IDvolution.org

Exploring a massive supercomplex in mitochondria comprising all four respiratory complexes

In the beginning was the Word: the Word was with God and the Word was God.

Information is prime… IDvolution - God “breathed” the super language of DNA into the “kinds” in the creative act.

“Information is information, neither energy nor matter. Any materialism that fails to take account of this will not survive one day.” – Norbert Weiner, MIT Mathematician and Founder of Cybernetics

More evidence for IDvolution.

Sweeping gene survey reveals new facets of evolution

It is textbook biology, for example, that species with large, far-flung populations—think ants, rats, humans—will become more genetically diverse over time.
But is that true?
"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.
For the planet's 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity "is about the same," he told AFP.
The study's most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.
"This conclusion is very surprising, and I fought against it as hard as I could," Thaler told AFP.

Read more at: https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html#jCp

It is textbook biology, for example, that species with large, far-flung populations—think ants, rats, humans—will become more genetically diverse over time.

But is that true?

"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.

For the planet's 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity "is about the same," he told AFP.

The study's most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.

"This conclusion is very surprising, and I fought against it as hard as I could," Thaler told AFP.

It is textbook biology, for example, that species with large, far-flung populations—think ants, rats, humans—will become more genetically diverse over time.
But is that true?
"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.

Read more at: https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html#jCp

It is textbook biology, for example, that species with large, far-flung populations—think ants, rats, humans—will become more genetically diverse over time.
But is that true?
"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.
For the planet's 7.6 billion people, 500 million house sparrows, or 100,000 sandpipers, genetic diversity "is about the same," he told AFP.
The study's most startling result, perhaps, is that nine out of 10 species on Earth today, including humans, came into being 100,000 to 200,000 years ago.
"This conclusion is very surprising, and I fought against it as hard as I could," Thaler told AFP.

Read more at: https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html#jCp

It is textbook biology, for example, that species with large, far-flung populations—think ants, rats, humans—will become more genetically diverse over time.
But is that true?
"The answer is no," said Stoeckle, lead author of the study, published in the journal Human Evolution.

Read more at: https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html#jCp

“another unexpected finding from the study—species have very clear genetic boundaries, and there’s nothing much in between."

“If individuals are stars, then species are galaxies,” said Thaler. “They are compact clusters in the vastness of empty sequence space.”

The absence of “in-between” species is something that also perplexed Darwin, he said."

Read more at: https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html#jCp

"If individuals are stars, then species are galaxies," said Thaler. "They are compact clusters in the vastness of empty sequence space."
The absence of "in-between" species is something that also perplexed Darwin, he said.

Read more at: https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html#jCp

Sweeping gene survey reveals new facets of evolution

The Latest from Ann Gauger and Doug Axe

Ann Gauger on the Limits of Evolutionary Optimization

They discuss trying to get to shapes with meaning. Can a scribble on a page mutate to a han character with meaning? (protein folds)

“mutations and natural selection have limits and they can’t innovate anything unless the function they are innovating is already present… you already have to have the designed feature there in order to get it to improve… you cannot improve a pigment cell to an eye unless you already have something like an eye there.”

Paper

Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention–Selection Itself Is Not Inventive

Abstract

Since biological inventions only benefit their possessors after they work, their origins cannot be attributed to their selective effects. One proposed solution to this conundrum is that selection perfects activities that already existed in rudimentary form before they became beneficial. An example of this idea for protein origins is the promiscuity hypothesis, which claims that minor aberrant side-reactions in enzymes can be evolutionary starting points for proficient new enzymes. Another example—the junk hypothesis—claims that proteins arising from accidental expression of non-genic DNA may likewise have slight activities that, through evolutionary optimization, lead to proficient enzymes. Here, we tested these proposals by observing how the endpoint of simple evolutionary optimization depends on the starting point. Beginning with optimization of protein-like constructs in the Stylus computational model, we compared promiscuous and junk starting points, where design elements specific to the test function were completely absent, to a starting point that retained most elements of a good design (mutation having disrupted some). In all three cases, evolutionary optimization improved activities by a large factor. The extreme weakness of the original activities, however, meant even large improvements could be inconsequential. Indeed, the endpoint was itself a proficient design only in the case where this design was largely present from the outset. Laboratory optimization of ampicillin-resistance proteins derived from a natural beta lactamase produced similar results. Our junk protein here was a deletion mutant that somehow confers weak resistance without the original catalytic mechanism (much of the active site having been lost). Evolutionary optimization was unable to improve that mutant. In contrast, a comparably weak mutant that retained the active site surpassed the natural beta lactamase after six rounds of selection. So, while mutation and selection can improve the proficiency of good designs through small structural adjustments, they seem unable to convert fortuitous selectable activities into good designs. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2015.2

Over and over we are finding repair mechanisms that fight mutations and copying errors. Complex language that has meaning forward, backward and with layering. Where is the evidence leading?

