evolutionnewsandviews--2020-03-13--Lesson from a Carnivorous Plant

Lesson from a Carnivorous Plant

I won ’ t pretend to you that this isn ’ t a stressful time .
In search of distraction , today I ’ ve been thinking about a rather odd water dweller .
It ’ s the carnivorous plant Utricularia , aka aquatic bladderwort .
Granville Sewell wrote about it here recently , citing plant geneticist Wolf-Ekkehard Lönnig and others , calling it “ Michael Behe ’ s ‘ Irreducibly Complex ’ Mousetrap in Nature.
” Its mechanism is not just complex , but irreducibly so .
Like a mousetrap , it requires purpose in its design .
Check @ @ @ @ @ @ @ the John Innes Centre in the U.K. concludes , “ Plants are seriously smart.
” I can ’ t tell if that ’ s supposed to be ironic , but the mechanism is indeed ingenious .
If your German skills are up for it , you can read Dr. Lönnig ’ s book on The Evolution of Carnivorous Plants , downloadable here , detailing the limits of what natural selection can do in this case of the “ fastest plant in the world , ” the “ most wonderful plant in the world @ @ @ @ @ @ @ movement of all carnivorous plants.
” ( These are some comments of his fellow scientists cited in the book . )
Aquatic bladderworts don ’ t have the charm of a rose , a lily , cherry blossoms , or many other plants you can think of .
Even the name is unlovely .
They don ’ t appear at all on a chart of symbolic plants , which bring to mind wonderful associations of love , passion , and other sentiments .
But in being such an in-your-face example of intelligent design @ @ @ @ @ @ @ recommend it .
As Michael Behe told me in an email , “ It ’ s craziness to think such wonders don ’ t require design.
” Dr. Sewell adds , “ All of the carnivorous plants are great examples of irreducible complexity , but the bladderwort is especially interesting because of its water-tight trap ( with trigger hair attached to a valve-like door ) .
How much of a selective advantage is there in an ‘ almost ’ water-tight bladder ?
” So too with the “ Lovable Venus Flytrap , ” @ @ @ @ @ @ @ , whose design can only reflect “ foresight.
” Lönnig and a colleague from the Max Planck Institute for Plant Breeding Research point to “ other carnivorous plant genera ( Dionaea , Aldovanda , Genlisea ) [ that ] come at least very near to ‘ such a case ’ of irreducible complexity.
” The lesson may be that while nature can be frightening — like a storm at sea , as Behe wrote here the other day — it also demonstrates that a plan , a design , is somehow at work @ @ @ @ @ @ @ plan , beyond our ability to fully comprehend .
Evolutionists may deny it .
But the world is not a place ruled by random forces alone .
Whether the rose or the bladderwort , the marvels of life did not come about solely by chance workings in the blind natural world .
Behind the veil there is a good plan .
Photo at the top : Utricularia aurea , by Meneerke bloem / CC BY-SA .

I won’t pretend to you that this isn’t a stressful time. In search of distraction, today I’ve been thinking about a rather odd water dweller. It’s the carnivorous plant Utricularia, aka aquatic bladderwort. Granville Sewell wrote about it here recently, citing plant geneticist Wolf-Ekkehard Lönnig and others, calling it “Michael Behe’s ‘Irreducibly Complex’ Mousetrap in Nature.” Its mechanism is not just complex, but irreducibly so. Like a mousetrap, it requires purpose in its design. Check out these videos:
The video from the John Innes Centre in the U.K. concludes, “Plants are seriously smart.” I can’t tell if that’s supposed to be ironic, but the mechanism is indeed ingenious.
If your German skills are up for it, you can read Dr. Lönnig’s book on The Evolution of Carnivorous Plants, downloadable here, detailing the limits of what natural selection can do in this case of the “fastest plant in the world,” the “most wonderful plant in the world,” with the “fastest trapping movement of all carnivorous plants.” (These are some comments of his fellow scientists cited in the book.)
Aquatic bladderworts don’t have the charm of a rose, a lily, cherry blossoms, or many other plants you can think of. Even the name is unlovely. They don’t appear at all on a chart of symbolic plants, which bring to mind wonderful associations of love, passion, and other sentiments.
In-Your-Face Intelligent Design
But in being such an in-your-face example of intelligent design, this plant has something else to recommend it. As Michael Behe told me in an email, “It’s craziness to think such wonders don’t require design.” Dr. Sewell adds, “All of the carnivorous plants are great examples of irreducible complexity, but the bladderwort is especially interesting because of its water-tight trap (with trigger hair attached to a valve-like door). How much of a selective advantage is there in an ‘almost’ water-tight bladder?” So too with the “Lovable Venus Flytrap,” as a Marcos Eberlin has put it, whose design can only reflect “foresight.” Lönnig and a colleague from the Max Planck Institute for Plant Breeding Research point to “other carnivorous plant genera (Dionaea, Aldovanda, Genlisea) [that] come at least very near to ‘such a case’ of irreducible complexity.”
The lesson may be that while nature can be frightening — like a storm at sea, as Behe wrote here the other day — it also demonstrates that a plan, a design, is somehow at work. It’s a highly complex plan, beyond our ability to fully comprehend. Evolutionists may deny it. But the world is not a place ruled by random forces alone. Whether the rose or the bladderwort, the marvels of life did not come about solely by chance workings in the blind natural world. Behind the veil there is a good plan.
Photo at the top: Utricularia aurea, by Meneerke bloem / CC BY-SA.


evolutionnewsandviews--2020-03-13--Blurring the Line Between Natural and Artificial

