Friday, 7 February 2025
Wednesday, 5 February 2025
The human evolution narrative does not compute?
Human Evolution by the Numbers: Chatbot Weighs In
Over at Vox Popoli, writer Vox Day tried putting an evolution question to a chatbot. As we all know, chatbots are not much good with logic but they tend to be able to handle calculations. He writes,
Although AI has many limitations, including the more serious ideological restraints imposed by its highly-converged creators, the requirement for it to be capable of correctly crunching numbers puts it leagues ahead of the average scientist, particularly the average biologist, in grasping the obvious fact that there is absolutely no chance that evolution by natural selection can account for more than a very small and insignificant fraction of the genetic diversity that separates one species from another.
“One Percent of Zero,” January 3, 2025
After Some Chugging
He gave Google’s Gemini a go and after some chugging, got this result:
Given the vast difference between the maximum possible number of fixations through natural selection (225) and the estimated number of fixations required to account for the genetic distance between humans and chimpanzees (360,000), it is extremely unlikely that natural selection alone could account for all those fixations. Therefore, the probability that 360,000 fixation events could have occurred solely through natural selection is extremely low, essentially approaching zero for any practical purposes.
“One Percent of Zero”
Day notes
Now, notice that despite arbitrarily reducing the size of the average fixation event to one percent of the observed 36,000,000 base pair differences between modern humans and modern chimpanzees on the basis of absolutely nothing, the AI still concluded that the probability that humans could have evolved from the Chimpanzee-Human Last Common Ancestor as “essentially approaching zero for any practical purposes”. But the real probability is around one percent of approaching zero…
He continues his dialogue with Gemini here.
For the True Believers
The probability calculations don’t matter much, though. The Darwinian story of human evolution from an ape-like creature is probably the most powerful modern secular myth. It’s a myth in the sense that it offers an account of human life in general, and can be applied to literally any topic.
Contrary evidence is irrelevant. What need not be proven true can’t be falsified either. For those who truly believe, Darwinism tends to organize their whole way of understanding life. It provides a justification for persecuting doubters as well. Those who would research life on Earth seriously must route around the edifice of faith erected around Darwinism
Against litigious XXV
Litigious:Your rejection of historical continuity in Christianity shows a misunderstanding of Christ’s promise in Matthew 16:18 that “the gates of hell shall not prevail” against His Church. You dismiss historical Christianity as corrupted and claim Jehovah’s Witnesses are the true faith,
Myself:As I pointed our Lord and his apostles rejected the argument from antiquity yet you keep recycling this argument that our Lord rejected the Jews could point to similar promises in the scriptures that the law and the priesthood were to continue to olam,
Exodus ch.40:15NIV"Anoint them as you did their father, so they may also serve me as priests. With their anointing, Aaron’s descendants are set apart for the priesthood forever, from generation to generation.”"
Why do you keep recycling this tired old argument that our Lord and his apostles rejected.
Litigious:yet your movement did not exist until the 19th century. The early Church Fathers, who lived far closer to the apostles, taught doctrines that Jehovah’s Witnesses reject, including the deity of Christ and the Trinitarian nature of God (cf. Justin Martyr, Irenaeus, Athanasius). The Watchtower Society’s ever-changing doctrines undermine its claim to divine authority. Jesus did not establish an organization that would later need to be "restored"—He founded a Church that has endured since the time of the apostles.
Myself:the Jews would also have raised the same argument against the Christians and would point to extra biblical authority for their man made tradition again Jesus rejected man made tradition not rooted in scripture no matter how old. See Matthew ch.15:2-6 none of the foundation teachings of our movement were invented by the brothers you know about arius,there is also ancient authority for conditional immortality,and premillenialism,baptism by immersion,substitutionary atonement ,so individuals did preserve elements of the truth though these were in the minority just as the first century church was a tiny and hated minority and they were scattered,jesus prophecy at Matthew ch.13:24-30 indicated that it would be the case that apostates and their disciples would outnumber fruitbearing Christians 2thessalonians ch.2:1-12 points to those leading the rebellion they claim supernatural signs and gifts long after those have passed away. But the bloodstained fruit they bear exposes them as weeds sown by the enemy.
Litigious:Your attempt to dismiss the documented changes in Jehovah’s Witness doctrine as “window dressing” ignores the serious theological inconsistencies within your organization. Doctrinal shifts such as the multiple post-hoc re-interpretations of the “generation” in Matthew 24:34 or failed prophetic predictions, such as the 1914 and 1975 end-times claims, show that your organization cannot claim to be God’s unerring voice. Contrast this with Catholic doctrine, which, despite human failings, has preserved the same core teachings on the Trinity, the sacraments, and salvation since the time of Christ.
