File under " well said" CXIII

 "And how can a man die better than facing fearful odds, for the ashes of his fathers, and the temples of his Gods" -

Thomas B. McCauley 

"For whoever does the will of God, he is my brother and sister and mother.”"

Jesus of Nazareth as rendered by the English Standard Version Mark ch.3 v.35. 

The testimony of population genetics

 Paper Digest: Addressing Flaws in Population Dynamic Models

Emily Reeves

Population genetics, the field that studies how alleles shift and spread in a population, can tell us something about our history. A genome functions like a unique fingerprint for every organism, allowing scientists to compare genomes and determine which genomes are similar. According to evolutionary biology, genome comparison can also allow one to trace the gradual accumulation of mutations (as proposed by Darwinian evolution) and reconstruct the history of life through common ancestry. 

An ID Perspective

However, intelligent design (ID), as a scientific theory, posits that the origin of certain features of living organisms — including many features of genomes — are better explained by an intelligent cause than solely by undirected processes like random mutations. Leading ID proponents, including Michael Behe, Douglas Axe, Winston Ewert, William Dembski, and Stephen Meyer, have raised concerns about the ability of random mutations to generate complex, information-rich systems. Behe argues that random mutations generally degrade, rather than enhance, genetic information. Additionally, researchers such as Winston Ewert, Ann Gauger, Paul Nelson, Casey Luskin, and others, although agreeing that genome comparison is extremely helpful, have also highlighted issues in phylogenetics, the field that uses genome comparisons to infer common ancestry.

An emerging perspective within the ID community, advanced by figures like Jonathan Bartlett (whose paper I’m covering today), Brian Miller, Steve Laufmann, and myself (here, here, and here), suggests that some genetic variation within a population of organisms represents programmed, parameterized adaptive potential. Bartlett discusses the issue in his recent peer-reviewed article, “Alternate mutation modalities in models of population dynamics” (Academia Biology). He first raises problems with population dynamic models. Bartlett then suggests integrating the parameterized genetic variation into population dynamic models to resolve inconsistencies and improve accuracy, providing a starting example for how this might be accomplished

Key Flaws in Current Models

Bartlett points out that reproductive fitness is often conflated with biophysical fitness. He defines biophysical fitness as the effectiveness of biophysical components to carry out their function. On the other hand, reproductive fitness he defines as “the relative ability of different genetic configurations to produce offspring.”

The problem with this conflation becomes evident when we consider that in two environmental contexts an organism with the exact same biophysical fitness may have different reproductive fitness. One example Bartlett provides is a genetic variation affecting an outer bacterial coat protein. In certain situations, this type of genetic variation can conserve the biophysical fitness of the protein (meaning the protein retains its ability to structurally reinforce the cell wall or outer membrane), even as it reduces reproductive fitness in the environmental context of a specific antibiotic to which the genetic variant makes the bacteria more susceptible. Hence, a genetic change can maintain biophysical fitness but reduce reproductive fitness. 

A second problematic assumption is that genetic change is random. Bartlett notes two types of genetic change that challenge this assumption: stress-induced genetic variation and cyclical genetic variation. As an aside, you might have noticed I personally don’t like to call genetic change “mutation” because I think the term “mutation” should be reserved for random genetic change that is known to negatively impact biophysical fitness. 

An example of stress-induced genetic variation is that single-celled organisms are known to activate polymerases that introduce genetic variation. This occurs when stress is detected but not in a random pattern. Instead, these polymerases target genetic variation to specific regions of the genome where it might be helpful.

Cyclical genetic variation, also called back mutation, is defined as genetic change which happens on a periodic cycle and may revert to a previous allele. These events happen in phase-variable genes. Bartlett explains one mechanism:

There are multiple mechanisms by which [cyclical genetic variation] occurs, one of which is inverting the promoter sequence. One direction turns the promoter on, and the other direction turns it off. By having a sequence with a bistable state, the organism will revisit both configurations repeatedly.

