Darwinism's conundrum: the objective distinction between natural and artificial selection.

 What’s “Natural”? Engineering Creates a Conundrum for Evolutionists

David Coppedge 

Are humans natural? Writing in PNAS, Juha Merilä comments on, “Human-induced evolution of salmon by means of unnatural selection.” According to his bio page at Research Portal, Dr. Merilä is Professor in the Organismal and Evolutionary Biology Research Programme in the Ecological Genetics Research Unit of the University of Helsinki. He begins, 

By modifying environmental conditions, human activities are generating novel selection pressures, which pose challenges to wildlife. When faced with novel selection pressures, organismal populations can respond to this through evolutionary adaptation, modifying their phenotype through plastic changes, or evading these new pressures by migrating to more beneficial environments. Otherwise, they will face loss of fitness and eventually, even extirpation. Although alteration of natural environments by humans has been long recognized as a potential source of novel and strong selection pressures, demonstrating human-induced evolution has proven to be challenging. 

The conundrum is obvious here. He refers to “unnatural selection” and “alteration of natural environments by humans” that demonstrate “human-induced evolution” — but why should this be any different from what beavers do to their environments? Are beavers natural? Are their dams natural? Many animals disrupt their environments; are those cases natural?

I do not know Dr. Merilä’s stance on human origins, but it is a safe bet that he (as an evolutionary biologist) denies intelligent design, and believes humans evolved from other natural animals. If so, it is strange to call anything humans do “unnatural.” There seems to be a subconscious recognition in his writing that humans are exceptional, and culpable for damage they cause to “natural” environments. Otherwise, “human-induced evolution” is plain old evolution by natural — not unnatural — selection. 

The Human Impact on Salmon 

In his commentary, Merilä is reflecting on work by Jensen et al. in PNAS that illustrated the impact humans have had on “natural” Atlantic salmon populations. At the end of his article, Merilä waffles on the “natural” designation and confers the term “agency” on what salmon did in response — a word that overlaps with intelligent design. One could say that beavers are the “agents” of “beaver-induced evolutionary change,” but they had no choice in the matter since the drive to build dams is instinctive, built into their genetic nature. In the case of the salmon, the agency could have been indirect, but Merilä seems to suggest that humans could have, and should have, left the natural salmon alone.  

Whatever the selective agent behind the observed body size decline, the study by Jensen et al. provides compelling evidence that the size change is genetically based, driven by natural selection, and clearly associated with human interference with their environment. While concerns about undesirable consequences of human-induced genetic changes in natural fish populations were raised in 1950s, a lot of the early research on this topic failed to provide evidence that observed phenotypic shifts have a genetic basis and hence, represent evolutionary changes. With this in mind, one of the major contributions of the work of Jensen et al. is in providing hard evidence for human-induced evolutionary change. 

The confusion remains. Are humans acting naturally when they become “selective agents”? Are humans thus culpable for the “undesirable consequences” of genetic changes to “natural” fish? Who decides what is “undesirable”? Evolutionists believe that many unsavory consequences of evolutionary change, such as extinctions, have occurred throughout natural history before humans emerged. That label undesirable is an ethically loaded word unique to humans. A “natural” beach stranding of whales might be undesirable for the whales, but highly “desirable” for bacteria.  

Still More Confusion 

The confusion is evident also in the Jensen paper. The last paragraph says, 

Our study provides unequivocal evidence of unintentional human-induced evolution in a natural population, in which the species managed to adapt to the altered environment. River Eira once harbored some of the largest salmon in the world but has now evolved into an ordinary salmon population. This successful adaptation comes at a cost of reduced life-history diversity, and, potentially, reduced population stability and resilience to further environmental change. 

“Unintentional” is an interesting word here. Design advocates identify intentionality as a discriminator between chance and design. If humans had intended to make the fish evolve, and it cost the salmon some of their adaptability and resilience, would that have been unethical? If not, then whatever happened was “natural” and hardly worth worrying about.

We can tell, however, that Merilä had more on his mind, because he praised the Jensen team for documenting human-induced evolutionary change which had raised “concerns about undesirable consequences” back in the 1950s. Now there is hard evidence. The concerns were valid. Humans are guilty as charged. I’ll have more to say on this tomorrow.

File under"Well said." LXXXV

 "He who knows only his own side of the case knows little of that" 

          John Stuart Mill 

Lamarck gets the last laugh?