Myself:We know that the apostles had wrong expectations and they were prophets see luke ch.24:20,21 John ch 21:23 before each of those expectations the brothers made it clear that they were cessationists and hence were not literal prophets your continue lie boldfacedly like this about this issue is not recommending you as good faith interlocutor https://aservantofjehovah.blogspot.com/2024/03/on-false-prophets-and-false-accusers.html
From the January 1908 watchtower"With regard to 1914: : "We are not prqophesying; we are merely giving our surmises . . . We do not even aver that there is no mistake in our interpretation of prophecy and our calculations of chronology. We have merely laid these before you, leaving it for each to exercise his own faith or doubt in respect to them"
This years prior to 1914 so it is definitely not a post hoc rationalization as you lyingly implied. It is you who claim infallibility and boldfacedly admit to necromancy claiming to receive dreams and visions from dead saints a clear violation of Deuteronomy ch.18:9-11
Like the apostles wrong expectations none of those had any theological consequences JEHOVAH Still remained supreme,Christ still remained subordinate to his anointed,the dead continued to sleep until the resurrection the millennium continued to be hoped for ,baptism continued to be by immersion on those qualified to make a covenant with JEHOVAH,the atonement continued to be substitutionary ,the final end of the wicked continued to be annihilation,we continued to remain separate from politics and nationalism and war,we continued to hope for a restoration of human perfection,I observed you made no specific claims as to what aspect of our theology was changed by these misunderstandings of recorded prophecy.
Litigious:You argue that “all of Christendom” is guilty of political and religious violence, yet you fail to distinguish between the actions of individuals and the teachings of the Church. The Catholic Church has always condemned unjust violence, as seen in papal encyclicals like Pacem in Terris (1963) and Evangelium Vitae (1995). While historical conflicts occurred, they were often driven by political, not theological, motivations. More importantly, Christ’s teachings remain unchanged. The Church does not justify the past sins of its members but rather seeks repentance and reform, unlike the Watchtower Society, which rewrites its history to cover past errors.
Myself:it is astounding that you think that the fact that your mass fratricide is driven by political and ethnic contentions some how excuses it, that makes it worse does it not? The tolerance of those who unrepentantly slaughter fellow believers even urging them on in the slaughter is a clear violation of what the Bible indicates ought to be expected of true Christians see John ch.13;34,35
Isaiah ch 2:2-4ASV"And it shall come to pass in the latter days, that the mountain of Jehovah's house shall be established on the top of the mountains, and shall be exalted above the hills; and all nations shall flow unto it.
3And many peoples shall go and say, Come ye, and let us go up to the mountain of Jehovah, to the house of the God of Jacob; and he will teach us of his ways, and we will walk in his paths: for out of Zion shall go forth the law, and the word of Jehovah from Jerusalem.
4And he will judge between the nations, and will decide concerning many peoples; and they shall beat their swords into plowshares, and their spears into pruning-hooks; nation shall not lift up sword against nation, neither shall they learn war any more."
Like I stated already the notion that Satan could get his people to precisely fulfill these expectations while Christ will so spectacularly fail to get his people to fulfill these expectations is utterly irrational
Litigious:Your appeal to John 13:35, claiming that Jehovah’s Witnesses show true Christian love by refusing to participate in military service, is misleading. The Catholic Church upholds just war principles, as seen in Augustine and Aquinas,
Myself: killing fellow believers is never just let the unbelievers fight their own wars we have JEHOVAH'S War to fight we can't take time away from that truly just war to meddle in the unbelievers' wars.
2Corinthians ch.10:4NIV"he weapons we fight with are not the weapons of the world. On the contrary, they have divine power to demolish strongholds."
Litigious:which permit self-defense and the protection of the innocent. The rejection of military service does not automatically equate to moral superiority. Jehovah’s Witnesses claim to be neutral, yet the organization has engaged in questionable legal and political maneuvers, such as its association with the United Nations as an NGO while publicly condemning political involvement.
Myself :in practice christendom's churches have been willing tools for the nationalist ambitions of which ever nation they happen to be part of we pay taxes and obey the law therefore we are entitled to access whatever our taxes pay for their is nothing political about that so this insinuation is an attempt to divert attention from the bloodstained history of christendom's churches including their implication in the violent persecution of JEHOVAH'S Servants, christendom has never met a bloodstained tyrant she didn't like provided he was ready to do her bidding
Litigious:You claim that Jehovah disciplines those in rebellion, but you fail to recognize that authority within the Church is meant to build up, not tear down. The Catholic Church does not reject discipline but implements it with mercy. Paul commands the Church to discipline the immoral brother in 1 Corinthians 5, yet in 2 Corinthians 2:6-8, he urges the Church to forgive and restore the sinner, demonstrating that discipline must lead to reconciliation, not indefinite exclusion.
You fail to realize the difference between mercy and license,mercy is when the truly repentant are help to regain spiritual health your attempt to excuse your church's lax attitude toward those hardened in open rebellion against JEHOVAH'S Law and who clearly have no interest in(or may not even recognize the need for) repentance is not mercy. Proverbs ch.28:13NLT"People who conceal their sins will not prosper, but if they confess and turn from them, they will receive mercy."