Life is super complex and has purpose. The information to direct it came from a mind.
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New class of DNA repair enzyme discovered October 29, 2015

A new class of DNA repair enzyme has been discovered which demonstrates that a much broader range of damage can be removed from the double helix in ways that biologists did not think were possible.

According to the researchers, the AlkD mechanism has some remarkable properties:

It can recognize damaged bases indirectly. AlkD identifies lesions by interacting with the DNA backbone without contacting the damaged base itself.
It can repair many different types of lesions as long as they are positively charged. By contrast, the base-flipping mechanism used by other glycosylases relies on a relatively tight binding pocket in the enzyme, so each glycosylase is designed to work with a limited number of lesions. AlkD doesn't have the same type of pocket so it isn't restricted in the same way. Instead, the catalytic mechanism that AlkD uses is limited to removing positively charged lesions.
It can excise much bulkier lesions than other glycosylases. Base excision repair is generally limited to relatively small lesions. A different pathway, called nucleotide excision repair, handles larger lesions like those caused by UV radiation damage. However, Eichman's team discovered that AlkD could excise extremely bulky lesions, such as the one caused by the antibiotic yatakemycin, which is beyond the capability of other glycosylases.

Front Loading? Genetic Entropy? Complexity to simplicity?

Phys.org)—The view that animals have become more complex over time could be a thing of the past, according to the latest research.

The new evidence, from scientists at the University of St Andrews, suggests that some modern day animals may have evolved instead by becoming less complex.

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Our Fragile Intellect

"Taken together, the large number of genes required for intellectual and emotional function, and the unique susceptibility of these genes to loss of heterozygosity, lead me to conclude that we, as a species, are surprisingly intellectually fragile and perhaps reached a peak 2000–6000 years ago. But if we are losing our intellectual abilities, how did we acquire them in the first place? This will be the topic of the next section [15]. "

You do the math.........

"The genome... is best described as a database used by organisms to generate the functions that you and I and others study as physiology."

"We inherit much more than DNA"

"The number of possible interactions , the number of possible circuits you could form 25,000 genes is 10^70,000. There wouldn't be enough time over the whole billions of years of the evolution of life on earth for nature to have explored but more than a tiny fraction of those."

On Dawkins and the selfish gene - "He is totally confused." "He has misused a metaphor" "He [Dawkins] is philosophically naive and I am afraid he has misled many people for a very considerable period of time." 40 minutes in

"There are no good or bad genes"

"There are reasons those genes are there"

"The great majority of people we are talking to were educated in biology 30 or 40 years ago and they really have no idea of the sea change that has occurred."

"the house of cards, the citadel if you like is empty, but many people still do not know that." 54 min

(more in comments below...)

“This book is groundbreaking in synthesizing the latest science. No other single book brings it all together so well.

Evolution 2.0 Breaking the Deadlock between Darwin and Design is a must read to those interested in the current state of the supposed conflict between faith and reason. It shows that where they intersect they are not in opposition.

Evolution 2.0 is the future. Beautifully written and engaging it is useful for the person who is eager to learn more and take the journey with Perry. It will especially appeal to engineers who design everyday and recognize it in the language of DNA and the sophistication of life. The Grand Design of life is fully appreciated on page after page.

In a prior post Genetic Piano Perhaps someone was listening........ A while ago I posted on the idea that we should look at genes like keys on a piano. The number of tunes that can be cranked out is astounding. Sometimes a single key is played or in combinations. Some are rarely played but still can produce beautiful music. Now someone else has picked up on this idea. More support for IDvolution.

Now from Nature:

Epigenome: The symphony in your cells

A slew of papers reveals the chemical tweaks to DNA in a wealth of different cells — as explained with the help of a small orchestra.

"Based on simple mathematical models, we think it may have happened suddenly, analogously to a heated gas abruptly bursting into flame."

IDvolution - God “breathed” the super language of DNA into the “kinds” in the creative act.

Paul Davies on the Origin of Life as an Information Problem

The Guardian features an interesting article by Paul Davies: “The secret of life won’t be cooked up in a chemistry lab: Life’s origins may only be explained through a study of its unique management of information.” Davies writes,

"If we cast the problem of life's origin in computer jargon, attempts at chemical synthesis focus exclusively on the hardware – the chemical substrate of life – but ignore the software – the informational aspect. To explain how life began we need to understand how its unique management of information came about.