Epigenetics Directs Genetics — And That’s a Problem for Darwinism 

David Coppedge 

The power of epigenetic processes over genes continues to be a big subject in biology. Epigenetic processes control which genes are translated and which are silenced, which concentrations of transcripts are required, and how molecular machines assemble at the right times and places to steer gene products to their operational destinations. If sheet music is an argument for design, how much more the organization that makes it come alive in a marching band’s halftime show? 

The Guardian of the Epigenome 

The p53 protein has long been called the “guardian of the genome” for its key role in tumor suppression. Now, some German researchers are calling it “the guardian of the (epi)genome.” News from the University of Konstanz tells how a research team led by Ivano Amelio took a painstaking look at how p53 works.  

Cells — and their DNA integrity — are particularly at risk when they divide, as they duplicate their DNA in the process. “Like in any other replication process, such as photocopying a document or copying a digital file, it is disastrous if the template moves or is changed while the copy is being made. For this reason, genes cannot be transcribed – i.e. used as templates for proteins – while the DNA is being copied,” Amelio explains. If they are transcribed anyway, serious disruptions occur, which can lead to cancer-promoting mutations. The results from Amelio and his team, now appearing as the cover story in Cell Reports, show that p53 inactivation favours such copy-related damage. They found that p53 normally acts by changing cell metabolism in a way that prevents activation of genome regions that should remain inactive.  

Their work found that p53 is an epigenetic regulator: it keeps genes silent that should not be translated during mitosis by locking them away in heterochromatin. Without this control, genes become accessible to translation machinery at the wrong time, such as during mitosis. “This causes so much damage,” they found, “that it will drive cells into a state of genomic instability that favours and worsens cancer progression.” 

“By unravelling this mechanism, we could demonstrate that there is a link between metabolism, epigenetic integrity and genomic stability. In addition, we provided evidence that p53 represents the switch controlling the on/off status of this protection system in the response to environmental stress,” Amelio summarizes the finding.

The question of how p53-inactivated tumours develop genomic instability has plagued the scientific community for quite some time. “Now we have certainty that, in these tumours, there is a problem at the metabolic level that is reflected in the integrity of the epigenome. Hence, p53 should actually be called guardian of the (epi-)genome. 

Epigenetics Compacts Genes in Gametes 

The John Innes Centre in the UK announced the solution to an enigma: how plants compact their DNA in sperm cells. Animals, which have swimming sperm cells, do it by replacing their histones with protamines. But plants, which spread their gametes via pollen, maintain their histone-based chromatin through fertilization. Why the difference, and how do plants compact the DNA in the male gametes?

The answer was found by a research team at the Centre led by Professor Xiaoqi Feng. It involves condensates (see my article on the Caltech study) that form by phase separation, intrinsically disordered regions of certain proteins, and epigenetics. “Professor Feng’s research team used super-resolution microscopy, comparative proteomics, single-cell-type epigenomic sequencing and 3D genome mapping to investigate this mystery.” Key to the solution was identification of a histone variant named H2B.8. It is specifically expressed in sperm nuclei. 

H2B.8 has a long intrinsically disordered region (IDR), a feature that frequently allows proteins to undergo phase separation. The research found nearly all flowering plant species have H2B.8 homologs (copies), all of which contain an IDR, suggesting important functions. 

So why do plants need DNA compaction, when the sperm don’t need to swim to the egg? Pollen grains land on a pistil and send long pollen tubes to reach the eggs. Compaction of the sperm cells, therefore, serve a purpose for angiosperms. Interestingly, gymnosperms, which use a different method of pollination, do not compact their sperm genomes, and lack H2B.8. 

Dr Toby Buttress first author of the study said: “We propose that H2B.8 is a flowering plant evolutionary innovation that achieves a moderate level of nuclear condensation compared to protamines, which sacrifice transcription for super compaction. H2B.8-mediated condensation is sufficient for immotile sperm and compatible with gene activity.” 

Epigenetics Runs the Office 

A lively follow-up to Caltech’s findings last year about condensates was published by Nature, “The shape-shifting blobs that shook up cell biology.” Reporter Elie Dolgin calls these membraneless organelles droplets, condensates, and granules. She uses the same office floor plan metaphor that Caltech used: 

For years, if you asked a scientist how they pictured the inner workings of a cell, they might have spoken of a highly organized factory, with different departments each performing specialized tasks in delineated assembly lines.

Ask now, and they might be more inclined to compare the cell to a chaotic open-plan office, with hot-desking zones where different types of cellular matter gather to complete a task and then scatter to other regions. 