What about those who have no shame at all in part because their church allows those advocating moral compromise to teach their slackness from the pulpit. None of this is true mercy
Litigious;In conclusion, your defense of Jehovah’s Witness practices relies on selective Scripture interpretation, theological inconsistencies, and a rejection of historical Christianity. Catholic doctrine maintains the balance between justice and mercy, acknowledging the necessity of repentance while preserving the dignity of individuals. Unlike Jehovah’s Witnesses’ rigid disciplinary system, which often results in broken families and emotional harm, the Catholic Church follows the biblical model of correction ordered toward restoration. Your rejection of historical Christianity and your organization's doctrinal instability undermine your claim to be the true faith. The Catholic Church, built upon the foundation of Christ and the apostles, remains the pillar and foundation of truth, offering God’s grace to all who seek it.
Myself: the churches of christendom's failure to promote the bible's morals and her being a willing cheerleader for nationalists and militarists is what has resulted in mass harm to families and nations. As I pointed out, but your bad faith continues to ignore, the sanction does not apply to spouses and their minor children,or children living under their roof.those who take the vow of dedication do so with full awareness of the consequence for defection from the vow, the vow must not be taken frivolously, as the proverb says it is better to not vow, ecclesiastes ch.5:4-6NIV"When you make a vow to God, do not delay to fulfill it. He has no pleasure in fools; fulfill your vow. 5It 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? "
Don't be a pretender you won't have anything to worry about ,those who are repentant will receive mercy for sure but those defiantly rebellious against JEHOVAH'S Law must be removed for the Church to remain in a sanctified state.
The foundation of our doctrine has not changed just as an incomplete understanding of prophecy see 1Corinthians ch.13:9 did not affect the fundamental theology of the first century church,so too an incomplete understanding of messianic prophecy has not affected the essentials of our faith,the identity of the one true God ,the identity of his subordinate Messiah,the atonement ,premillenialism etc. All remained unaffected. Your church has also had some doctrinal changes ,I'm sure you have some ad hoc rationalization as to why your infallible pope ever needs to make such adjustments and why your claim that such adjustments are disqualifying don't apply in that instance,but it all seems like special pleading to me.
Tuesday, 4 February 2025
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
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"
Monday, 3 February 2025
Sunday, 2 February 2025
Forensic examination of the explosion that demolished Darwin's house continues
Dodging the Main Issue in the Cambrian Explosion
Concerning the well-known and persistent problem of the Cambrian explosion, Stephen Meyer stated the issue as clearly and succinctly as possible in his best-selling book Darwin’s Doubt: “the origin of new biological information” (p. ix). He has repeated this issue in videos, interviews, debates, articles and speeches before and after 2013, the book’s publication date. Indeed, it was the central issue in Meyer’s Smithsonian paper that led to Richard Sternberg’s ouster in 2004. With scientists in the ID movement stating this issue continually for more than two decades, evolutionary biologists cannot claim ignorance of it. Yet to the present day, they dodge it. In three recent papers, we see how they talk about everything and anything but the issue: the origin of new biological information. Let’s consider these papers in order of publication.
Molecular Clock Fiddling
Last November, Philip C. J. Donoghue of the University of Bristol (mentioned by Bechly here) with three colleagues struggled to calibrate the Ediacaran and Cambrian fossil record to the “molecular clock” hypothesis (see my discussion of the molecular clock here). Getting these two data sources to fit has been a pervasive challenge along the entire evolutionary timeline. The abstract of their paper in Science Advances1 claims success, but ends with a quizzical statement:
Integrating across uncertainties including phylogenetic relationships, clock model, and calibration strategy, we estimate Metazoa to have originated in the early Ediacaran, Eumetazoa in the middle Ediacaran, and Bilateria in the upper Ediacaran, with many crown-phyla originating across the Ediacaran-Cambrian interval or elsewise fully within the Cambrian. These results are in much closer accord with the fossil record, coinciding with marine oxygenation, but they reject a literal reading of the fossil record.
By that, they mean that if you calibrate the molecular clock to certain fossils, they do not fit most of the other fossils. Is their conclusion as anti-empirical as it sounds? You be the judge:
Our results suggest that there was a radiation of metazoans beginning in the middle Ediacaran, with all major phyla originating by the late Cambrian (Fig. 5), although this may have taken a little under 100 Myr based on the maximum and minimum age estimates for all of the phyla, suggesting the “Cambrian explosion” was more drawn-out than a literal reading of the fossil record would suggest. Although crown-Metazoa originated in the Ediacaran, many of the crown-phyla did not originate until the Cambrian; Euarthropoda, Echinodermata, Ctenophora, Hemichordata, Rotifera, and Chaetognatha likely originated in the Cambrian, while Chordata, Cnidaria, and Mollusca have late Ediacaran origins.
What this means is that the Cambrian explosion is evident from the fossils, but you cannot trust the observational evidence — the “literal” reading of the fossils — to perceive the truth of evolution. Don’t believe your eyes. Belief in evolution requires the belief in the existence of ancestors. Since evolutionists cannot see them, they must infer their presence from the molecular clock. But since the molecular clock hypothesis is built on the assumption of evolution, this is circular reasoning.2
Nowhere do these four evolutionists address the main issue: the origin of new biological information. Score: Dodgers, 1. (No opponent score given, since they are playing against themselves. Darwin skeptics have been disqualified by fiat, so they watch the game from the sidelines and call fouls.)