In 2010 , Craig Venter ’ s lab embedded text and images into the DNA of a bacterium .
Would a future investigator be able to tell ?
It would take special tools to see the insertion , but the difference should be detectable .
What if bioengineers invent new genes that use the cell ’ s translation machinery to build non-natural proteins ?
This is already coming to pass with CRISPR/Cas9 methods .
If the insertion were made in an embryo , all the adult cells would inherit the change .
The line between natural and artificial is getting @ @ @ @ @ @ @ the new bioengineering developments are similar in principle to longstanding cases of artificial interference in nature , as in agriculture , camouflage , or construction of simple dwellings with available materials like grass or fallen branches .
The Design Filter takes into account what chance and natural law can do .
There will always be difficult cases ; ID errs on the side of non-intelligent causes when the degree of specified complexity is borderline .
But now , specified complexity exists in both “ natural ” DNA and DNA altered by human intelligence @ @ @ @ @ @ @ between human intelligent causes and non-human intelligent causes , whether those be space aliens , spirit beings , or a transcendent Creator .
In their epilogue to the book The Mystery of Life ’ s Origin ( newly updated and expanded by Discovery Institute Press ) , Charles Thaxton , Walter Bradley , and Roger Olsen considered five sources for a “ more satisfactory theory of origins.
” These included : new natural laws , panspermia , directed panspermia , “ special creation by a creator within the cosmos , ” and “ @ @ @ @ @ @ @ cosmos.
” The last four involve intentional , mind-directed activity ; only # 5 necessarily involves the supernatural .
To the investigator , though , the output of the Design Filter would be the same .
It boils down to natural versus artificial : unguided , or mind-directed .
But what happens when the mind-directed interference of bioengineers gets so good , it looks natural ?
It becomes a case of the perfect crime , leaving the investigator baffled .
Today ’ s Mars rovers are easily distinguished from the rocky , dusty @ @ @ @ @ @ @ future designers made them look like rocks , functioning when they roll over in the wind ?
This is a growing challenge for ID as bioengineering progresses .
News from ETH Zurich says : This implies that an investigator will have to search the ancestry of an organism to make a design inference .
The author , Dr .
Beat Christen of ETH , says this is not science fiction .
The tools to do this are already in place .
“ I am convinced that they will soon be a reality , @ @ @ @ @ @ @ require designing every molecular machine de novo .
Darwin Got Something Right How would an investigator in such cases be able to differentiate a synthetic organism from known examples of “ mosaic organisms ” or natural organisms containing orphan genes ?
On ID the Future recently , Paul Nelson acknowledged from his trip to the Galápagos Islands that Darwin got something right : organisms have a history .
There can be some natural modification in a lineage over time , as in the case of flightless cormorants , he said , and ID @ @ @ @ @ @ @ theory of design .
With bioengineering entering the mix , they will also have to distinguish natural history from artificial history in the codes of life .
This is an extension of what they must do in distinguishing the artificial history of cultivated crops and animal breeds .
The dachshund looks very different from the wolf from which domestic dogs descended .
The ears of corn we buy in supermarkets differ substantially from the maize or teosinte from which farmers selectively bred them .
But now that bioengineers can selectively edit the genes @ @ @ @ @ @ @ history in the genotype as well as the phenotype .
The ability to do this could become very important .
Another challenge will arise as human history progresses .
Right now , we have more clues to trace genetic editing to particular labs .
But as the number of gene editing labs grows over time , and editing becomes routine — maybe even to individuals — it may become impossible to trace the edits to their source .
This happens with artificial breeding as well ; unless particular breeders documented their work , @ @ @ @ @ @ @ clues to the time and place of origin for a particular breed .
It could have started in ancient Babylon , Egypt , or Rome .
It ’ s not ID ’ s job to identify the agent , the books explain ( e.g.
, The Design Revolution , Chapter 26 ) ; the investigator should be able to detect design from its effects alone .
Genetic tinkering will make that inference more difficult , if genetic engineers continue to blur the line between natural genetic information and edited genetic information .
Moreover @ @ @ @ @ @ @ work .
As in the case of bioweapons , the source may intentionally try to conceal its designs .
In Nature , three scientists wrote a review titled , “ The coming of age of de novo protein design.
” The opening sentence of the article by Huang , Boyken , and Baker makes a point that Douglas Axe and Ann Gauger would agree with : functional space is dwarfed by sequence space .
The summary on Phys.org has the title , “ Scientists can now design new proteins from scratch with specific @ @ @ @ @ @ @ de novo protein design involves evolutionary algorithms , in which the intelligent agent provides the “ selective pressure ” to find the fittest protein for the chosen goal .
If engineers succeed in taking an amino acid sequence that folds in silico and then can reverse engineer the genetic code for it so that it can be translated by a natural bacterium ’ s cellular machinery , does it become indistinguishable from an orphan gene ?
In both instances , the Design Filter would register a positive , but should ID advocates be @ @ @ @ @ @ @ it matter ?
Another blurring of lines between the natural and the artificial occurs in cases of guiding organisms to do unnatural things .
At the Israel Institute of Technology ( Technion ) , biotechnicians have turned a bacterial cell into a biological computer .
Once again , telling the difference will require a robust design inference .
This type of tinkering might be compared to animal training .
Shown two wolves , one trained to respond to human words and one in its wild state , could the investigator tell them apart @ @ @ @ @ @ @ but discriminating biological computers from wild bacteria could be a lot tougher , tractable only to molecular biologists .
These examples in the news present both challenges and opportunities .
As lines blur between the natural and the synthetic in the 21st century , the design inference must be tightened accordingly .
The specified-complexity criterion is robust against false positives ( “ This is designed ” when it ’ s not ) , but not against false negatives ( “ This isn ’ t designed ” when it is ; see William Dembski @ @ @ @ @ @ @ 22-28 ) .
To avoid a growing number of false negatives , the investigator must now become aware of the history of the genotype as well as the phenotype .
It ’ s well and good to lump all instances of complex specified information into the “ designed ” category , whether a gene was edited by humans or designed by a transcendent entity .
But these rapidly growing capabilities for bioengineering raise additional challenges for the ID community .
Fortunately , with the challenges come opportunities .
The very act of genetic @ @ @ @ @ @ @ the scientific community of the degree of specified complexity in “ natural ” organisms , and the extremely limited tolerances for success .
Nature confesses : The design inference is not changing in principle ; it only needs clarification to fit more challenging cases .
It also affords opportunities to communicate design principles to those still clinging to the hope that blind , unguided processes are capable of navigating endless fields of haystacks for a tiny number of needles .

