR, HDR, PSY1, CRTISO, CYCB, CYP97A, NCED) in yft3 and CRISPR knockout lines. However, biochemical assays revealed severely reduced lycopene and total carotenoid levels, indicating that the gene upregulation could not compensate for enzymatic deficiency. 

Molecular docking revealed that the Ser126 mutation alters the active site conformation, impairs Mg²⁺ cofactor binding, and diminishes catalytic efficiency. These findings suggest Ser126 is critical for the correct positioning and function of substrate-enzyme interactions in carotenoid biosynthesis. Moreover, the impaired chromoplast ultrastructure in yft3 and YFT3-KO lines further underscores YFT3‘s role in fruit color development and quality.

This discovery holds significant potential for agricultural biotechnology and breeding programs. Understanding the role of YFT3 in regulating the isoprenoid pathway offers breeders a precise genetic handle to enhance fruit pigmentation and carotenoid content—key traits for market appeal and nutrition." 

SciTechDaily

Valley of Fire

 ...because of the waters of the flood. Genesis 7:7

"Valley of Fire is located 50 miles northeast of Las Vegas.
The name Valley of Fire comes from the red sandstone formations in the valley, called the Aztec Sandstone, which often appear to be on fire beneath the rays of the sun.
Consulting the reinterpretation chart of figure 2 we can see that a

“uniformitarian age” of 150 million years is somewhere around the Jurassic. Alongside this age the green arrow indicates it is towards
the top of “Floodwaters rising”.
In other words, the sandstone was deposited during Noah’s Flood some 4,500 years ago as the floodwaters were rising and as they were nearing their peak. On this diagram, notice the blue arrow, which indicates that after the Cretaceous the floodwaters were falling. 

Also notice that there is some overlap on the arrows to indicate that the exact location (e.g. between rising and falling) can vary depending on the area we are considering.

Long-age geologists will automatically assume that these beds were deposited by wind, rather than by water, because it would take a flood of Biblical proportions to deposit such huge dunes from water.

However, this is no problem for a Biblical interpretation because we would expect to see lots of evidence of large-scale watery catastrophe.
And that is what we see.

The enormous beds of sandstone were deposited by great volumes of

flowing floodwaters. 

The Wikipedia article on the Valley of Fire reports that other important rock formations in the area include limestones, shales, and conglomerates (composed of large rocks). 

All these were deposited as the waters of Noah’s Flood were rising."
CMI

Time Crystals Found at the Quantum Level

"From the orderly orbit of the planets to the finely tuned rhythm of our own internal circadian cycles, centuries of discoveries have confirmed that the universe operates within a framework of orderly and time-bound precision. 

--While these systems have long been a source of wonder, new discoveries suggest that timely order is not confined to macro-scale interactions; rather, even nano-scale subatomic particles exhibit intrinsic, orderly and rhythmic oscillations, suggesting that temporal structure is an embedded feature within matter itself.

In a momentous breakthrough published in Physical Review Letters

(September 2025), researchers Ruso and Pohl at TU Wien University uncovered that orderly patterns of particle movement exist at the quantum level. These “time crystals” oscillate without being acted upon by any known external driver, but “self-organize” in rhythmic behavior, based on physical correlations between the particles themselves.

The discovery of these “time crystals” defies previous assumptions that quantum behavior is chaotic with random noise. These observations therefore open significant questions on interpretations of order, origins, and design.

The Evolutionary View of Time and Rhythm

In evolutionary frameworks (whether cosmological, physical, or

biological) time and rhythm are viewed as emergent properties, not fundamental features of the universe. Time is treated as only one dimension of a matter and space continuum that began with the Big Bang, unfolding as the universe expanded.
While the second law of thermodynamics introduced the concept of the “arrow of time” (systems naturally evolving from order to disorder), evolutionary models propose that order arises temporarily and locally, being directed from energy gradients and environmental conditions that allow systems to self-organize. In an evolutionary framework therefore, rhythm is not embedded in matter itself but emerges from repeating interactions shaped by environmental conditions.

Despite this prevailing view, the discovery of time crystals contrasts with the evolutionary perspective. In quantum time crystals, rhythmic order arises internally without external drivers, challenging the assumption that time-based structure must be externally imposed.