Tracking the Explosion
The next paper, published in Current Biology3 this month, tries to tease out differences between animal tracks and environmental traces on an exposed benthic deposit in Canada that lies on the boundary of the late Ediacaran and “the onset of the Cambrian explosion.”
The Cambrian explosion was a time of groundbreaking ecological shifts related to the establishment of the Phanerozoic biosphere. Trace fossils, which are the products of animals interacting with their substrates, provide a key record of the diversification of the benthos and the evolution of behavioral complexity through this interval.
The seven authors accumulate “The most extensive ichnologic dataset compiled from any Ediacaran-Cambrian section.” They believe that their resulting matrix of ichnofossils (some interpretation was required) will help with “refining our understanding of the early stages of the Cambrian explosion.” Mentions of evolution: 15. Mentions of biological or genetic information: zero.3
Notice their choice of noun phrases to dodge the cause of all the novelty:
The Cambrian explosion was a time of groundbreaking ecological shifts related to the establishment of the Phanerozoic biosphere.
Score: Dodgers, 2.
Getting Permission to Evolve
The third paper by seven authors, mostly from the University of Edinburgh, was published in Science Advances a few days later5. A refinement of the old Oxygen Theory for the Cambrian explosion (here, here), this new paper presents the notion that “Low oxygen but dynamic marine redox conditions permitted the Cambrian Radiation.”
The team inferred oxygen abundances and fluctuations on the Siberian Platform by proxy measurements. Surprise; the earliest Cambrian body plans were not dependent on oxygenation.
Whether metazoan diversification during the Cambrian Radiation was driven by increased marine oxygenation remains highly debated. Repeated global oceanic oxygenation events have been inferred during this interval, but the degree of shallow marine oxygenation and its relationship to biodiversification and clade appearance remain uncertain. To resolve this, we interrogate an interval from ~527 to 519 Ma, encompassing multiple proposed global oceanic oxygenation events…. We document primarily dysoxic water column conditions, suggesting that early Cambrian metazoans, including motile skeletal benthos, had low oxygen demands. We further document oxygenation events coincident with positive carbon isotope excursions that led to modestly elevated oxygen levels. These events correspond to regional increases in species richness and habitat expansion of mainly endemic species, offering a potentially globally applicable model for biodiversification during the Cambrian Radiation.
By stating without dispute that “A causal relationship between increasing shallow marine oxygenation and the Cambrian Radiation has long been proposed,” they essentially agree with the Oxygen Theory. Only the degree of oxygenation needed their clarification: “but it is not clear whether oxygen availability rose progressively through this interval and, if so, how this promoted biotic innovation and the radiation of early metazoans.” In other words, they want to answer how much oxygen was needed to trigger the explosion. You can’t just add oxygen. You have to add the right amount of oxygen. Then, bang!
One novel twist in their hypothesis is that evolution is permitted with or without oxygen; but with it, animals can move around. More noun phrases conceal their notion that oxygen gives animals permission to evolve. It enables them. It promotes them.
There has been much debate as to the actual drivers of an evolutionary response to oxygenation. Rising oxygen levels (potentially driven by increased productivity and organic matter burial) may have deepened the redoxcline, thereby extending habitable water depths. Enhanced oxygenation may also have enabled the evolution of more metabolically costly ecologies such as mobility and carnivory, as well as the ability to produce skeletal hard parts, thus promoting animal-sediment mixing and evolutionary escalation. Conversely, the presence of shallow marine anoxia itself might have formed physical barriers to dispersal and, thus, dynamic redox variability over evolutionary timescales may have promoted reproductive isolation and speciation.
Oxygen is like a ticket to ride. With oxygen, animals are permitted to evolve and swim. Without it, they have to stay put and evolve in place. These authors continue using other synonyms for permission: oxygen facilitates evolution; it makes animals able to expand and diversify. They almost catch themselves thinking the notion is crazy.
While a rise in oxygen levels has been suggested to facilitate the evolution of costly ecologies, it does not offer a definitive mechanism for the origination of new clades or the appearance of key evolutionary innovations, such as a biomineralization, bilaterality, and segmentation, but may rather provide a viable mechanism by which existing metazoan clades are able to expand their habitat range and so diversify.
Translation: Oxygen didn’t cause the Cambrian explosion. It just gave animals their “get up and go.” What did cause the Cambrian explosion, then? No answer.
Evolution gets 11 mentions by this team; biological or genetic information gets (again) zero. Score: Dodgers 3.
Until the Darwinians address the main issue in the Cambrian explosion, the expelled opposing team needs to keep shouting to the Dodgers through bullhorns from the sidelines, “But what about the origin of biological information?”
