Humans may have lost abilities that our ancestors had

If our ancestors had the ability to regenerate teeth and limbs and now we can't; would this be evolution?   Or is it devolution?

From ScienceDaily:

Genetic elements that drive regeneration uncovered

Limb or organ regrowth may be hidden in our genes
 

"If you trace our evolutionary tree way back to its roots -- long before the shedding of gills or the development of opposable thumbs -- you will likely find a common ancestor with the amazing ability to regenerate lost body parts."

"Lucky descendants of this creature, including today's salamanders or zebrafish, can still perform the feat, but humans lost much of their regenerative power over millions of years of evolution."   (hmmmm)

"We want to find more of these types of elements so we can understand what turns on and ultimately controls the program of regeneration," said Poss (programs are designed)

A prior post here by John Sanford and genetic entropy - "the human race is degenerating at 1-5% per generation"

"so it's kind of a trade secret amongst population geneticists,any well informed population geneticist understands man is degenerating"

"so in deep geological time we should have been extinct a long time ago"

The latest from Scientific American.  Is the Copernican Principle being overturned?  Stay tuned....

Exoplanet Census Suggests Earth Is Special after All

A new tally proposes that roughly 700 quintillion terrestrial exoplanets are likely to exist across the observable universe—most vastly different from Earth

"But the average age of these planets—well above Earth’s age—and their typical locations—in galaxies vastly unlike the Milky Way—just might turn the Copernican principle on its head.

"But Max Tegmark from the Massachusetts Institute of Technology, who also was not part of the research, thinks Earth is a colossal violation of the Copernican principle..."

-and-

Planck Satellite Confirms WMAP Findings: Universe is not Copernican

The Modern World is Faced with the Breach of a Far Reaching Paradigm

 "The question is ‘what will modern science do now’? Will they invent additional parameters to keep the current theories alive (in addition to those already added: dark matter, dark energy, redshift as expansion, big bang inflation, etc.) or will they consider the possibility that we are in a special place as observations clearly indicate?"

-and-

Do We Live in a Giant Cosmic Bubble? 


"This idea that we live in a void would really be a statement that we live in a special place," Clifton told SPACE.com. "The regular cosmological model is based on the idea that where we live is a typical place in the universe. This would be a contradiction to the Copernican principle."
"This idea that we live in a void would really be a statement that we live in a special place," Clifton told SPACE.com. "The regular cosmological model is based on the idea that where we live is a typical place in the universe. This would be a contradiction to the Copernican principle."

Biology of the Baroque

Can Darwinism explain beauty in nature?  God is an artist of such beauty.  IDvolution - God “breathed” the super language of DNA into the “kinds” in the creative act reflecting His beauty.

"The Biology of the Baroque" is a documentary that explores the amazing patterns, order, and beauty in biology that go beyond what can be explained by Darwinian evolution. It features geneticist Michael Denton and is inspired by Denton's new book Evolution: Still a Theory in Crisis"

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

New class of DNA repair enzyme discovered

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. 

-and-

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 death of NeoDarwinism, No Selfish Gene

"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...)

More John Lennox: God is Irrelevant

Once again, Lennox takes it to the house.

God is Irrelevant: Discuss by John Lennox  

Is nature mostly a tinkerer or an inventor? or was it all front loaded? by Who?

Who did the front loading?  

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

This accounts for the diversity of life we see. The core makeup shared by all living things have the necessary complex information built in that facilitates rapid and responsive adaptation of features and variation while being able to preserve the “kind” that they began as. Life has been created with the creativity built in ready to respond to triggering events.

Phys.org August 18, 2015 published the following.

Is nature mostly a tinkerer or an inventor?  

The Krüppel-like factor and specificity protein (KLF/SP) genes are found across many species, ranging from single cell organisms to humans. This gene family has been conserved during evolution, because it plays a vital role in regulating the expression of other genes.

"Our study paints a picture of nature innovating largely through sharing the functional bits of genes—tinkering with molecular genetic material that already exists," said William E. Browne, assistant professor of Biology at UM's College of Arts & Sciences and principal investigator of the study.

Read more at: http://phys.org/news/2015-08-nature-tinkerer-inventor.html#jCp

"Our study paints a picture of nature innovating largely through sharing the functional bits of genes—tinkering with molecular genetic material that already exists," said William E. Browne, assistant professor of Biology at UM's College of Arts & Sciences and principal investigator of the study.

"This is interesting because it supports the idea that the appearance of new types of cells in a lineage of organisms as they evolve may be, more commonly, a consequence of turning off genes in unique temporal and spatial combinations," Browne said. "Large numbers of unique cell types are required to support the development of complex tissues and organs."


A prior finding

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. 

-and-

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......... 

 

"Our study paints a picture of nature innovating largely through sharing the functional bits of genes—tinkering with molecular genetic material that already exists," said William E. Browne, assistant professor of Biology at UM's College of Arts & Sciences and principal investigator of the study.

Read more at: http://phys.org/news/2015-08-nature-tinkerer-inventor.html#jCp

"This is interesting because it supports the idea that the appearance of new types of cells in a lineage of organisms as they evolve may be, more commonly, a consequence of turning off genes in unique temporal and spatial combinations," Browne said. "Large numbers of unique cell types are required to support the development of complex tissues and organs."

Read more at: http://phys.org/news/2015-08-nature-tinkerer-inventor.html#jCp

"This is interesting because it supports the idea that the appearance of new types of cells in a lineage of organisms as they evolve may be, more commonly, a consequence of turning off genes in unique temporal and spatial combinations," Browne said. "Large numbers of unique cell types are required to support the development of complex tissues and organs."

Read more at: http://phys.org/news/2015-08-nature-tinkerer-inventor.html#jCp

Natural Selection can impede speciation

In a prior post Natural selection is a conservative process not a creative one. it was argued that natural selection is a conservative process not a creative one.  Now we see that it can actually impede speciation.

Natural selection, key to evolution, also can impede formation of new species

 

 

Rationality of Belief in God

At around 1:00 Dr Kreeft explains faith and reason and the intersection where both are true. (see illustration below)

How Could God Interact with the World? (William Dembski)

Closer to Truth

   

How Could God Interact with the World? (William Dembski)

 

 

Evolution 2.0 New Book

“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.

Genetic Piano Again

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.

Does Richard Dawkins Exist? - Answers to "Scientific" Materialism

Dr. Bonnette gets to the heart of the matter, illustrating the absurdity and irrationalism of scientific materialism. Richard Dawkins by his own ideas of the universe does not exist! Does Richard Dawkins Exist? An Introduction to Atheistic Materialism to Theistic Hylemorphism"

The Moral and Kalam Argument