Design in the Deepest Realms: 

A Contrast with Evolutionary Theory

While describing the phenomenon of time crystals, the authors unintentionally expose various philosophical and scientific implications relevant to questions of origins and design.
For instance, in attempting to explain their findings, the authors stated that:

“…the emergence of a continuous time-crystal (CTC) phase in this setting is directly connected to the physics of dissipative quantum systems…”

While the authors describe the link between the “physics ofdissipative quantum systems” and the behaviors of time crystals, there remains a vagueness about the root cause of such “emergence”. While the authors use the term “emergence” to describe how complex order arises, the use of this term often bypasses the discussion of processes that would sufficiently explain the origin of this process.

*As time crystals challenge the assumption that quantum systems begin in static or equilibrium states, it may suggest that rhythmic, correlated motion could be embedded from the outset, even in the early universe. However, a cosmological evolutionary framework provides inadequate explanatory power as to why particles should be predisposed to organize themselves.

Notwithstanding, this research shows that quantum systems defy randomness and produce coherence – a coherence that is not imposed from outside but arises from within the system.

Another major marker of design that has been revealed through this study is that the behavior of these time crystals is extremely nuanced – not being accounted for by merely averaging the field effects. In the words of the authors:

“We identify a second type of qCTC that is not predicted by mean-field theory but instead is driven by correlations.” …Remarkably, one of them emerges only in the presence of correlations, upon accounting for beyond-mean-field effects… The found qCTC phases do not rely on symmetries of the underlying master equation and are robust to perturbations, both of which are essential aspects for potential experiments.”

As its name implies, “mean-field theory” approximates each system’s component via the average influence of its constituents—thereby erasing the subtle interactions that drive complex behavior. Standard cosmological perturbation theory treats fluctuations linearly, akin to mean-field approximations that neglect correlations. However, as the authors note, “two distinct time-crystal phases … cannot be described within mean-field theory”. This failure signals greater complexity than standard quantum physics models account for: as something essential is lost when one merely relies on the single mean-field figure.

The simulations in this paper reveal that one of these two phases “emerges only in the presence of correlations, upon accounting for beyond-mean-field effects”. This implies that particle behavior is not randomly homogenous, estimable by isolated averages but is linked in a finely tuned network. Ignoring any connection would produce inaccurate estimations for the oscillations as each link plays a critical role. The emergence of a qCTC phase driven by correlations underscores that higher-order interactions can qualitatively change outcomes. The further finding that these phases are “robust to perturbations” may suggest an in-built resilience.

These discoveries in time crystals are yet one more example of modern science pointing us away from the concept of randomness and disorder, and toward the notion of design. 

--Interestingly, these discoveries at the fine quantum scale, uncovers depth to the Scripture that declares “To everything there is a season, and a time to every purpose under the heaven.” (Ecclesiastes 3:1). Scripture has remained resonant with scientific observations, affirming that time is not random, rather, it is purposeful and governed by divine wisdom.

Rather than undermining faith, discoveries like time crystals deepen the case for intelligent design, as they reveal a universe where order is intrinsic. As Job was reminded, “Do you know the laws of the heavens? Can you set up God’s dominion over the earth?” (Job 38:33)." 

CEH/Dr. Sarah Buckland-Reynolds

Rapid Radiations

 And God made the beast of the earth after his kind, and cattle after their kind, and every thing that creepeth upon the earth after his kind: and God saw that it was good. Genesis 1:25

"In the most extensive published examination of animal and plant diversification rates to date, Dr John J. Wiens, professor at the University of Arizona, and Dr Daniel Moen, an assistant professor at the University of California Riverside found that “the majority of earth’s species stem from a few evolutionary explosions”. The study published in the journal Frontiers in Ecology and Evolution examined a taxonomic scope of over 2,000,000 species, from 2,545 families and 17 kingdoms, including over 300,000 species of plants, a million species of insects, over 66,000 species of vertebrates and 1.5 million invertebrates.