In summary, within the field of population genetics, Bartlett notes assumptions are made that aren’t necessarily true in every situation of genetic change. Specifically, fitness is ill-defined, and genetic variation is not always random (scientists have known this for a while).

Modeling Population Dynamics

There are two major ways of modeling genetic variation for population dynamics: origin fixation models and standing genetic variation models. Standing genetic variation models seek to explain current allele frequencies based on pre-existing genetic diversity in the population due to recombination or gene flow. These models largely ignore novel genetic variants. 

Origin fixation models assume that novel genetic variants are random events that can contribute to fitness and accumulate in a population. These models aim to describe the process beginning with a novel variant’s introduction, through to its eventual elimination or fixation within the population.

In order to improve modeling of population dynamics, Bartlett argues we must incorporate other known modes of genetic variation. He then makes an attempt at doing this for cyclical genetic variation. He develops a mathematical model for a single locus to model cyclical genetic variation. What he learns from doing this is that the ratio of beneficial to deleterious variants does not depend on the rate at which variants appear, but on the number of genotypes and the sizes of the subpopulations of a specific genotype. This causes an interesting effect.

As long as the cyclical variation rate is not too high, the most reproductively fit individuals dominate the population. As time goes on, most of the variation accumulating in the dominant population is deleterious, moving individuals to less fit genotypes. This means the majority of variants will be leaving this subpopulation and joining a less fit population. So if the environment is constant, then the dominant genotype increases in number and the ratio of beneficial to deleterious variants drops for that subpopulation. In other words, the number of deleterious variants goes up overall in the subpopulation.

However, if the environment changes to a situation where the dominant population is no longer the most reproductively fit, another subpopulation will begin to rise in dominance. That would cause the previously favored subpopulation’s ratio of beneficial to deleterious variants to decrease.

Reframing Genetic Variation

Bartlett has raised excellent points and concerns for the field of population genetics and he has developed an important preliminary model for cyclical mutation at a single locus. The parameterized form of genetic variation discussed in this paper may function as a population-level (think: cloud-based) potential for organismal adaptation, different from random mutation induced by ionizing radiation. Bartlett and other ID proponents hypothesize that conflating this non-random genetic variation with random variation has led to unresolved problems in both population genetics and phylogenetics. Reframing genetic variation as falling into separate categories — random and non-random — could provide new insights into how organisms adapt and how the history of life is interpreted. Future work by Bartlett or others will help shed light on how this can be accomplished.

Against Litigious XXIV

Litigous:You emphasize repentance as a prerequisite for mercy and grace, citing Matthew 4:17. This is a valid point but does not negate the Catholic Church’s emphasis on repentance and the transformative power of grace. The Catholic Church continually calls its members to repentance through the sacraments, particularly Confession (Reconciliation). Jesus’ call to “Repent, for the kingdom of heaven is at hand” (Matthew 4:17) is echoed in the Church’s liturgy, teaching, and pastoral care. The Church teaches that God’s mercy and justice are not in opposition. While repentance is necessary, mercy is always available to those who seek it sincerely. The parable of the Prodigal Son (Luke 15:11-32) illustrates that God welcomes sinners who return to Him, even after grievous offenses. While the Church practices discipline, it avoids the harshness of shunning or permanent ostracism, which risks violating Christ’s command to forgive “seventy times seven” (Matthew 18:22). Even excommunicated individuals are always invited to repent and return to full communion with the Church.

Myself: same here you repent you return to full fellowship you don't repent you endure the rebuke of JEHOVAH and his son,the person who has repented and taken the vow is not in the same position as the person who has never taken the vow, 

Ecclesiastes ch.5:5,6NIV"It is better not to make a vow than to make one and not fulfill it. 6Do not let your mouth lead you into sin. And do not protest to the temple messenger, “My vow was a mistake.” Why should God be angry at what you say and destroy the work of your hands? "

Luke ch.12:47NKJV"“And a servant who knows what the master wants, but isn’t prepared and doesn’t carry out those instructions, will be severely punished."