In 2010, Craig Venter’s lab embedded text and images into the DNA of a bacterium. Would a future investigator be able to tell? It would take special tools to see the insertion, but the difference should be detectable. What if bioengineers invent new genes that use the cell’s translation machinery to build non-natural proteins? This is already coming to pass with CRISPR/Cas9 methods. If the insertion were made in an embryo, all the adult cells would inherit the change. The line between natural and artificial is getting more blurry.
In a sense, the new bioengineering developments are similar in principle to longstanding cases of artificial interference in nature, as in agriculture, camouflage, or construction of simple dwellings with available materials like grass or fallen branches. The Design Filter takes into account what chance and natural law can do. There will always be difficult cases; ID errs on the side of non-intelligent causes when the degree of specified complexity is borderline. But now, specified complexity exists in both “natural” DNA and DNA altered by human intelligence. There should be ways to distinguish between human intelligent causes and non-human intelligent causes, whether those be space aliens, spirit beings, or a transcendent Creator.
Thaxton, Bradley, and Olsen
In their epilogue to the book The Mystery of Life’s Origin (newly updated and expanded by Discovery Institute Press), Charles Thaxton, Walter Bradley, and Roger Olsen considered five sources for a “more satisfactory theory of origins.” These included: new natural laws, panspermia, directed panspermia, “special creation by a creator within the cosmos,” and “special creation by a creator outside the cosmos.” The last four involve intentional, mind-directed activity; only #5 necessarily involves the supernatural. To the investigator, though, the output of the Design Filter would be the same. It boils down to natural versus artificial: unguided, or mind-directed. But what happens when the mind-directed interference of bioengineers gets so good, it looks natural? It becomes a case of the perfect crime, leaving the investigator baffled. Today’s Mars rovers are easily distinguished from the rocky, dusty environment of Mars. But what if future designers made them look like rocks, functioning when they roll over in the wind?
This is a growing challenge for ID as bioengineering progresses. News from ETH Zurich says:
Every living creature on earth has parents, grandparents, great-grandparents and so on — representing an unbroken line of ancestry all the way back to the very first organisms that lived here billions of years ago. Soon we will have life forms that have no such direct lineage. The first of these organisms will be bacteria. Bioengineers will use computers to develop such bacteria and specifically tailor them for applications in medicine, industry or agriculture. With the help of DNA synthesisers, they will build these bacteria’s genomes from the ground up to produce artificial life forms. [Emphasis added.]
This implies that an investigator will have to search the ancestry of an organism to make a design inference.
I don’t mean organisms in which only individual genes have been altered – a technique that has been applied in biotechnology and crop breeding for decades, and that today’s CRISPR gene scissors have made very simple. No, I mean organisms for which bioengineers have literally developed the genome from scratch so that they can synthesise it in the lab.
The author, Dr. Beat Christen of ETH, says this is not science fiction. The tools to do this are already in place. “I am convinced that they will soon be a reality,” he says. It may not require designing every molecular machine de novo.
Digital databases store over 200,000 genome sequences from a broad range of organisms providing us access to a wealth of molecular building plans. By cleverly combining or modifying known genetic functions, bioengineers can develop microorganisms with new and useful characteristics.
Darwin Got Something Right
How would an investigator in such cases be able to differentiate a synthetic organism from known examples of “mosaic organisms” or natural organisms containing orphan genes? On ID the Future recently, Paul Nelson acknowledged from his trip to the Galápagos Islands that Darwin got something right: organisms have a history. There can be some natural modification in a lineage over time, as in the case of flightless cormorants, he said, and ID advocates need to build that into their theory of design. With bioengineering entering the mix, they will also have to distinguish natural history from artificial history in the codes of life.
This is an extension of what they must do in distinguishing the artificial history of cultivated crops and animal breeds. The dachshund looks very different from the wolf from which domestic dogs descended. The ears of corn we buy in supermarkets differ substantially from the maize or teosinte from which farmers selectively bred them. But now that bioengineers can selectively edit the genes, they will have to discern the history in the genotype as well as the phenotype. The ability to do this could become very important.
Another challenge will arise as human history progresses. Right now, we have more clues to trace genetic editing to particular labs. But as the number of gene editing labs grows over time, and editing becomes routine — maybe even to individuals — it may become impossible to trace the edits to their source. This happens with artificial breeding as well; unless particular breeders documented their work, historians and archaeologists can only gain indirect clues to the time and place of origin for a particular breed. It could have started in ancient Babylon, Egypt, or Rome. It’s not ID’s job to identify the agent, the books explain (e.g., The Design Revolution, Chapter 26); the investigator should be able to detect design from its effects alone. Genetic tinkering will make that inference more difficult, if genetic engineers continue to blur the line between natural genetic information and edited genetic information. Moreover, not all gene editors publish their work. As in the case of bioweapons, the source may intentionally try to conceal its designs.
Functional Space and Sequence Space
In Nature, three scientists wrote a review titled, “The coming of age of de novo protein design.” The opening sentence of the article by Huang, Boyken, and Baker makes a point that Douglas Axe and Ann Gauger would agree with: functional space is dwarfed by sequence space.
There are 20200 possible amino-acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the physical principles that underlie protein folding. Computational methodology has advanced to the point that a wide range of structures can be designed from scratch with atomic-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnology.
The summary on Phys.org has the title, “Scientists can now design new proteins from scratch with specific functions.” One of the techniques of de novo protein design involves evolutionary algorithms, in which the intelligent agent provides the “selective pressure” to find the fittest protein for the chosen goal. If engineers succeed in taking an amino acid sequence that folds in silico and then can reverse engineer the genetic code for it so that it can be translated by a natural bacterium’s cellular machinery, does it become indistinguishable from an orphan gene? In both instances, the Design Filter would register a positive, but should ID advocates be able to tell the difference? Does it matter?
Another blurring of lines between the natural and the artificial occurs in cases of guiding organisms to do unnatural things. At the Israel Institute of Technology (Technion), biotechnicians have turned a bacterial cell into a biological computer.
In recent decades, the barriers between engineering and life sciences have been falling, and from the encounter between the two different disciplines, a new science — synthetic biology — was born. Synthetic biology introduces engineering into biology, makes it possible to design and build biological systems that don’t exist in nature, and supplies an innovative toolbox for reprogramming the genetic code in living creatures, including humans…. “We built a kind of biological computer in the living cells. In this computer, as in regular computers, circuits carry out complicated calculations,” said Barger. “Only here, these circuits are genetic, not electronic, and information are [sic] carried by proteins and not electrons.”
Once again, telling the difference will require a robust design inference. This type of tinkering might be compared to animal training. Shown two wolves, one trained to respond to human words and one in its wild state, could the investigator tell them apart by their behavior alone? Probably, but discriminating biological computers from wild bacteria could be a lot tougher, tractable only to molecular biologists.
Challenges and Opportunities
These examples in the news present both challenges and opportunities. As lines blur between the natural and the synthetic in the 21st century, the design inference must be tightened accordingly. The specified-complexity criterion is robust against false positives (“This is designed” when it’s not), but not against false negatives (“This isn’t designed” when it is; see William Dembski, No Free Lunch, pp. 22-28). To avoid a growing number of false negatives, the investigator must now become aware of the history of the genotype as well as the phenotype.
It’s well and good to lump all instances of complex specified information into the “designed” category, whether a gene was edited by humans or designed by a transcendent entity. But these rapidly growing capabilities for bioengineering raise additional challenges for the ID community. Fortunately, with the challenges come opportunities. The very act of genetic engineering must surely be raising awareness in the scientific community of the degree of specified complexity in “natural” organisms, and the extremely limited tolerances for success. Nature confesses:
It is useful to begin by considering the fraction of protein sequence space that is occupied by naturally occurring proteins [1012 out of 20200]…Evidently, evolution has explored only a tiny region of the sequence space that is accessible to proteins.
The design inference is not changing in principle; it only needs clarification to fit more challenging cases. It also affords opportunities to communicate design principles to those still clinging to the hope that blind, unguided processes are capable of navigating endless fields of haystacks for a tiny number of needles.
Photo: Topiary animals, by Doko Jozef Kotulič / CC BY.


evolutionnewsandviews--2020-03-12--China Credibly Accused of Organ-Harvesting Atrocity

Last week , the Independent Tribunal into Forced Organ Harvesting from Prisoners of Conscience in China issued its final report concluding that China engages in the systematic human-rights atrocity of killing political and other prisoners and harvesting their organs .
( I wrote about the preliminary report here . )
It is a horrific account to which woefully inadequate attention has been paid .
Over more than 500 detailed pages , the report presents shocking evidence of horrific human-rights abuses , including from witness testimony , analyses of public records , and reviewing of scholarly reports .
The question presented @ @ @ @ @ @ @ the final “ Judgment ” : If the accusations are true , then thousands of innocent people have been killed…having their bodies — the physical integrity of their beings — cut open while still alive for their kidneys , livers , hearts , lungs , cornea and skin to be removed and turned into commodities for sale .
Those innocents were killed by doctors simply because they believed , for example , in truthfulness , compassion , and forbearance and lived lives of healthy exercise and meditation and because the way they lived @ @ @ @ @ @ @ and objectives of the totalitarian state of the People ’ s Republic of China .
And yet the People ’ s Republic of China has done little to challenge the accusations except to say that they were politically motivated lies .
The Judgment convincingly concludes that China is guilty as charged .
According to the report , beginning at page 415 , there are four methods by which China kills prisoners and harvests their organs .
• Organ harvesting under the pretext of brain death ( taking organs from people not really dead @ @ @ @ @ @ @ , if anything , will be done about it ?
So far , the depressing answer is , “ Not much.
” Oh , the U.S. has imposed certain sanctions .
But , as the old saying goes , that and six bits will buy you a cup of coffee .
Under the current circumstances , the private sector may possess greater soft power than governments to mitigate this evil .
Remember when corporations tripped over each other to threaten Indiana with loss of business for passing the Religious Freedom Restoration Act , @ @ @ @ @ @ @ LGBT community ?
Remember when private companies threatened to pull out of South Carolina for its transgender “ bathroom ” law ?
China ’ s abuses are exponentially worse .
So , why haven ’ t these companies threatened the same “ canceling ” of China for its truly heinous and murderous human-rights abuses ?
We all know that the answer is money .
Far more is at stake for these companies in China than ever was in Indiana and South Carolina .
But that road flows both ways .
China needs our @ @ @ @ @ @ @ them , meaning that enterprises such as Apple , Nike , and Boeing may have greater ability to save persecuted Chinese than the United States Department of State .
The time has come for public pressure to be placed on these companies to put their business decisions where their PR departments claim their values are .
We could start with appropriate Congressional committees holding hearings on this issue and inviting CEOs of these companies to attend and answer some pointed questions .