Using a “nearly complete” sample comprising of an estimated ~70% of known species (~67% animals, and ~78% vertebrates), the researchers found that “…among the major clades of living organisms and among land plant phyla and animal phyla, >80% of known species richness is contained within the few clades in the upper 90th percentile for diversification rates in each group.” These striking findings led the researchers to the following conclusion: 

“…these results show for the first time that most of the known species’ richness of life is explained by rapid radiations.”

Q:What do these ‘rapid radiations’ mean for evolutionary theory?
A: The Significance of Rapid Radiations: An Affront to Gradualism
Uniformitarian assumptions influence the interpretation of almost all data in the realm of both biological and geological evolution. This long-held interpretation of slow, incremental and continuous change over millions of years, driven by random mutation and natural selection, was made famous by Charles Darwin himself. When Darwin wrote his seminal ‘On the Origin of Species’, he specifically regarded gradualism as a cornerstone of his theory. 

In his words:
“As natural selection acts solely by accumulating slight, successive, favorable variations, it can produce no great or sudden

modifications; it can only act by very short and slow steps.” — Charles Darwin, The Origin of Species (1859)
And again, he wrote:
“If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”

***From these quotes, it is evident that Darwin sets a clear testable boundary for his theory: if gradualism fails to explain complexity, then natural selection collapses. This underscores how foundational gradualism was to his evolutionary framework.

However, rapid radiation theory suggests the opposite–that most species emerged in short bursts, not through gradual steady accumulation. If true, this directly undermines uniformitarian assumptions and raises further key questions about the plausibility of theorized evolutionary mechanisms to explain these observations. For instance: 

Q: Why do most species belong to a few clades, and why are such rapid speciation events said to be ‘rare’ yet dominant?

Intelligent Design theory presents a predictive contrast, as rapid radiation aligns more naturally with the idea of front-loaded potential or purposeful diversification. 

*If life was designed with an embedded capacity to adapt and flourish in new environments, then bursts of speciation would reflect activation of latent, in-built design, not random chance.

Retention of Evolutionary Assumptions…

While Invoking Miraculous Thinking!

Although the authors acknowledge rapid speciation, they retain an evolutionary framework in their core assumptions throughout the paper. For example, the article repeatedly invokes the alleged antiquity of species—hundreds of millions of years old—in at least three separate instances.
Another example is found in the commentary of the same article on ScienceDaily, where the researchers stated:
“’Rapid radiations’ of species are thought to occur when a new ecological niche opens up: for example, when a flock of grassquit birds dispersed from Central America to the virgin territory of the Galápagos Islands approximately 2.5 million years ago to diversify into the famous Darwin’s finches; or when an evolutionary innovation like powered flight prompted the radiation of bats 50 million years ago.”
Let’s deconstruct this reasoning: While on the one hand, the authors find that short bursts of speciation fully account for the vast majority of known species, on the other hand, they appeal to evolutionary processes and timelines as somehow (miraculously) explaining the origins of massive engineering wonders such as flight in bats!

Q: Who Is the Innovator?
Inserting the word ‘innovation’ is quite telling, as it implicitly admits an attribution of evolution as an ‘innovator’! 

Humans require intelligent minds simply to copy these inventions into our own technologies, for the engineering of flight involves significant irreducible complexity—the interdependence of numerous systems, without which functionality would collapse. 

Humans require intelligent minds to merely copy these inventions into our own technologies, as the engineering of flight ability entails significant irreducible complexity – the interdependence of numerous systems, without which, functionality would fail.
Q: Is it not a conundrum then to attribute such innovative power to the blind force of evolution, which depends on the ‘selection’ of random mutations to somehow work together to invent powered flight? The appeal to Darwinism offers no real explanatory power for these observations.

Philosophical Implications

Wein and Moen’s study once again reinforces findings that challenge

the validity of uniformitarian assumptions. The revelation that most of Earth’s species stem from a handful of explosions invites us to reconsider the oft propagated story about life’s gradual unfolding. If biodiversity arises not through slow, steady change but through explosive bursts triggered by pivotal traits or ecological upheavals, then evolutionary theory must confront its own inherent contradictions. 

Q: Would this mounting evidence against gradualism—the very test Darwin sought to falsify his theory—cause it to ‘absolutely break down,’ in his own words?" 

