2018/05/10

Intense breeding has eroded genetic diversity - No evolution observed

Intense breeding has eroded genetic diversity

https://www.cell.com/trends/plant-science/abstract/S1360-1385(17)30089-4

Excerpt: "Broadening crop phenotypic diversity is a key issue facing the challenge of sustainable food security and crop adaptation to ongoing climate changes.

Chromatin marks and epigenetic regulatory mechanisms are essential to the control of plant developmental processes and in shaping plant phenotypic plasticity, including adaptive responses to environmental stresses.

Stability and heritability features of epigenetic marks and knowledge of epigenetic regulatory mechanisms are crucial for breeding applications.

Modeling epigenetic variations requires understanding epigenetic regulatory mechanisms to further predict their impact on plant performances.
 
Modeling epigenetic variations with a process-based approach could help to assess and quantify their impacts on plant performances and then to guide the decision to either induce or repress them. This modeling feedback is central to model-driven breeding strategies.

Crop modelers are urged to take epigenetic variations into account to assist breeding strategies.

Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits."

My comment: Breeding means epigenetic intensification or debilitation of desired traits. Shifting with epigenetic information profiles, in an artificial or adaptational way, results in erosion of genetic information layers. Any change in organisms occurs due to epigenetic regulation of existing biological information OR gradual but inevitable corruption of information. That's why there's no mechanism for evolution. Don't get lost.

2018/05/04

Organisms need genetic rescue because evolution is not happening

Adaptation results in a weakened gene pool - There is no mechanism for evolution

https://www.edge.org/response-detail/27232

Excerpt: "Wildlife populations are most threatened when their numbers become reduced to the point that their genetic diversity is lost. Their narrowing gene pool can accelerate into what is called an “extinction vortex.” With ever fewer gene variants (alleles), the ability to adapt and evolve declines. As inbreeding increases, deleterious genes accumulate, and fitness plummets. The creatures typically have fewer offspring, many of them physically or behaviorally impaired, susceptible to disease, increasingly incapable of thriving. Most people assume they are doomed, but that no longer has to be what happens.

“Genetic rescue” restores genetic diversity. Conservation biologists are warming to its use with growing proof of its effectiveness. One study of 156 cases of genetic rescue showed that 93% had remarkable success. The most famous case was a dramatic turnaround for the nearly extinct Florida panther. By the mid-1990s only 26 were left, and they were in bad shape. In desperation, conservationists brought in 8 female Texas cougars (which are closely related to the Florida cats). Five of the females reproduced. The result of the outcrossing was a rapid increase in litter success—424 panther kittens born in the next 12 years. The previous population decline of 5% a year reversed to population growth of 4% a year. Signs of inbreeding went away, and signs of increasing fitness grew. Scientists noticed, among other things, that the genetically enriched panthers were becoming harder to capture.
 
Often genetic diversity can be restored by means as straightforward as connecting isolated populations with wildlife corridors or larger protected areas, but new technological capabilities are broadening the options for genetic rescue. Advanced reproductive technology offers an alternative to transporting whole genetically-distinct parents—artificial insemination has brought genetic refreshment to cheetahs, pandas, elephants, whooping cranes, and black-footed ferrets. With the cost of genome sequencing and analysis coming down, it is becoming possible to examine each stage of genetic rescue at the gene level instead of having to wait for external traits to show improvement. This has already been done with Rocky Mountain bighorn sheep.

Another strategy being considered is “facilitated adaptation.” Different populations of a species face different local challenges. When a particular population can’t adapt fast enough to keep up with climate change, for example, it may be desirable to import the alleles from a population that has already adapted. With gene editing becoming so efficient (CRISPR etc.), the desired genes could be introduced to the gene pool directly. If necessary, the needed genes could even come from a different species entirely. That is exactly what has been done to save the American chestnut from the fungus blight that killed four billion trees early in the 20th century and reduced the species to functional extinction. Two fungus-resistant genes were added from wheat, and the trees were made blight-proof. They are now gradually in the process of being returned to their keystone role in America’s great eastern forest.

One further reservoir of genetic variability has yet to be employed. In museums throughout the world there are vast collections of specimens of species that have been reduced to genetically-impoverished remnant populations in the wild or in captive breeding programs. Those museum specimens are replete with “extinct alleles” in their preserved (though fragmented) DNA. Ancient-DNA sequencing and analysis is becoming so precise, the needed alleles can be identified, reproduced, and reintroduced to the gene pool of the current population, restoring its original genetic diversity. The long-dead can help rescue the needful living."