Last week, the Independent Tribunal into Forced Organ Harvesting from Prisoners of Conscience in China issued its final report concluding that China engages in the systematic human-rights atrocity of killing political and other prisoners and harvesting their organs. (I wrote about the preliminary report here.) It is a horrific account to which woefully inadequate attention has been paid.
Shocking Evidence
Over more than 500 detailed pages, the report presents shocking evidence of horrific human-rights abuses, including from witness testimony, analyses of public records, and reviewing of scholarly reports. The question presented could not be more disturbing. From the final “Judgment”:
If the accusations are true, then thousands of innocent people have been killed…having their bodies — the physical integrity of their beings — cut open while still alive for their kidneys, livers, hearts, lungs, cornea and skin to be removed and turned into commodities for sale. Those innocents were killed by doctors simply because they believed, for example, in truthfulness, compassion, and forbearance and lived lives of healthy exercise and meditation and because the way they lived was seen as dangerous to the interests and objectives of the totalitarian state of the People’s Republic of China. And yet the People’s Republic of China has done little to challenge the accusations except to say that they were politically motivated lies.
The Judgment convincingly concludes that China is guilty as charged. According to the report, beginning at page 415, there are four methods by which China kills prisoners and harvests their organs.
Organ harvesting from prisoners incompletely executed by shooting; Organ harvesting from prisoners after lethal injection; Execution by organ explantation (killing by organ harvesting); Organ harvesting under the pretext of brain death (taking organs from people not really dead).
The question becomes, what, if anything, will be done about it? So far, the depressing answer is, “Not much.” Oh, the U.S. has imposed certain sanctions. But, as the old saying goes, that and six bits will buy you a cup of coffee.
A Role for the Private Sector
Under the current circumstances, the private sector may possess greater soft power than governments to mitigate this evil. Remember when corporations tripped over each other to threaten Indiana with loss of business for passing the Religious Freedom Restoration Act, which critics claimed was discriminatory against the LGBT community? Remember when private companies threatened to pull out of South Carolina for its transgender “bathroom” law?
China’s abuses are exponentially worse. So, why haven’t these companies threatened the same “canceling” of China for its truly heinous and murderous human-rights abuses?
We all know that the answer is money. Far more is at stake for these companies in China than ever was in Indiana and South Carolina.
But that road flows both ways. China needs our private sector more than these companies need them, meaning that enterprises such as Apple, Nike, and Boeing may have greater ability to save persecuted Chinese than the United States Department of State.
The time has come for public pressure to be placed on these companies to put their business decisions where their PR departments claim their values are. We could start with appropriate Congressional committees holding hearings on this issue and inviting CEOs of these companies to attend and answer some pointed questions.
Photo credit: McKay Savage [CC BY 2.0], via Wikimedia Commons.
Cross-posted at The Corner.


evolutionnewsandviews--2020-03-12--Listen: Biophysicist and Philosopher Kirk Durston on Experimental Science

On a new episode of ID the Future , biophysicist and philosopher Kirk Durston discusses his recent article series about @ @ @ @ @ ( 1 ) experimental science , which is generally very trustworthy , with some exceptions @ @ @ @ @ science , which can be trustworthy but often takes huge leaps into the doubtable and @ @ @ @ @ ) fantasy science , which is essentially science fiction masquerading as actual science .
In @ @ @ @ @ , Durston focuses on experimental science .
Such science is , at its best , @ @ @ @ @ says he has yet to find a true conflict between experimental , reproducible scientific observations @ @ @ @ @ The contradictions he encountered were all between his faith and the inferences that some scientists @ @ @ @ @ .
Durston and host Andrew McDiarmid then move into a discussion of the reproducibility crisis @ @ @ @ @ Durston explains , without a healthy scientific culture and the right incentives , experimental science @ @ @ @ @ .
Download the podcast or listen to it here .

On a new episode of ID the Future, biophysicist and philosopher Kirk Durston discusses his recent article series about three types of science — (1) experimental science, which is generally very trustworthy, with some exceptions; (2) inferential science, which can be trustworthy but often takes huge leaps into the doubtable and dodgy; and (3) fantasy science, which is essentially science fiction masquerading as actual science.
In this first of three episodes, Durston focuses on experimental science. Such science is, at its best, reproducible and verifiable. Durston says he has yet to find a true conflict between experimental, reproducible scientific observations and his religious faith. The contradictions he encountered were all between his faith and the inferences that some scientists were drawing from experimental science.
Durston and host Andrew McDiarmid then move into a discussion of the reproducibility crisis in experimental science. As Durston explains, without a healthy scientific culture and the right incentives, experimental science can quickly fall into disrepair. Download the podcast or listen to it here.
Photo credit: CDC via Unsplash.


evolutionnewsandviews--2020-03-11--With a Hopeful Message About Life’s “X Factor,” Episode 5 of Secrets of the Cell Is Well Timed

Michael Behe is a biochemist , leading proponent of intelligent design , and a wise guide to understanding the wonders of life with its mysterious “ purposeful arrangement of parts.
” The new series from Discovery Institute , Secrets of the Cell with Michael Behe , concludes today with a last consideration of the “ X Factor ” that appears to lie behind the wonderful , irreducible complexity of biology .
That “ X Factor , ” he explains , is an intelligence inconceivably beyond our own : Secrets distills the argument for intelligent design in five-to-eight minute episodes , @ @ @ @ @ @ @ sure ID has never been presented more accessibly , in a way anyone can easily understand .
Share Secrets of the Cell with your family , friends , and social media network !
What a remarkable thing that the design of the universe was almost universally appreciated , by scientists , philosophers , and everyone else , whether religious or not , until the middle of the 19th century .
Charles Darwin wove an argument that strangely changed the culture of thinking , around the globe , in ways that corroded many people @ @ @ @ @ @ @ is a good and benevolently ordered place .
So it ’ s fortuitous to be releasing this now — more welcome than the producers could have expected .
With our country and much of the world stressed by worries about a sickness , on a scale we ’ ve never seen before , it ’ s a reminder that the universe is not governed by random accidents only .
Behe is the first to admit , as he does in this episode , that science can ’ t offer answers to all our @ @ @ @ @ @ @ to good people , ” for one , is a secret that philosophy and theology can seek to address , perhaps not successfully .
Certainly it ’ s beyond what science can say .
It is reassuring , then when we are upset this way , to think that there is indeed a design behind our existence , that a designer cared to instill a purpose in all the forms of life we see , which are of overwhelming beauty and marked everywhere with hints of an underlying love .
Thank you to @ @ @ @ @ @ @