2Peter ch.2:20,21NIV"If they have escaped the corruption of the world by knowing our Lord and Savior Jesus Christ and are again entangled in it and are overcome, they are worse off at the end than they were at the beginning. 21It would have been better for them not to have known the way of righteousness, than to have known it and then to turn their backs on the sacred command that was passed on to them. "

The truly wise man will recieve the rebuke of JEHOVAH and his priest with the proper spirit. 

Revelation ch.3:19NIV"Those whom I love I rebuke and discipline. So be earnest and repent."

Psalm ch.141:5NLT"Let the godly strike me! It will be a kindness! If they correct me, it is soothing medicine. Don’t let me refuse it. But I pray constantly against the wicked and their deeds."

Litigious:You imply that the Catholic Church “tolerates” sin while Jehovah’s Witnesses enforce stricter standards. However, several aspects of JW theology and practice merit critique. Jehovah’s Witnesses practice disfellowshipping, which often results in total isolation of individuals, even from family members. This goes beyond biblical correction (Matthew 18:15-17) and violates the command to honor one’s parents (Exodus 20:12). Catholic discipline, in contrast, seeks repentance and restoration, not permanent exclusion. Jehovah’s Witnesses deny core Christian doctrines, such as the deity of Christ. These denials contradict Scripture (e.g., John 1:1, Matthew 28:19) and the teachings of the early Church, as evidenced by the Nicene Creed. The Watchtower Society’s claim to be the true faith is undermined by its lack of historical continuity with the apostolic Church. In contrast, the Catholic Church traces its origins directly to Christ and the Apostles (Matthew 16:18, Acts 2:42).

The one flesh bond between spouses and their minor children is not affected by the sanction required by the Bible. This sanction is quite clear : 1corithians ch.5:5ASV"to deliver such a one unto Satan for the destruction of the flesh, that the spirit may be saved in the day of the Lord Jesus"

1Corinthians ch.5:12,13NIV"For what have I to do with judging them that are without? Do not ye judge them that are within? 13But them that are without God judgeth. Put away the wicked man from among yourselves."

Note a distinction is made with those who are outside never having taken the vow of dedication and those who have dedicated themselves, the purpose of the sanction is to deter the frivolous taking of the vow it can't do that if it is a bluff. No it must be clear that JEHOVAH Means business.

Well you are arguing in a circle as usual the "our beliefs are true because we say they are" ,who cares what logic and the inspired scriptures have to say. Our Lord and his apostles rejected the argument from antiquity 2000 years ago,I don't know why you insists on trying to recycle it?

Litigious:You accuse me of failing to “remove the plank from your own eye” (Matthew 7:5). However, this accusation applies equally to the Jehovah’s Witness organization, which has faced its own scandals and controversies, including child abuse cases and doctrinal changes as well. Allegations of mishandling child abuse cases have plagued the Watchtower Society. These failures reveal that no organization, including Jehovah’s Witnesses, is immune to human sinfulness. The Watchtower Society has repeatedly altered its teachings, raising questions about its claim to be God’s sole channel of truth. For example, its shifting interpretation of the “generation” mentioned in Matthew 24:34 has led to confusion and disillusionment among its members. The Catholic Church acknowledges its human failings while remaining steadfast in its divine mission. As St. Paul wrote, “We have this treasure in jars of clay, to show that the surpassing power belongs to God and not to us” (2 Corinthians 4:7).

Myself :the plank in your eye is preventing you from seeing that the secret sins which no leadership can prevent, cannot be compared to tolerance for public corruption, and worse yet mass murder of coreligionists over political and ethnic differences and the scheming of state sponsored repression of religious minorities, and again I am not singling out the Catholic here I will even concede that it has not all things considered been the worst offender ALL of the churches of Christendom bear community guilt in these regards. Your claim that the global peace we enjoy not even retaliating against the violent persecution of politicised religions,and our uncompromising stand for the bible's morals are the fruit of a tree planted by Satan, while your mass fratricide over political and ethnic differences and your constant compromising over the bible's moral standards are the fruit of a tree planted by the God and Father of Jesus is irrational.