CEH/Dr. Sarah Buckland-Reynolds

Helium in Radioactive Rocks

 In the beginning God created.... Genesis 1:1

"During the radioactive decay of uranium and thorium contained in rocks, lots of helium is produced. Because helium is the second lightest element and a noble gas—meaning it does not combine with other atoms—it readily diffuses (leaks) out and eventually escapes into the atmosphere. 

Helium diffuses so rapidly that all the helium should have leaked out in less than 100,000 years. 

Q: So why are these rocks still full of helium atoms?

While drilling deep Precambrian (pre-Flood) granitic rocks in New Mexico, geologists extracted samples of zircon (zirconium silicate) crystals from different depths. The crystals contained not only uranium but also large amounts of helium. 

The hotter the rocks, the faster the helium should escape, so researchers were surprised to find that the deepest, and therefore hottest, zircons (at 387°F or 197°C) contained far more helium than expected. Up to 58% of the helium that the uranium could have ever generated was still present in the crystals.

The helium leakage rate has been determined in several experiments. All measurements are in agreement. Helium diffuses so rapidly that all the helium in these zircon crystals should have leaked out in less than 100,000 years. 

---The fact that so much helium is still there means they cannot be 1.5 billion years old, as uranium-lead dating suggests. Indeed, using the measured rate of helium diffusion, these pre-Flood rocks have an average “diffusion age” of only 6,000 (± 2,000) years.

These experimentally determined and repeatable results, based on the well-understood physical process of diffusion, thus emphatically demonstrate that these zircons are only a few thousand years old. The supposed 1.5-billion-year age is based on the unverifiable assumptions of radioisotope dating that are radically wrong.

Another evidence of a young earth is the low amount of helium in the atmosphere. The leakage rate of helium gas into the atmosphere has

been measured. Even though some helium escapes into outer space, the amount still present is not nearly enough if the earth is over 4.5 billion years old. In fact, if we assume no helium was in the original atmosphere, all the helium would have accumulated in only 1.8 million years even from an evolutionary standpoint. But when the catastrophic Flood upheaval is factored in, which rapidly released huge amounts of helium into the atmosphere, it could have accumulated in only 6,000 years.

***So glaring and devastating is the surprisingly large amount of helium that old-earth advocates have attempted to discredit this evidence.
One critic suggested the helium didn’t all come from uranium decay in the zircon crystals but that a lot diffused into them from the surrounding minerals. But this proposal ignores measurements showing that less helium gas is in the surrounding minerals. Due to the well-established diffusion law of physics, gases always diffuse from areas of higher concentration to surrounding areas of lower concentration.

Another critic suggested the edges of the zircon crystals must have stopped the helium from leaking out, effectively “bottling” the helium within the zircons. 

However, this postulation has also been easily refuted because the zircon crystals are wedged between flat mica sheets, not wrapped in them, so that helium could easily flow between the sheets unrestricted. All other critics have been answered. Thus all available evidence confirms that the true age of these zircons and their host granitic rock is only 6,000 (± 2,000) years." 

AIG

The Tonto Group

And it came to pass after seven days, that the waters of the flood were upon the earth. Genesis 7:10

"......about new research on the Grand Canyon.
The new research looked at the Tonto Group, a 500-meter-thick formation, containing the Tapeats sandstone, Bright Angel Shale, and Muav Limestone (as well as two other minor) strata, that is conventionally assigned to the Cambrian layer (this represents the initial stages of the global flood). 

While evolutionists believe it to be 540 million years old, listen to

how they interpret this area based on their studies at Grand Canyon and other places:

“The Tonto Group holds a treasure trove of sedimentary layers and fossils chronicling the Cambrian Explosion some 540 million years ago, when the first vertebrates and animals with hard shells rapidly proliferated and sea levels rose to envelop continents with emerging marine life.”

“From the Tonto Group’s 500-meter-thick strata, we’re learning about sea-level rise and the effects of catastrophic tropical storms – probably more powerful than today’s devastating hurricanes – during a period of very hot temperatures when the Earth was ice-free.”
“Sea levels were so high during this time period, Dehler says, that rocks like the Tonto Group were deposited atop every continent on Earth, as seas bathed the continents in a complex mosaic of shallow marine, coastal, and terrestrial environments.”