Michael Behe is a biochemist, leading proponent of intelligent design, and a wise guide to understanding the wonders of life with its mysterious “purposeful arrangement of parts.” The new series from Discovery Institute, Secrets of the Cell with Michael Behe, concludes today with a last consideration of the “X Factor” that appears to lie behind the wonderful, irreducible complexity of biology. That “X Factor,” he explains, is an intelligence inconceivably beyond our own:
Secrets distills the argument for intelligent design in five-to-eight minute episodes, five in all. I’m sure ID has never been presented more accessibly, in a way anyone can easily understand. Share Secrets of the Cell with your family, friends, and social media network!
What a remarkable thing that the design of the universe was almost universally appreciated, by scientists, philosophers, and everyone else, whether religious or not, until the middle of the 19th century. Charles Darwin wove an argument that strangely changed the culture of thinking, around the globe, in ways that corroded many people’s previous confidence that the world is a good and benevolently ordered place.
So it’s fortuitous to be releasing this now — more welcome than the producers could have expected. With our country and much of the world stressed by worries about a sickness, on a scale we’ve never seen before, it’s a reminder that the universe is not governed by random accidents only. Behe is the first to admit, as he does in this episode, that science can’t offer answers to all our questions. “Why bad things happen to good people,” for one, is a secret that philosophy and theology can seek to address, perhaps not successfully. Certainly it’s beyond what science can say.
It is reassuring, then when we are upset this way, to think that there is indeed a design behind our existence, that a designer cared to instill a purpose in all the forms of life we see, which are of overwhelming beauty and marked everywhere with hints of an underlying love. Thank you to Professor Behe for this well-timed series!


evolutionnewsandviews--2020-03-11--Researchers: It Exists; Therefore, It Evolved

The way some evolutionary biologists and some uncritical reporters in the media talk , probabilistic miracles are routine events .
Natural selection is omnipotent so it can handle any observation in biology .
Since evolution is already a fact , no other explanation or argument is needed .
It exists ; therefore it evolved .
Take the case of de novo genes .
Darwin skeptics argue that the origin of a new gene or protein by chance is so fantastically improbable , it will never happen anywhere in the history of the universe , even under the most favorable circumstances @ @ @ @ @ @ @ evolutionists ; since evolution is a fact , it happened .
This is a variation on a formulation offered here last year , “ To solve a problem , declare it solved.
” Watch the faith of evolutionists at Trinity College Dublin when they consider the origin of orphan genes .
They report , “ Genes from scratch — far more common and important than we thought.
” Over time , genes change via random mutations .
Some of these changes result in serious defects and are rarely passed on to the next @ @ @ @ @ @ @ and others confer significant advantages , which become favoured due to natural selection and end up being passed on to future generations .
This is the main source of genetic novelty and how organisms differ from each other .
However , genetic novelty can also be generated by totally new genes evolving from scratch .
[ Emphasis added . ]
They exist ; therefore they evolved .
Totally new genes evolved from scratch .
These evolutionists are aware that the existence of orphan genes looks like a tough problem for Darwinism .
But @ @ @ @ @ @ @ a tough evolutionary problem though .
They don ’ t look like other genes , so where do they come from ?
One idea is that they can originate seemingly from nothing : over long , evolutionary timescales , a completely novel gene can emerge de novo out of a region in the genome that is made up of junk DNA .
Alternatively , with enough time , two ‘ cousin ’ genes can diverge so much that we can no longer identify the relationship between them .
Thus , a gene may @ @ @ @ @ @ @ orphan without having really emerged de novo .
Surely they are not going to pursue option 1 , that orphan genes appeared out of junk DNA ?
And yet we see them discount option 2 , that orphan genes are descendants of genes that diverged long ago .
Only about a third of them seem to have come about from pre-existing genes , they reckon .
What can they do ?
Their method of determining how orphan genes originated is simple .
Here it is : they counted them .
Since they exist @ @ @ @ @ @ @ for evolution to create them .
Professor of genetics Aoife McLysaght explains : From the junkpile of non-coding DNA , strands with “ potential ” to be functional exist , waiting for their moment in the light .
Once they show some function , natural selection is fully capable of amplifying them into genes from scratch .
Assistant professor of computational systems biology Anne-Ruxanda Carvunis has no problem with declaring the problem solved .
Evolution is a fact , remember ?
It ’ s the Darwin skeptics ’ fault if they can ’ @ @ @ @ @ @ @ refresher on the difference between order and complexity would help .
Their paper in Nature Communications shows that the team of 16 , including Carvunis and McLysaght , did perform some busy work to argue for the innovative power of evolution .
For instance , they found an orphan gene in yeast that was not present in its assumed evolutionary ancestor .
Simple answer : its existence served as “ confirming the de novo origination of ” the gene .
Why , all that non-coding junk must be pregnant with “ proto-genes ” @ @ @ @ @ @ @ !
Once they show a little talent ( are “ preadapted ” ) , natural selection is sure to make them masters of fitness .
These emerging proto-genes , rather than being stumbling beginners , must be even more likely to race to the fitness goal .
Mutations that cause changes to the sequence or expression of established genes are typically constrained by preexisting selected effects—the specific physiological processes mediated by the gene products that are maintained by natural selection .
In contrast , emerging proto-genes are expected to mostly lack such constraints @ @ @ @ @ @ @ .
This would leave them more readily accessible to evolutionary changes that have the potential to increase fitness ( adaptive changes ) .
We reasoned that this initial potential for adaptive changes would give way as proto-genes mature and the adaptive changes engender novel selected effects , in turn increasing constraints and reducing the possibility of future change .
This reasoning is akin to Sartre ’ s “ existence precedes essence ” dictum , and predicts that mutations affecting the sequence or regulation of proto-genes should impact fitness differently than mutations affecting the @ @ @ @ @ @ @ Specifically , proto-genes are predicted to evolve under weaker constraints , and thereby to display a higher potential for adaptive change , than established genes ( Fig .
1a ) .
Well .
If Jean-Paul Sartre , the famous biochemist , says it , it must be so .
There may be no Designer , but there is adaptive potential in junk DNA .
And so these proto-genes , like rowdy youngsters full of unconstrained energy , are more likely to increase their fitness rapidly without being bogged down by the hang-ups of @ @ @ @ @ @ @ functional , innovative genes is established by their existence .
Who needs thermodynamics to overcome the configurational entropy hurdle described by Charles Thaxton , Walter Bradley and Roger Olsen in the new expanded edition of The Mystery of Life ’ s Origin ?
Genes exist de novo .
Therefore , they evolved .
** Listen to Paul Nelson on ID the Future describe the extent of orphan genes , with examples from various genomes .
He considers both options evolutionists use for their origins : divergence from common ancestry and de novo appearance @ @ @ @ @ @ @ for Science & Culture biologist Ann Gauger answers the question , “ Is it easy to get a new protein ?
” with Doug Axe ’ s calculations about probability of a new protein fold by chance .
She also addresses the example of nylonase , which is often put forward as an icon of evolutionary potential for innovation .
For an illustration of the improbability of a functional protein , see “ The Amoeba ’ s Journey ” from Illustra Media ’ s film Origin .
**A companion paper in eLife by @ @ @ @ @ @ @ open access ) , “ Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes , ” argues that sequence divergence is an insufficient explanation for orphan genes : Horizontal transfer “ is not known to be frequent in metazoa , ” they say .
By conservatively underestimating the number of orphans , and overestimating the number originating by sequence divergence , they find the divergence explanation inconsistent with the data .
The eLife paper focuses on refuting the divergence explanation , but does not conclude that de novo @ @ @ @ @ @ @ answer to the “ mystery of orphan genes ” to future studies :