My comment: A gene pool of an organism stays about the same or it experiences gradual but inevitable weakening due to adaptation to changing conditions. At molecular biological level, adaptation always occurs due to epigenetic mechanisms and factors and it typically results in alterations in DNA sequence. But as we can see, sequence modifications don't lead to evolution but accumulation of harmful mutations, loss of diversity, loss of functions and genetic degradation. In the future, thousands of species will need genetic rescue, including human populations. It's interesting to see when people realize that evolution is not happening.

https://onlinelibrary.wiley.com/doi/full/10.1111/icad.12235
https://bigcatrescue.org/wp-content/uploads/2014/10/Accumulation-of-Deleterious-Mutations-Due-to-Inbreeding-in-Tiger-Population.pdf
http://grayareathefilm.com/wp-content/uploads/2012/10/HedrickFredrickson-GeneticRescueGuidelines-2010.pdf
https://phys.org/news/2016-03-island-foxes-genetic.html
https://www.smithsonianmag.com/science-nature/threatened-species-science-genetic-rescue-180963040/

2018/05/02

Biological forward-planning and epigenetic memory point to Design

Biological forward-planning and epigenetic memory point to Design

https://www.sciencealert.com/scientists-observe-epigenetic-memories-passed-down-for-14-generations-most-animal

Excerpt: "To study how long the environment can leave a mark on genetic expression, a team led by scientists from the European Molecular Biology Organisation (EMBO) in Spain took genetically engineered nematode worms that carry a transgene for a fluorescent protein. When activated, this gene made the worms glow under ultraviolet light.

Then, they switched things up for the nematodes by changing the temperature of their containers. When the team kept nematodes at 20° Celsius (68° F), they measured low activity of the transgene - which meant the worms hardly glowed at all.

But by moving the worms to a warmer climate of 25° C (77° F), they suddenly lit up like little wormy Christmas trees, which meant the fluorescence gene had become much more active.

Their tropical vacation didn't last long, however. The worms were moved back to cooler temperatures to see what would happen to the activity of the fluorescence gene.

Surprisingly, they continued to glow brightly, suggesting they were retaining an 'environmental memory' of the warmer climate – and that the transgene was still highly active.

Furthermore, that memory was passed onto their offspring for seven brightly-glowing generations, none of whom had experienced the warmer temperatures. The baby worms inherited this epigenetic change through both eggs and sperm.
 
The team pushed the results even further - when they kept five generations of nematodes at 25° C (77° F) and then banished their offspring to colder temperatures, the worms continued to have higher transgene activity for an unprecedented 14 generations.

That's the longest scientists have ever observed the passing-down of an environmentally induced genetic change (My addition: this is an epigenetic change) . Usually, environmental changes to genetic expression only last a few generations.

"We don't know exactly why this happens, but it might be a form of biological forward-planning," said one of the team, Adam Klosin from EMBO and Pompeu Fabra University, Spain.

"Worms are very short-lived, so perhaps they are transmitting memories of past conditions to help their descendants predict what their environment might be like in the future," added co-researcher Tanya Vavouri from the Josep Carreras Leukaemia Research Institute in Spain.

There's a reason why scientists turn to C. elegans as a model organism - after all, those 14 generations would only take roughly 50 days to develop, but can still give us important clues on how environmental genetic change is passed down in other animals, including humans.

There are many examples of this phenomenon in worms and mice, but the study of environmental epigenetic inheritance in humans is a hotly debated topic, and there's still a lot we don't know.

"Inherited effects in humans are difficult to measure due to the long generation times and difficulty with accurate record keeping," stated one recent review of epigenetic inheritance.

But some research suggests that events in our lives can indeed affect the development of our children and perhaps even grandchildren - all without changing the DNA.

For example, studies have shown that both the children and grandchildren of women who survived the Dutch famine of 1944-45 were found to have increased glucose intolerance in adulthood.

Other researchers have found that the descendants of Holocaust survivors have lower levels of the hormone cortisol, which helps your body bounce back after trauma.
The 2017 study on nematodes is an important step towards understanding more about our own epigenetic inheritance - especially because it serves as a remarkable demonstration of how long-lasting these inter-generational effects may be.
"

My comment: The inheritance of acquired characteristics is based on epigenetic memory. The fact that the cell has a memory, a changing state of information it can transfer to its offspring, tells about designed mechanisms. Using memory requires extremely complex information management systems:

- What kind of memory format is to be used?
- What is the mechanism that writes the memory?
- Which mechanism chooses what to write about?
- By which media and mechanism is the memory transferred to offspring?
- What mechanism reads the written memory?
- How will the information written in memory be converted to such a form that it leads to the desired outcome, that is, to the correct gene regulation?

Epigenetic memory is controlled by co-operation of histone epigenetic markers and non-coding RNA molecules (lncRNAs, piRNAs, siRNAs, miRNAs) that transmit the necessary information. 

The memory management system must be ready at once. Such complex information management systems don't evolve. Evolution theory is the most serious heresy of our time.