Notes
Carlisle, Donoghue et al., Ediacaran origin and Ediacaran-Cambrian diversification of Metazoa. Science Advances, 13 Nov 2024 (open access). DOI: 10.1126/sciadv.adp7161.
“There is no shortage of rhetoric that pitches molecular clock methodology and the fossil record as opposed and incompatible, but, given that molecular clock analyses are usually calibrated using fossil evidence, this is self-evidently false. Molecular clock methods provide a means of interpreting the fossil record in establishing a timescale for evolutionary history and, hence, they are in tension only with alternative approaches to inferring evolutionary time from the fossil record [like ID?]. There can be no doubt that the fossil record requires interpretation since it can be demonstrated intrinsically to be an imperfect temporal archive of evolutionary history.” Translation: Because evolution requires ancestors, and fossils do not provide them, we have to infer their existence without literal fossil evidence by “interpreting” the molecular clock (which assumes evolution).
They mention “novel architectural designs in ichnotaxa” but explain them as a “novel evolutionary event”— which sounds like, “Bang! New body plans! No intelligence allowed.”
Gougeon, Minter et al., Environmental and evolutionary controls in animal-sediment interactions at the onset of the Cambrian explosion. Current Biology, 20 Jan 2025 (open access). DOI: 10.1016/j.cub.2024.11.028.
Alexander, Wood et al., Low oxygen but dynamic marine redox conditions permitted the Cambrian Radiation. Science Advances, 24 Jan 2024 (open access). DOI: 10.1126/sciadv.ads2846
Saturday, 1 February 2025
Friday, 31 January 2025
Thursday, 30 January 2025
Pterosaurs: yet more magical thinking from Darwin?
Magical Thinking: Can Pterosaurs Be Darwinized
Baloney detecting is a skill we all learn to some degree and can sharpen with practice. It’s useful, among other areas, in detecting logical and evidentiary flaws in evolutionary interpretations of fossils. Here, let’s think about how evolutionary paleontologists use and abuse concepts of evolution in recent discoveries about pterosaurs.
Neil Thomas has written about “Evolutionary Theory as Magical Thinking” and there is no shortage of examples in the literature on fossils. When reading a scientific paper, one of the first things I do is search through for the use of the word evolution and related words like origin, mutation, transition, and selection. This gives me a sense of the authors’ outlook and where they are headed when it comes to interpreting the data and putting it in context. We start with an article in Current Biology by David Martill, professor of paleobiology at the University of Portsmouth in England.
Keep the Main Thing the Main Thing
When it comes to pterosaurs, surely the most remarkable trait they possessed was powered flight. This multi-faceted, irreducibly complex marvel, Martill informs us, evolved. It just evolved! He couches the magical aspect of his belief in synonyms that not only assume evolution but distract from the marvel of flight and all the engineering requirements to achieve it. A Boeing 747 is said to consist of six million non-flying parts. It’s the engineered arrangement of the parts that permits the function.
Flight, moreover, is an all-or-nothing feat. “You don’t just partly fly,” Paul Nelson quipped in the Illustra film Flight. For a pterosaur to fly, everything about its body had to be designed for that function. Evolutionary paleontologists distract from this most important point through the use of magic words. Martill says (emphasis added),
“Pterosaurs…were the first vertebrates to take to the air”
“Pterosaurs… were the first vertebrates to evolve powered flight”
“Birds… overcame similar problems related to flight”
“…. by becoming better walkers, pterosaurs overcame an evolutionary obstacle”
Did they do these things with foresight and planning? Obviously not. In Darwinism, organisms are the passive beneficiaries of sheer dumb luck. Natalia Jagielska at the University of Edinburgh, whose team found a pterosaur fossil on the Island of Skye (see BBC News), continues the use of magic words in her post at The Conversation:
“…. the first vertebrates to master flight.”
“It took some time for active flight to evolve in the natural world.”
“[in the Triassic,] the first bony animals took to the skies.”
“Birds flapped into existence sometime in the Jurassic….”
“Bats were the last to the race….”
“Pterosaurs were pioneers of flight….”
Günter Bechly referred to this kind of explanation as “Darwinian magic” and found it in probability words such as likely, potentially, and maybe. Jagielska illustrates this talent:
My team’s new study may help solve the evolutionary mystery, revealing how a vane on the tip of their tails may have helped these ancient animals fly more efficiently.
Martill also employs this skill, as do other papers we will look at.
Hiding Gaps with Tarp
Dr. Bechly often pointed out the “explosions” of diversity that are seen in the fossil record: complex organisms and body plans fully formed without ancestors (e.g., here). The pterosaur record is a prime example (here), where the first one was already capable of powered flight. It “looks like they appeared out of thin air,” wrote Bechly (here), as he examined proposed flightless ancestors like Scleromochlus and Venetoraptor. Here, in a Fossil Friday article about Ludodactylus, he said,
Outside of Darwinian fantasy land, we indeed lack any transitional fossils that would document an assumed gradual evolutionary development of characteristic pterosaur wings. In my view this strongly suggests that the transition happened very quickly as an abrupt saltation rather than mediated by hundreds of transitional species, for which there is not a shred of empirical evidence.