The way some evolutionary biologists and some uncritical reporters in the media talk, probabilistic miracles are routine events. Natural selection is omnipotent so it can handle any observation in biology. Since evolution is already a fact, no other explanation or argument is needed. It exists; therefore it evolved.
Genes from Scratch
Take the case of de novo genes. Darwin skeptics argue that the origin of a new gene or protein by chance is so fantastically improbable, it will never happen anywhere in the history of the universe, even under the most favorable circumstances.* No problem, say these evolutionists; since evolution is a fact, it happened. This is a variation on a formulation offered here last year, “To solve a problem, declare it solved.” Watch the faith of evolutionists at Trinity College Dublin when they consider the origin of orphan genes. They report, “Genes from scratch — far more common and important than we thought.”
Over time, genes change via random mutations. Some of these changes result in serious defects and are rarely passed on to the next generations, others have little impact, and others confer significant advantages, which become favoured due to natural selection and end up being passed on to future generations. This is the main source of genetic novelty and how organisms differ from each other. However, genetic novelty can also be generated by totally new genes evolving from scratch. [Emphasis added.]
They exist; therefore they evolved. Totally new genes evolved from scratch.
Evolution Supplied the Miracles
These evolutionists are aware that the existence of orphan genes looks like a tough problem for Darwinism. But looks are deceiving.
Orphan genes pose a tough evolutionary problem though. They don’t look like other genes, so where do they come from? One idea is that they can originate seemingly from nothing: over long, evolutionary timescales, a completely novel gene can emerge de novo out of a region in the genome that is made up of junk DNA. Alternatively, with enough time, two ‘cousin’ genes can diverge so much that we can no longer identify the relationship between them. Thus, a gene may at a glance appear to be an orphan without having really emerged de novo.
Surely they are not going to pursue option 1, that orphan genes appeared out of junk DNA? And yet we see them discount option 2, that orphan genes are descendants of genes that diverged long ago. Only about a third of them seem to have come about from pre-existing genes, they reckon. What can they do?
Their method of determining how orphan genes originated is simple. Here it is: they counted them. Since they exist, it must have been a cinch for evolution to create them. Professor of genetics Aoife McLysaght explains:
“To our surprise, at most, around one third of orphan genes result from divergence. So, in turn, this suggests that most unique genes in the species we looked at are the result of other processes, including de novo emergence, which is therefore much more frequent than scientists initially thought.”
From the junkpile of non-coding DNA, strands with “potential” to be functional exist, waiting for their moment in the light. Once they show some function, natural selection is fully capable of amplifying them into genes from scratch. Assistant professor of computational systems biology Anne-Ruxanda Carvunis has no problem with declaring the problem solved. Evolution is a fact, remember? It’s the Darwin skeptics’ fault if they can’t see the logic.
“Order seems like something that’s hard to achieve, but our results go completely opposite to that. We found that simple order is rampant everywhere in the genome. The propensity to make simple shapes that are stable is already there, waiting to be exposed. De novo gene birth is thus becoming less and less mysterious as we better understand molecular innovation.”
Perhaps a refresher on the difference between order and complexity would help.
Masters of Fitness
Their paper in Nature Communications shows that the team of 16, including Carvunis and McLysaght, did perform some busy work to argue for the innovative power of evolution. For instance, they found an orphan gene in yeast that was not present in its assumed evolutionary ancestor. Simple answer: its existence served as “confirming the de novo origination of” the gene. Why, all that non-coding junk must be pregnant with “proto-genes” just waiting for their moment to emerge! Once they show a little talent (are “preadapted”), natural selection is sure to make them masters of fitness.
Recent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection.
These emerging proto-genes, rather than being stumbling beginners, must be even more likely to race to the fitness goal.
Mutations that cause changes to the sequence or expression of established genes are typically constrained by preexisting selected effects—the specific physiological processes mediated by the gene products that are maintained by natural selection. In contrast, emerging proto-genes are expected to mostly lack such constraints because they do not have selected effects. This would leave them more readily accessible to evolutionary changes that have the potential to increase fitness (adaptive changes). We reasoned that this initial potential for adaptive changes would give way as proto-genes mature and the adaptive changes engender novel selected effects, in turn increasing constraints and reducing the possibility of future change. This reasoning is akin to Sartre’s “existence precedes essence” dictum, and predicts that mutations affecting the sequence or regulation of proto-genes should impact fitness differently than mutations affecting the sequence or regulation of established genes. Specifically, proto-genes are predicted to evolve under weaker constraints, and thereby to display a higher potential for adaptive change, than established genes (Fig. 1a).
Who Needs Probability?
Well. If Jean-Paul Sartre, the famous biochemist, says it, it must be so. There may be no Designer, but there is adaptive potential in junk DNA. And so these proto-genes, like rowdy youngsters full of unconstrained energy, are more likely to increase their fitness rapidly without being bogged down by the hang-ups of their elderly fuddy-duddies. Their essence as functional, innovative genes is established by their existence. Who needs thermodynamics to overcome the configurational entropy hurdle described by Charles Thaxton, Walter Bradley and Roger Olsen in the new expanded edition of The Mystery of Life’s Origin? Genes exist de novo. Therefore, they evolved.**
Listen to Paul Nelson on ID the Future describe the extent of orphan genes, with examples from various genomes. He considers both options evolutionists use for their origins: divergence from common ancestry and de novo appearance.
*On ID the Future, Center for Science & Culture biologist Ann Gauger answers the question, “Is it easy to get a new protein?” with Doug Axe’s calculations about probability of a new protein fold by chance. She also addresses the example of nylonase, which is often put forward as an icon of evolutionary potential for innovation. For an illustration of the improbability of a functional protein, see “The Amoeba’s Journey” from Illustra Media’s film Origin.
**A companion paper in eLife by Vakirlis, Carvunis, and McLysaght (open access), “Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes,” argues that sequence divergence is an insufficient explanation for orphan genes:
The persistent presence of orphans and TRGs [taxonomically restricted genes] in almost every genome studied to date despite the growing number of available sequence databases demands an explanation. Studies in the past 20 years have mainly pointed to two mechanisms: de novo gene emergence and sequence divergence of a pre-existing gene, either an ancestrally present or one acquired by horizontal transfer.
Horizontal transfer “is not known to be frequent in metazoa,” they say. By conservatively underestimating the number of orphans, and overestimating the number originating by sequence divergence, they find the divergence explanation inconsistent with the data.
As a result, we can be confident that those genes without detectable similarity really are orphans and TRGs, but in turn we also know that some will have spurious similarity hits giving the illusion that they have homologues when they do not in reality.
The eLife paper focuses on refuting the divergence explanation, but does not conclude that de novo appearance is likely. They leave the answer to the “mystery of orphan genes” to future studies:
Overall, our findings are consistent with the view that multiple evolutionary processes are responsible for the existence of orphan genes and suggest that, contrary to what has been assumed, divergence is not the predominant one. Investigating the structure, molecular role, and phenotypes of homologues in the ‘twilight zone’ will be crucial to understand how changes in sequence and structure produce evolutionary novelty.
Image credit: Arek Socha via Pixabay.