--Sea levels rose all around the world, 

--bathing the continents 

--and depositing vast rock layers that stretch across continents. 

That’s all coming from evolutionary scientists—but it almost sounds like they’re describing the initial stages of the global flood as waters began to rise and sea creatures were rapidly buried by these rising floodwaters." 

AIG

Exodus 20:11 an insurmountable stone wall to Long Age Chronology

For in six days the Lord made heaven and earth, the sea, and all that is in them, and rested on the seventh day. Therefore the Lord blessed the Sabbath day and made it holy. Exodus 20:11

"Exodus 20:11 -- this verse is critical to the question of the age of

the creation. 

It stands as an insurmountable stone wall to block every attempt to add millions of years anywhere into the Bible. 

Therefore, to be faithful to Scripture, Christians must reject the “big bang” theory and the billions of years of cosmological and geological history as myths.
Exodus 20:11 is very important because it is God’s Word in a special way: it was not written through Moses but rather directly on tablets of stone by God Himself." 

AIG

Soft Tissue in Dinosaurs [PROVES Not Millions of Years Old]

And all flesh died that moved upon the earth,

 both of fowl, and of cattle, and of beast, 

and of every creeping thing that creepeth upon the earth,

and every man:

Genesis 7:21

"Ask the average layperson how he knows that the earth is millions or billions of years old, and that person will probably mention the dinosaurs, which nearly everybody “knows” died off 65 million years ago.
--A recent discovery by Dr. Mary Schweitzer, however, has given reason for all but committed evolutionists to question this assumption.
Bone slices from the fossilized thigh bone (femur) of a

Tyrannosaurus rex found in the Hell Creek formation of Montana were studied under the microscope by Schweitzer. 

To her amazement, the bone showed what appeared to be blood vessels of the type seen in bone and marrow, and these contained what appeared to be red blood cells with nuclei, typical of reptiles and birds (but not mammals). 

The vessels even appeared to be lined with specialized endothelial cells found in all blood vessels.
Amazingly, the bone marrow contained what appeared to be flexible tissue. 

Initially, some skeptical scientists suggested that bacterial biofilms (dead bacteria aggregated in a slime) formed what only appear to be blood vessels and bone cells. Schweitzer and coworkers found biochemical evidence for intact fragments of the protein collagen, which is the building block of connective tissue. 

This is important because collagen is a highly distinctive protein not made by bacteria. (See Schweitzer’s review article in Scientific American [December 2010, pp. 62–69] titled “Blood from Stone.”)
Q: Is it even remotely plausible that blood vessels, cells, and protein fragments can exist largely intact over 68 million years?

While many consider such long-term preservation of tissue and cells to be very unlikely, the problem is that no human or animal remains are known with certainty to be 68 million years old.
But if creationists are right, dinosaurs died off only 3,000–4,000 years ago.
Q: So would we expect the preservation of vessels, cells, and complex molecules of the type that Schweitzer reports for biological tissues historically known to be 3,000–4,000 years old?
A: The answer is yes.
--Many studies of Egyptian mummies and other humans of this old age (confirmed by historical evidence) show all the sorts of detail Schweitzer reported in her T. rex.
--In addition to Egyptian mummies, the Tyrolean iceman, found in the Alps in 1991 and believed to be about 5,000 years old, shows such incredible preservation of DNA and other microscopic detail.
*We conclude that the preservation of vessels, cells, and complex molecules in dinosaurs is entirely consistent with a young-earth creationist perspective but is highly implausible with the evolutionist’s perspective about dinosaurs that died off millions of years ago."
AIG

Hox genes = DESIGNER

For by Him were all things created.... Colossians 1:16

"Hox genes are clusters of “master switches” in the genome that act like body-plan architects.
Each gene produces a protein that turns other genes on or off, telling

cells where they are along the head-to-tail axis.
Strikingly, the order of Hox genes on the chromosome matches the order of the body parts they control — a phenomenon called colinearity.
In mammals there are four clusters (Hox A–D), conserved across animals from flies to humans.
Even small shifts in their regulation can make the difference between a fin, a limb, or a digit."
CEH