Darwinians, by habit, accentuate the positive and eliminate the negative, presenting a distorted view of the record. Do the recent papers present a transitional form from flightless to flying? Do any of the Darwinian experts on pterosaurs use the word transitional? Yes! David Martill does, but only when discussing changes between pterosaurs fully capable of flight, not before them. Moreover, the transition, he argues, happened only in the feet. From this he assumes that grandpappy wing-lizard (the meaning of “pterosaur”) was evolving from landing in trees to walking on the ground. Think of the Darwinian magic such a transition permitted!
Intriguingly, this new pterosaur [Skiphosaura bavarica, announced by David Hone and colleagues] does show some significant modification of the foot skeleton, with dramatic changes to the fifth toe. In basal pterosaurs, the fifth toe is highly elongate, complex, with a 100 degree or more flexure that redirects it posteriorly. In the new pterosaur this fifth toe is reduced, and the bend has all but disappeared, showing a radical restructuring of the foot. This feature also occurs in two other non-pterodactyloids, Douzhanopterus and Propterodactylus, and hints at a more terrestrial lifestyle for these transitional forms.
More Magic Words
All of these specimens were flyers. Martill mentions other differences between them and fellow fossil pterosaurs. Do any of these differences create new organs or flight capabilities? Employing more magic words, Martill makes much ado about some non-flying parts.
This evolutionary transition from climbing to walking was accompanied by other changes achieved at different evolutionary speeds. Notable among these shifts was an increase in the size of the skull, an elongation of the neck, lengthening of the carpus and a reduction in the length of the tail. Later, among the pterodactyloids even more radical shifts occurred, including the evolution of dental filters (as in Pterodaustro from the Cretaceous of Argentina), loss of the dentition in at least two major clades (azhdarchids and pteranodontians), the development of elaborate head crests, as well as ultra-gigantism where wingspans reached more than 9 m in at least two clades: Azhdarchidae and Ornithocheiridae. The analysis of Smyth and colleagues, and the new discovery of Hone and colleagues (and many other pterosaur studies over the last decades) make clear that by becoming better walkers, pterosaurs overcame an evolutionary obstacle that was limiting their ecological diversity. Once over this hurdle, pterosaurs seem to have come down from the trees, became aquatic, adopted an incredible range of feeding strategies, as exemplified by their diverse dentitions, and became giants. Who would have believed that the secret to their evolutionary success was the feet?
Yes, there is diversity among pterosaur species, but Martill assumes those differences in head, teeth, and body size occurred by Darwin’s mutation and selection process.
In their paper in Current Biology, David Hone and colleagues make a big deal about transitions between their prize fossil Skiphosaura and other species, which he says “helps document the transition from early pterosaurs to the pterodactyloids.” This is like pointing out different flight characteristics of jet fighters while ignoring the origin of powered flight in manned aircraft.
In an earlier Current Biology paper, Smyth, Unwin, and colleagues use the word “transition” in a similar way: alleging transitions between pterosaur families while ignoring the origin of flight (though sneaking in Scleromochlus in their phylogenetic tree diagram). While trading in magic words, why not multiply them fourfold?
This transition to predominantly ground-based locomotor ecologies did not occur as a single event coinciding with the origin of short-tailed forms but evolved independently within each of the four principal radiations: euctenochasmatians, ornithocheiroids, dsungaripteroids, and azhdarchoids. Invasion of terrestrial environments by pterosaurs facilitated the evolution of a wide range of novel feeding ecologies, while the freedom from limitations imposed by climbing permitted an increase in body size, ultimately enabling the evolution of gigantism in multiple lineages.
Permission Granted
It’s amazing what little changes in foot bones and finger bones “permitted” Darwin to do with these four groups. They were all powerful flyers, however, before the diversity appeared in the fossils. Smyth says in news from the University of Leicester, “Unlike birds, which must grow before achieving flight, even the smallest Pterodactylus were capable of flight from an early age.” Like Martill and Hone, Smyth only addresses transitions from arboreal to cursorial lifestyles and diets, inferred (not observed, because they are extinct) on the basis of foot bones.
Of interest on a side note, Smyth and Unwin dispute the classification of two species, Pterodactylus antiquus and Diopecephalus kochi, which they regard as “two troublesome taxonomic concepts” (Journal of Systematic Paleontology). We can only wonder what the future will hold for re-evaluating pterosaur phylogeny.
Monday, 27 January 2025
Sunday, 26 January 2025
Here's what needs to happen before any of Christendom’s minions attempt to remove the straw from my eye.
Luke ch.6:42NIV"How can you say to your brother, ‘Brother, let me take the speck out of your eye,’ when you yourself fail to see the plank in your own eye? You hypocrite, first take the plank out of your eye, and then you will see clearly to remove the speck from your brother’s eye."