The first century disciples also had wrong expectations see Luke ch.24:21 as I pointed out some of christendom's leading lights Martin Luther,tertullian also had false expectations, 1corinthians ch.13:9NIV"Now our knowledge is partial and incomplete, and even the gift of prophecy reveals only part of the whole picture!"

Where the interpreting of prophecy us concerned the scriptures indicate that an incomplete understanding is the default , so we are not stumbled by the default,the foundation of our faith is the identity of the one true God JEHOVAH,the identity of his only High priest Jesus Christ, the mechanism of the ransom, conditional immortality, the peace that only JEHOVAH'S spirit can give and which Satan never can,the restoration of human perfection to our race, the total reassertion of JEHOVAH'S Sovereignty over all the earth, this foundation has remained steadfast from the outset,the changes you like to make much of are not fundamental ,they are window dressing by comparison

John ch.13:35NKJV"By this all will know that you are My disciples, if you have love for one another.”"

The kind of love that will move us to choose death rather than obey any command from any prince yo slay our brothers.

Litigious:In conclusion, the Catholic Church does not deny the need for repentance or discipline but balances these with mercy, grace, and a commitment to the truth of the Gospel. The sins of individuals, whether Catholic or Jehovah’s Witness, do not invalidate the truth of Christ’s message.

Myself:the truth of christ message was never the issue the person who has dedicated himself to the holy service of JEHOVAH on the basis of christ ransom is not on the same plain as the person who has no claims of any such dedication,and that needs to be made plain to anyone contemplating such a dedication. Those who turn their back on their vow publicly or whose secret defections become public must be expelled if they refuse to repent. Upon repentance full fellowship can be restored,but it must be clear to all who are contemplating a vow of dedication that the vow is not to be taken frivolously. Any failure to implement JEHOVAH'S Clear instructions in this regard will bring community guilt on the Church.see 1Corinthians ch.5:11-13

 Litigious:The Church remains the “pillar and foundation of the truth” (1 Timothy 3:15), offering God’s grace to all who seek it. Your interlocutor’s arguments misunderstand the nature of the Church, the process of sanctification, and the balance between justice and mercy that defines authentic Christianity.

Myself:JEHOVAH'S Rebuke of those who are hardened in rebellion against his righteous law is an example of his love for his loyalists,he separates possible contaminants to ensure that his true church remains in a sanctified state,

John ch.15:2NIV"He cuts off every branch in me that bears no fruit, while every branch that does bear fruit he prunes so that it will be even more fruitful."

1Corinthians ch.5:6,7NIV"Your boasting about this is terrible. Don’t you realize that this sin is like a little yeast that spreads through the whole batch of dough? 7Get rid of the old “yeast” by removing this wicked person from among you. Then you will be like a fresh batch of dough made without yeast, which is what you really are. Christ, our Passover Lamb, has been sacrificed for us.g "

If JEHOVAH'S Rebuke is received with the right spirit it can prove to be healing to the spiritually sick.

Psalm ch.141:5NLT"Let the godly strike me!

It will be a kindness!

If they correct me, it is soothing medicine.

Don’t let me refuse it.

But I pray constantly

against the wicked and their deeds."

2Chronicles ch.33:10-13ASV"And JEHOVAH spake to Manasseh, and to his people; but they gave no heed. 11Wherefore JEHOVAH brought upon them the captains of the host of the king of Assyria, who took Manasseh in chains, and bound him with fetters, and carried him to Babylon. 12And when he was in distress, he besought JEHOVAH his God, and humbled himself greatly before the God of his fathers. 13And he prayed unto him; and he was entreated of him, and heard his supplication, and brought him again to Jerusalem into his kingdom. Then Manasseh knew that JEHOVAH he was God"