The picture is less one of robots anchored to the floor on an assembly line, and more one of intelligent actors gathering on the fly, interacting, sharing materials, and solving problems. Isn’t that just like squishy biology anyway? Cells seem like chaotic blobs at one level, but they somehow give rise to a flying owl, a leaping dolphin, and a mathematician at a chalkboard. Clearly things are working at levels of engineering beyond our current ability to fathom. 

“We have the observations that condensates form,” says Jonathon Ditlev, a cellular biophysicist at the Hospital for Sick Children in Toronto, Canada. “Now we need to show why they are important.” 

Dolgin relates how these “blobs” self-organize through phase separation, but many questions remain. How do the right ingredients get into these “molecular crucibles” that speed up interactions by orders of magnitude? How do they separate when the work is done? He doesn’t mention epigenetics in his article, but the implication is clear that genetics alone cannot explain this. 

Epigenetics Challenges Evolution 

Whether plant DNA compaction can be called an “evolutionary innovation” as opposed to a designed solution can be debated. Regarding that controversy, at The Scientist, Katarina Zimmer asks, “Do Epigenetic Changes Influence Evolution?”  

Evidence is mounting that epigenetic marks on DNA can influence future generations in a variety of ways. But how such phenomena might affect large-scale evolutionary processes is hotly debated. 

After telling about a case where nematodes inherited a stress response, Zimmer delves into the current “fierce debate” between believers and doubters about whether epigenetics requires revisions to evolutionary theory. 

No one doubts the examples of epigenetic inheritance, but some in the old guard consign them to minor roles in long-term evolution. Zimmer mentions the buzz generated by the  article by Stephen Buranyi at The Guardian asking, “Do we need a new theory of evolution?” (see David Klinghoffer’s analysis here). One of the revisionists Zimmer quotes is Alyson Ashe at the University of Sydney, who also observed epigenetic inheritance in C. elegans. 

Specifically, the Modern Synthesis developed in the 1940s supposes that evolution is driven solely by random DNA mutations. While many scientists question whether non-DNA-based mechanisms could be meaningful contributors to evolutionary processes, some say that textbooks are due for an update.

“We don’t need to rewrite and throw away the current theories, but they’re incomplete,” says Ashe. “They need adjustment to show how epigenetics can interplay with those theories.” 

Epigenetics Makes the Band Play 

Zimmer leaves the controversy unresolved, but it’s likely that Darwinians will have to face the epigenetic music soon as its drumbeat gets louder. If the instrumentalists are like the genes, other entities must be telling the band members what music to play, when to start, and how to scatter and gather into the next formation on the field, or else there would be cacophony. If neo-Darwinism cannot even get random notes on a page to result in a melody, how can it account for a drum major, manager, librarian, programmer, drill team and all the other entities needed for a coherent performance? Thanks to epigenetics, all the players condense in the right positions, move around while playing, and give a crowd-pleasing performance of “Strike Up the Band.” 

 

Design Detection by the numbers?

William Dembski Offers an Updated Edition of an Intelligent Design Classic

Evolution News @DiscoveryCSC 

On a new episode of ID the Future, mathematician and philosopher William Dembski talks with host Eric Anderson about a revised and updated edition of Dembski’s pioneering 1998 Cambridge University Press book, The Design Inference. Dembski says he stands by that work and his early contributions to intelligent design theory, but adds that he has learned a lot more in the intervening years, particularly from his work with Robert J. Marks and Winston Ewert at the Evolutionary Informatics Lab. Lessons from that and other research, Dembski explains, will enrich the new edition. What light do these design-detecting methods shed on modern evolutionary theory? To find out, download the podcast or listen to it here. 

 

One more thing re: the Bible's antitrinitarian bias.

 The advocates of the dogma of the trinity claim that its constituents are persons but not beings. For the sake of continuity we'll ignore that assault on the lexicon only to point out that at 

Revelation1:4KJV"John to the seven churches which are in Asia: Grace be unto you, and peace, from him which is(Grk. Ho On: the being), and which was, and which is to come; and from the seven Spirits which are before his throne; "  

The God and Father of Jesus Christ is identified as the supreme being. Also how can one be anyone(let alone the most high God) without first having concrete existence. If one is not a BEING one certainly can't BE a person with whom anyone can have a relationship. Christendom's absurdity has the effect of reducing JEHOVAH to an abstraction, like numbers or colors only even more nonspecific.