By it's fruits a tree is known
Acts ch.7:15-27NIV"“Watch out for false prophets. They come to you in sheep’s clothing, but inwardly they are ferocious wolves. 16By their fruit you will recognize them. Do people pick grapes from thornbushes, or figs from thistles? 17Likewise, every good tree bears good fruit, but a bad tree bears bad fruit. 18A good tree cannot bear bad fruit, and a bad tree cannot bear good fruit. 19Every tree that does not bear good fruit is cut down and thrown into the fire. 20Thus, by their fruit you will recognize them.
21“Not everyone who says to me, ‘Lord, Lord,’ will enter the kingdom of heaven, but only the one who does the will of my Father who is in heaven. 22Many will say to me on that day, ‘Lord, Lord, did we not prophesy in your name and in your name drive out demons and in your name perform many miracles?’ 23Then I will tell them plainly, ‘I never knew you. Away from me, you evildoers!’
24“Therefore everyone who hears these words of mine and puts them into practice is like a wise man who built his house on the rock. 25The rain came down, the streams rose, and the winds blew and beat against that house; yet it did not fall, because it had its foundation on the rock. 26But everyone who hears these words of mine and does not put them into practice is like a foolish man who built his house on sand. 27The rain came down, the streams rose, and the winds blew and beat agains"
Galatians ch.5:22,23NIV"But the fruit of the Spirit is love, joy, peace, forbearance, kindness, goodness, faithfulness, 23gentleness and self-control. Against such things there is no law."
Galatians ch.5:19-21NIV"The acts of the flesh are obvious: sexual immorality, impurity and debauchery; 20idolatry and witchcraft; hatred, discord, jealousy, fits of rage, selfish ambition, dissensions, factions 21and envy; drunkenness, orgies, and the like. I warn you, as I did before, that those who live like this will not inherit the kingdom of God."
Ps. No Spamming allowed,I hope I'm not talking over anyone's head.
The thumb print of JEHOVAH :molecular edition.
Recurring Design Logic in Gene Regulation
A feature of biology that has struck me over the years is the phenomenon of recurring design logic, even across systems that do not appear to be related by descent. This is a feature that is quite surprising on the supposition that a mindless process is responsible for life’s origins, but is precisely what we might predict on the hypothesis that a mind played an important role. In other realms of experience, when we encounter recurring design logic, we habitually associate it with intelligent causes. For example, there are features of paintings that characterize a particular painter’s work, and features of buildings that are common between edifices designed by the same architect. There are even aspects of one’s writing that are distinctive of an individual author. This, then, is an example of a prediction made by the hypothesis of purposeful design — something we expect to see on the supposition of the involvement of an intelligent mind. There are plenty of examples of this sort of phenomenon in biology. For illustration purposes, I will focus here on one class of recurring design logic — two-component regulatory systems in bacteria.
What Are Two-Component Regulatory Systems?
Bacterial cells use two-component systems to sense and respond to environmental changes. As their name suggests, two-component systems characteristically involve two components — a sensor kinase and a response regulator. The sensor kinase, in response to a chemical or physical stimulus, undergoes autophosphorylation, whereby a phosphate group is transferred from ATP to a histidine residue on the kinase. The histidine protein kinase has two domains: an input domain and a transmitter domain. The former is located on the outside of the cell, and is ideally situated to detect incoming environmental signals. The latter is situated on the cytoplasmic face of the cell membrane, and is positioned such that it can interact with the response regulator. The phosphate group is transferred to the response regulator, which then drives a cellular response, such as turning genes on or off.
Two-component systems are extremely common among bacteria, and each utilizes the same basic design logic. In what follows, I shall provide a short survey of a few such examples.
Regulation of Outer Membrane Proteins in Escherichia coli
A two-component system regulates the expression of porins in response to environmental osmolarity (a measure of the concentration of solute particles in a solution). The sensor kinase for this system, located in the inner membrane, is EnvZ. EnvZ detects osmolarity changes and undergoes autophosphorylation. The response regulator, OmpR, receives the phosphate group from EnvZ and regulates the expression of genes.
When osmolarity is high, the kinase activity of EnvZ is activated, resulting in the phosphorylation of OmpR. When osmolarity is low, the phosphatase activity of EnvZ is activated, reducing levels of phosphorylated OmpR.
Upon phosphorylation, OmpR becomes an active dimer that has enhanced DNA-binding ability specific to ompC and ompF gene promoters. These are are porin genes that encode outer membrane proteins (which allow the passage of metabolites across the outer membrane of gram-negative bacteria). The pore diameter of OmpF is larger than OmpC. This allows for a ten-fold faster diffusion rate, which is advantageous under conditions of low osmolarity where nutrients are scarce. If osmotic pressure is low, the synthesis of OmpF is increased. If osmotic pressure is high, the expression of OmpC is increased. Moreover, transcription of micFantisense RNA is initiated. micF blocks translation of ompF by complementary binding – the synthesis of OmpF is thereby repressed.
Regulation of Chemotaxis
Bacteria are able to move towards a food source, such as glucose, by a process known as “chemotaxis.” A requisite for this process to work is the ability of the bacterial flagellar motor to literally shift gears so that it switches from spinning counter-clockwise to rotating clockwise. This change in rotation is brought about in response to chemical stimuli from the cell’s exterior. These chemical signals are detected by a two-component signal transduction circuit that operates to induce the switch in flagellar rotation.