evolutionnewsandviews--2020-03-10--Cosmos 3.0 Revisits Themes of the Past, with Familiar Historical Mythmaking

With its ode to the superior rationality of the modern secular mind , last night ’ s debut of the third season of Cosmos 3.0 came amid a full-scale national panic attack about a virus .
As David Klinghoffer commented here yesterday , the timing could be better .
The first two episodes , with Neil deGrasse Tyson returning as host , have now aired on Fox and National Geographic .
In contrast to Cosmos 2.0 , the President of the United States does not introduce this remake .
The overall theme of these episodes is our eventual exploration and @ @ @ @ @ @ @ , All the Time Episode 1 is titled “ Ladder to the Stars.
” We learn that this ladder is the DNA molecule .
Very poetic .
Great visuals .
The episode begins with Carl Sagan admonishing us to follow the evidence wherever it leads and to question everything .
If only the show ’ s writers and producers would take these lessons to heart .
Apart from a couple of sermonettes from St. Carl , it ’ s all Neil all the time .
We are told that the first DNA molecule @ @ @ @ @ @ @ .
As with Cosmos 2.0 , when the topic is life , we get sprinkles of fact mixed with heaps of speculation .
But only the rare TV viewer , who has read Signature in the Cell perhaps , will know how to separate these .
Tyson goes quickly from the origin of life to the first mammals to the origin of big brains .
On the former , for a sober view , listen to a podcast released coincidentally the same day with chemist James Tour , “ Why Science Can not @ @ @ @ @ @ @ to Tyson , all our thoughts , feelings , and achievements are explained by one random mutation in a single rung of 13 atoms in DNA .
That change lead to the growth in brain size in mammals over millions of years and to the origin of mind .
Is that all there is to the origin of mind ?
Tyson ’ s own thoughts , too , would then owe their origin to this and many other accidents .
If so , why should we believe that Neil Tyson , or anyone @ @ @ @ @ @ @ deriving rational conclusions , about the origin of mind or anything else ?
Alvin Plantinga ’ s “ Evolutionary Argument Against Naturalism ” shows that the naturalist can not justify his reason and beliefs .
One common theme in almost every episode of Cosmos 2.0 was “ science good , religion bad.
” So too with this third season .
Thus a jarring transition in episode 1 of the new season leaps from the origin and growth of cities to free thinkers to … you guessed it , Giordano Bruno !
He ’ @ @ @ @ @ @ @ time .
He made his first lengthy appearance in episode 1 of Cosmos 2.0 .
See Jay Richards ’ s comments here , “ Cosmos Revives the Scientific Martyr Myth of Giordano Bruno.
” Tyson uses him to set the mood for the historical interlude that follows .
The scientifically intolerant Catholic Church executes free thinking Bruno in 1600 for daring to believe that the stars are other suns with planets around them .
Tyson then skips forward to Christiaan Huygens , the great Dutch astronomer , physicist , mathematician , and inventor @ @ @ @ @ @ @ noting that Huygens also believed stars were other suns orbited by their own systems of planets .
He briefly mentions Van Leeuwenhoek and his early work with microscopes .
Unsurprisingly , Tyson never mentions the Christian faith of these great scientists .
It seems curious that Tyson would skip over the better known astronomers Kepler and Galileo without any mention .
But it soon becomes clear why he does so .
Huygens was a friend of Baruch Spinoza , the patron saint of modern skeptics .
We are then treated to one of @ @ @ @ @ @ @ Spinoza rejecting the faith of his Jewish community .
Somehow , his rejection of the miracles narrated in the Bible leads him to become a great thinker .
At one point , the animation shows Spinoza being attacked by a knife-wielding assailant , presumably one of the synagogue worshipers Tyson had just talked about .
The problem is , the attack , if it ever actually occurred , may not have been from one of the Jewish worshipers .
Indeed , this appears to be more mythmaking on the part of Cosmos .
@ @ @ @ @ @ @ author of Spinoza : A Life ( Cambridge University Press ) .
He concludes about the knife episode : It seems quite possible , then , that the attempt on Spinoza ’ s life…was ( if it happened ) not a zealous attack on a dangerous heretic .
More likely , it was a simple case of vengeance by unscrupulous , thuggish businessmen .
Tyson also notes that Spinoza ground lenses for microscopes and telescopes .
This , combined with his friendship with Huygens , leads the casual viewer to infer that Spinoza @ @ @ @ @ @ @ Huygens .
Just to clinch the connection , the segment ends with a visit by Einstein to Spinoza ’ s home in Leiden in 1920 .
But Spinoza , like Bruno , was not a scientist .
He was an early Enlightenment philosopher .
At a couple of points in this episode , Tyson employs the “ Book of Nature ” metaphor , but he never gives its proper historical context .
It ’ s actually a Christian concept , going back at least to Augustine .
It was widely believed by the @ @ @ @ @ @ @ studying the “ Book of Nature ” to learn about God , as an act of worship .
There is a segment on the flowers and the bees .
This is revisiting a topic from Cosmos 2.0 where they had mistakenly argued for the coevolution of insects and flowers based on timing .
As an explanation for true biological novelties , coevolution is a favored evolutionary chestnut .
As Brian Miller has remarked here , though , “ Such scenarios may sound plausible , but they only result in trivial adjustments to preexisting @ @ @ @ @ @ @ Information and Coevolution : New BIO-Complexity Article by Ewert and Marks.
” And so it goes with Cosmos .
There is , admittedly , less to object to in episode 2 .
More on that , perhaps , another time .
Overall , despite the sharp graphics , as with many of the Cosmos 2.0 episodes , there is a certain shapelessness to the production .
The transitions between topics are weak .
They seem haphazard .
The fanfare leading up to the release of Cosmos 3.0 was much more subdued than with @ @ @ @ @ @ @ content to settle for low viewership on its release , reasoning that it will go straight into the public schools anyway .
Image : Screenshot from the trailer for Cosmos 3.0 , “ Possible Worlds .
”