To take a simple example; whether a cell expresses a gene can depend on mechanical stresses or electric fields acting on the whole cell by its environment. Thus, a change in global information (a pattern of force) at the macroscopic level translates into a change in local information movement at the microscopic level (switching on a gene). More generally, a range of signals received from its environment help to dictate how a cell's DNA is distributed and transcribed. Walker and I propose that the key transition on the road to life occurred when top-down information flow first predominated. Based on simple mathematical models, we think it may have happened suddenly, analogously to a heated gas abruptly bursting into flame"

Past 5,000 years prolific for changes to human genome

A study published today in Nature³ now helps to clarify when many of those rare variants arose. Researchers used deep sequencing to locate and date more than one million single-nucleotide variants — locations where a single letter of the DNA sequence is different from other individuals — in the genomes of 6,500 African and European Americans. The findings confirm their earlier work suggesting that the majority of variants, including potentially harmful ones, were picked up during the past 5,000–10,000 years. Researchers also saw the genetic stamp of the diverging migratory history of the two groups.

Slowly but surely we are finding life is more complex than we ever thought. From the review: Darwinism and Materialism: They Sink or Swim Together He quotes the information theorist Henry Quastler who stated that “the creation of information is habitually associated with conscious activity.”

"Will Stephen Meyer’s Darwin’s Doubt be “the most despised science book” of 2013?"

"Recently the Discovery Institute’s Stephen Meyer published Darwin’s Doubt, a book that raises many questions about the theory of evolution. As his title tells us, Darwin himself shared one of these doubts. The book has sold well, reaching #7 on the New York Times bestseller list, #4 on the Los Angeles Times list, and #10 on Publishers Weekly." “Darwin said that speciation occurred too slowly for us to see it. Gould and Eldredge said it occurred too quickly for us to see it. Either way we don’t see it.”

"Organisms are intelligently designed, says Meyer, who has a PhD from Cambridge University in the philosophy of science. His book is an education, demanding attentive reading but no specialized knowledge. To a large extent it uses the facts and arguments of professional biologists, some bordering on open dissent from the orthodoxy."

So we see more support for IDvolution - God “breathed” the super language of DNA into the “kinds” in the creative act.

This is a video worth watching. The Q an A is also interesting. The tide is turning....

More support for IDvolution - God “breathed” the super language of DNA into the “kinds” in the creative act.

"the displacement problem - where every attempt to explain the origin of information absent an intelligent agent either fails or it surreptitiously smuggles in the effect of intelligent agency...."

... "a byproduct of this artificial restriction on reasoning that excludes the reality of something of which we all know, which is mind, agency has certain causal powers that nature itself by itself does not have and when we encounter effects that we know only agents can produce it is rational to infer the activity of agency not to exclude it on principle and say well we must be scientific"

'Intelligent Design: The Most Credible Idea?' A Lecture by Dr Stephen C Meyer

This paper shows that some "mutations" are designed changes directed by cellular machinery.

Genomic "tuning knobs" with implicit range are strategies for organisms to change and adapt as needed. We know about fine tuning in the universe, now we see it in life.

Remember the Genetic Piano post (here)? Which keys are chosen to play? What decides?

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and

How Bees Decide What to Be: Reversible 'Epigenetic' Marks Linked to Behavior Patterns

and

Harvard cracks DNA storage, crams 700 terabytes of data into a single gram -Must see.....

and

Is There Enough Time For Humans to have Evolved from Apes? Dr. Ann Gauger

For some time I have been claiming that epigenetic inheritance is a problem for evolution. Here we have Science Daily agreeing.This rapid ability to produce variation is in agreement with IDvolution.

From the article: "The results suggest that domestication has led to epigenetic changes. For more than 70 % of the genes, domesticated chickens retained a higher degree of methylation. Since methylation is a much faster process than random mutations, and may occur as a result of stress and other experiences, this may explain how variation within a species can increase so dramatically in just a short time."

Inherited Epigenetics Produced Record Fast Evolution

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens

Professor Walton takes us through the chemistry and shows us the RNA world scenario is impossible. Life was complex at the earliest times.

The Origin of Life

Conclusions:

Statistically, the chance of forming even one “useful” RNA sequence can be shown to be essentially zero in the lifetime of the earth.
The complexity of the first self-replicating system, and the information needed to build it, imply intelligent design.
Hope of beating the colossal odds against random formation of replicating RNA is based on ideology rather than science.
As lab experiments on model replicators become more complex they demonstrate the need for input from intelligent mind(s).
Acceptance of an early earth atmosphere free of oxygen atoms strains belief beyond breaking point!
No chemically or geologically plausible routes to nucleotides or RNA strands have been developed.
Geological field work shows no support for a “prebiotic soup.” It favors little change in the atmosphere over time. Living things have been present since the first crustal rocks.
After over 50 years of sterile origin of life research it is time to give intelligent design a fair hearing.

A video on the inner workings of the cell. See the molecular machinery in action.