Readers may find it helpful to refer to the following diagram while reading the descriptions that follow:
Image credit: Wikimedia Commons
How do bacteria detect a chemical gradient? The answer lies in a certain class of transmembrane receptors called methyl-accepting chemotaxis proteins (hereafter, MCPs). Different MCPs can detect different types of molecules, and are able to bind attractants or repellents. These receptors then communicate with — and activate — the so-called “Che proteins.”.
Proteins called CheA and CheW are bound to the receptor. The former is the histidine kinase for this system. Upon activation of the receptor, the CheA’s conserved histidine residue undergoes autophosphorylation. There are two response regulators called CheB and CheY. There is a transfer of a phosphoryl group to their conserved aspartate residue from CheA. CheY subsequently interacts with the flagellar switch protein called FliM. This induces the switching in flagellar direction from counterclockwise to clockwise.
This clockwise rotation upsets the entire flagella bundle and causes it to break up. The result is that the bacterium “tumbles.” This means that bacteria are able to re-direct their course and repeatedly re-evaluate and adjust their bearings in response to environmental stimuli such as food or poisons.
As for the other response regulator I mentioned, CheB, what does it do? When CheB is activated by the histidine kinase CheA, it operates as a methylesterase. This means that it actively removes methyl groups from glutamate residues on the receptor’s cytoplasmic surface. Meanwhile, another protein (called CheR) actively adds methyl residues to these same glutamate residues — that is to say, it works as a methyltransferase.
At this point the engineering shows a stroke of genius. If the stimulus is at a high level, there will be a corresponding decline in the level of phosphorylation of the CheA protein — and, as a consequence, of the response regulators CheY and CheB as well. Remember that the role of CheB is to remove methyl groups from glutamate residues on the receptor’s cytoplasmic surface. But now, phosphorylated CheB is not available and so this task is not performed. The degree of methylation of the MCPs will thus be raised. When the MCPs are fully methylated, the cell will swim continuously because the MCPs are no longer responsive to the stimuli.
This entails that the level of phosphorylated CheA and CheB will increase even when the level of attractant remains high, and the cell will commence the process of tumbling. But now, the phosphorylated CheB is able to demethylate the MCPs, and the receptors are again able to respond to the attracting chemical signals. In the case of repellents, the situation is similar — except that it is the least methylated MCPs which respond least while the fully methylated ones respond most. This kind of regulation also means that the bacterium has a memory system for chemical concentrations from the recent past and compares them to its currently receiving signals. It can thus detect whether it is moving towards or away from a chemical stimulus.
Quorum Sensing
The purpose of quorum sensing is essentially to ensure that sufficient cell numbers of a given species are present before initiating a response that requires the population density to be above a certain threshold. A single bacterial cell secreting a toxin into a eukaryotic organism is not likely to do the host any harm and would waste resources. If, however, all of the bacterial cells in a large population co-ordinate the expression of the toxin, the toxin is more likely to have the desired effect.
Each species that employs quorum sensing — which includes most gram-negative bacteria, and also some gram-positive bacteria — synthesizes a tiny signaling molecule (technically called an “autoinducer”), which diffuses freely across the cell’s membrane. Autoinducers are species-specific, which means that each cell of the same species makes the same molecule. This means that the autoinducer is only present in high concentrations inside the cell when there are many cells of the same species nearby. Inside the cell, the autoinducer binds to an activator protein which is specific for that particular molecule and thus signals the bacteria to begin transcription of specific genes.
For example, consider the case of the bioluminescent bacterium, Aliivibrio fischeri (pictured at the top of this article). The light that this species of bacteria emits results from the action of the enzyme, luciferase. An activator protein, called LuxR, is responsible for controlling the lux operons, which are in turn responsible for the transcription of the proteins required for luminescence. These operons are induced when the concentration of the autoinducer specific to Aliivibro fischeri reaches a high enough concentration. This autoinducer is itself synthesized by the enzyme which is encoded by the LuxI gene.
Image credit: Wikimedia commons
Quorum sensing is very widespread, particularly in gram negative bacteria. Pseudomonas aeruginosa, for example, uses such “population sampling” processes to trigger the expression of a significant number of unrelated genes when the population density reaches a certain threshold. These genes subsequently allow the cells to form a biofilm (which increases the pathogenicity of the organism and prevents the penetration of antibiotics). See the figure above on the role of two-component quorum sensing in bacterial biofilm formation
Recurring Design Logic
Here, I have described only a few examples of two-component regulatory systems, of which many more examples could be provided. Across these diverse systems, we see a recurring design logic, despite the fact that these systems are not related by evolutionary descent. This is precisely what we might expect to see if the same intelligent mind was involved in their origins, but is really quite surprising on the postulate of an undirected process of chance and physical necessity
Saturday, 25 January 2025
Friday, 24 January 2025
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