The movie "The Central Dogma: From Genomic Information to Protein Synthesis" is made by RIKEN Omics Science Center (RIKEN OSC) for the exhibition titled "Beyond DNA" held at National Science Museum of Japan. We tried to illustrate how molecular machines interact each other in the central dogma by giving "Japanese robot-anime" style representation to the molecules. By using this approach, people (especially kids) can easily distinguish between those molecules and understand how they function in our body.

Perhaps someone was listening........

A while ago I posted on the idea that we should look at genes like keys on a piano. The number of tunes that can be cranked out is astounding. Sometimes a single key is played or in combinations. Some are rarely played but still can produce beautiful music.

Now someone else has picked up on this idea.

More support for IDvolution.

Study gives clue as to how notes are played on the genetic piano

The NOVA U.S. public television program described epigenetics as “The Ghost In Your Genes.” It is the study of changes in gene expression that occur without changes in DNA sequence. Like keys on a piano, DNA is the static blueprint for all the proteins that cells produce. Epigenetic information provides additional dynamic or flexible instructions as to how, where and when the blueprint will be used. “It corresponds to a pianist playing a piece of music,” said Kohzoh Mitsuya, Ph.D., postdoctoral fellow in the School of Medicine at The University of Texas Health Science Center San Antonio.

Why Some Genes Are Silenced: Researchers Find Clue as to How Notes Are Played On the 'Genetic Piano' 'Like keys on a piano, DNA is the static blueprint for all the proteins that cells produce. Epigenetic information provides additional dynamic or flexible instructions as to how, where and when the blueprint will be used. "It corresponds to a pianist playing a piece of music," said Kohzoh Mitsuya, Ph.D., postdoctoral fellow in the School of Medicine at The University of Texas Health Science Center San Antonio.'

Timely peer reviewed paper - more support for IDvolution

Andy McIntosh’s Peer-Reviewed ID Paper–Note the Editor’s Note!

“Information and Entropy—Top-Down or Bottom-Up Development in Living Systems?” International Journal of Design & Nature and Ecodynamics 4(4) (2009): 351-385

Abstract: This paper deals with the fundamental and challenging question of the ultimate origin of genetic information from a thermodynamic perspective. The theory of evolution postulates that random mutations and natural selection can increase genetic information over successive generations. It is often argued from an evolutionary perspective that this does not violate the second law of thermodynamics because it is proposed that the entropy of a non-isolated system could reduce due to energy input from an outside source, especially the sun when considering the earth as a biotic system. By this it is proposed that a particular system can become organised at the expense of an increase in entropy elsewhere. However, whilst this argument works for structures such as snowflakes that are formed by natural forces, it does not work for genetic information because the information system is composed of machinery which requires precise and non-spontaneous raised free energy levels – and crystals like snowflakes have zero free energy as the phase transition occurs. The functional machinery of biological systems such as DNA, RNA and proteins requires that precise, non-spontaneous raised free energies be formed in the molecular bonds which are maintained in a far from equilibrium state. Furthermore, biological structures contain coded instructions which, as is shown in this paper, are not defined by the matter and energy of the molecules carrying this information. Thus, the specified complexity cannot be created by natural forces even in conditions far from equilibrium. The genetic information needed to code for complex structures like proteins actually requires information which organises the natural forces surrounding it and not the other way around – the information is crucially not defined by the material on which it sits. The information system locally requires the free energies of the molecular machinery to be raised in order for the information to be stored. Consequently, the fundamental laws of thermodynamics show that entropy reduction which can occur naturally in non-isolated systems is not a sufficient argument to explain the origin of either biological machinery or genetic information that is inextricably intertwined with it. This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate.

Pages

Saturday, July 22, 2023

Friday, April 29, 2022

Saturday, March 19, 2022

Saturday, May 9, 2020

Friday, August 17, 2018

Sweeping gene survey reveals new facets of evolution

Wednesday, January 13, 2016

Friday, December 18, 2015

You do the math.........

Tuesday, December 15, 2015

Saturday, May 23, 2015

Saturday, February 28, 2015

Tuesday, January 7, 2014

"Based on simple mathematical models, we think it may have happened suddenly, analogously to a heated gas abruptly bursting into flame."

IDvolution - God “breathed” the super language of DNA into the “kinds” in the creative act.

The Guardian features an interesting article by Paul Davies: “The secret of life won’t be cooked up in a chemistry lab: Life’s origins may only be explained through a study of its unique management of information.” Davies writes,

Friday, November 22, 2013

Saturday, September 21, 2013

Saturday, January 5, 2013

'Intelligent Design: The Most Credible Idea?' A Lecture by Dr Stephen C Meyer

Friday, November 23, 2012

Friday, March 2, 2012

Tuesday, January 24, 2012

Tuesday, December 27, 2011

Friday, May 13, 2011

Thursday, January 13, 2011