With its ode to the superior rationality of the modern secular mind, last night’s debut of the third season of Cosmos 3.0 came amid a full-scale national panic attack about a virus. As David Klinghoffer commented here yesterday, the timing could be better.
The first two episodes, with Neil deGrasse Tyson returning as host, have now aired on Fox and National Geographic. In contrast to Cosmos 2.0, the President of the United States does not introduce this remake. The overall theme of these episodes is our eventual exploration and colonization of other planets.
All Neil, All the Time
Episode 1 is titled “Ladder to the Stars.” We learn that this ladder is the DNA molecule. Very poetic. Great visuals. The episode begins with Carl Sagan admonishing us to follow the evidence wherever it leads and to question everything. If only the show’s writers and producers would take these lessons to heart. Apart from a couple of sermonettes from St. Carl, it’s all Neil all the time.
We are told that the first DNA molecule somehow formed and evolved by natural selection. As with Cosmos 2.0, when the topic is life, we get sprinkles of fact mixed with heaps of speculation. But only the rare TV viewer, who has read Signature in the Cell perhaps, will know how to separate these. Tyson goes quickly from the origin of life to the first mammals to the origin of big brains. On the former, for a sober view, listen to a podcast released coincidentally the same day with chemist James Tour, “Why Science Cannot Explain the Origin of Life.”
According to Tyson, all our thoughts, feelings, and achievements are explained by one random mutation in a single rung of 13 atoms in DNA. That change lead to the growth in brain size in mammals over millions of years and to the origin of mind. Is that all there is to the origin of mind? Tyson’s own thoughts, too, would then owe their origin to this and many other accidents. If so, why should we believe that Neil Tyson, or anyone else, is a being capable of deriving rational conclusions, about the origin of mind or anything else? Alvin Plantinga’s “Evolutionary Argument Against Naturalism” shows that the naturalist cannot justify his reason and beliefs.
Science Good, Religion Bad
One common theme in almost every episode of Cosmos 2.0 was “science good, religion bad.” So too with this third season. Thus a jarring transition in episode 1 of the new season leaps from the origin and growth of cities to free thinkers to … you guessed it, Giordano Bruno! He’s back, but only briefly this time. He made his first lengthy appearance in episode 1 of Cosmos 2.0. See Jay Richards’s comments here, “Cosmos Revives the Scientific Martyr Myth of Giordano Bruno.” Tyson uses him to set the mood for the historical interlude that follows. The scientifically intolerant Catholic Church executes free thinking Bruno in 1600 for daring to believe that the stars are other suns with planets around them.
Blessed Baruch Spinoza
Tyson then skips forward to Christiaan Huygens, the great Dutch astronomer, physicist, mathematician, and inventor. He links him to Bruno by noting that Huygens also believed stars were other suns orbited by their own systems of planets. He briefly mentions Van Leeuwenhoek and his early work with microscopes. Unsurprisingly, Tyson never mentions the Christian faith of these great scientists. It seems curious that Tyson would skip over the better known astronomers Kepler and Galileo without any mention. But it soon becomes clear why he does so. Huygens was a friend of Baruch Spinoza, the patron saint of modern skeptics. We are then treated to one of those historical animated segments showing the brave Spinoza rejecting the faith of his Jewish community. Somehow, his rejection of the miracles narrated in the Bible leads him to become a great thinker.
At one point, the animation shows Spinoza being attacked by a knife-wielding assailant, presumably one of the synagogue worshipers Tyson had just talked about. The problem is, the attack, if it ever actually occurred, may not have been from one of the Jewish worshipers. Indeed, this appears to be more mythmaking on the part of Cosmos. Historian and biographer Steven Nadler is the author of Spinoza: A Life (Cambridge University Press). He concludes about the knife episode:
It seems quite possible, then, that the attempt on Spinoza’s life…was (if it happened) not a zealous attack on a dangerous heretic. More likely, it was a simple case of vengeance by unscrupulous, thuggish businessmen.
Tyson also notes that Spinoza ground lenses for microscopes and telescopes. This, combined with his friendship with Huygens, leads the casual viewer to infer that Spinoza was a scientist of the caliber of Huygens. Just to clinch the connection, the segment ends with a visit by Einstein to Spinoza’s home in Leiden in 1920. But Spinoza, like Bruno, was not a scientist. He was an early Enlightenment philosopher.
The Book of Nature
At a couple of points in this episode, Tyson employs the “Book of Nature” metaphor, but he never gives its proper historical context. It’s actually a Christian concept, going back at least to Augustine. It was widely believed by the scientists of the period that they were studying the “Book of Nature” to learn about God, as an act of worship.
There is a segment on the flowers and the bees. This is revisiting a topic from Cosmos 2.0 where they had mistakenly argued for the coevolution of insects and flowers based on timing. As an explanation for true biological novelties, coevolution is a favored evolutionary chestnut. As Brian Miller has remarked here, though, “Such scenarios may sound plausible, but they only result in trivial adjustments to preexisting structures.” See, “Conservation of Information and Coevolution: New BIO-Complexity Article by Ewert and Marks.”
And so it goes with Cosmos. There is, admittedly, less to object to in episode 2. More on that, perhaps, another time.
Overall, despite the sharp graphics, as with many of the Cosmos 2.0 episodes, there is a certain shapelessness to the production. The transitions between topics are weak. They seem haphazard. The fanfare leading up to the release of Cosmos 3.0 was much more subdued than with its predecessor. Maybe the producers are content to settle for low viewership on its release, reasoning that it will go straight into the public schools anyway.
Image: Screenshot from the trailer for Cosmos 3.0, “Possible Worlds.”


evolutionnewsandviews--2020-03-10--Evolution, Design, and COVID-19

Evolution, Design, and COVID-19

I ’ ve been asked to comment on the coronavirus epidemic and evolution .
Much of what I wrote six years ago during an outbreak of Ebola virus applies to the current predicament as well.1 The bottom line is that , while of course the virus is dangerous , the situation can be compared to a strong storm on the ocean .
The waves may be huge and the surface roiling , but the deeper waters continue as they always have , essentially undisturbed .
In a similar way , although superficially it changes very rapidly , some researchers think @ @ @ @ @ @ @ types3 have remained basically the same for tens of millions of years .
Viruses are scraps of genetic material ( some composed of DNA , some of RNA , usually wrapped in a protein coat ) whose total genetic information ranges from about one ten-thousandth to about one millionth that of the human genome .
A virus can not reproduce by itself ; rather , it has to hijack a host cell ’ s molecular machinery to do so .
The immune system fights it every step of the way , but sometimes @ @ @ @ @ @ @ the replication and release of its progeny can trash a cell .
If many cells are damaged by the multiplying particles , serious health consequences result .
In order to enter a cell , a protein on the surface of the virus particle must bind specifically to a “ receptor ” protein sticking out from the surface of the cell .
It can be likened to a skeleton key that can fit a few kinds of locks , allowing a burglar to enter a home .
Once inside , the burglar can use @ @ @ @ @ @ @ .
But the key is key — unless the key fits , the home is safe .
Viral mutations can change the shape of the skeleton key at random .
Most of the time the process doesn ’ t work but , every once in a while , the virus hits the jackpot .
In some cases , a viral key that had bound to a wild-animal protein mutates and becomes able to bind to a similar human protein .
If a human is in close contact with the animal , the virus @ @ @ @ @ @ @ Then , like an invasive species in a new environment , the virus can multiply until the immune system learns to deal with it .
Various common strains of coronavirus infect humans and cause the usually mild symptoms of the common cold .
But when an animal coronavirus strain crosses over to humans ( such as the SARS virus of the early 2000s , the MERS virus a decade later , and the current COVID-19 ) , it can be much more virulent.4 So , do I think viruses were designed ?
Yes @ @ @ @ @ @ @ viruses of which we are aware — including the coronaviruses , Ebola , and HIV — are exquisitely , purposively arranged , which is the clear signature of intelligent design .
Well , then does that mean the designer is evil and wants people to suffer ?
No , not necessarily .
I ’ m a biochemist , not a philosopher .
Nonetheless , I see no reason why a designer even of such things as viruses should be classified as bad on that basis alone .
I started this post with an @ @ @ @ @ @ @ .
Certainly , if we were on a ship in a powerful storm , we might be excused for thinking storms are bad .
But in calmer moments we understand that on balance the ocean is very good and that , given an ocean and the laws of nature , storms will arise from time to time .
What ’ s more , we just might get caught in one .
In the same way , most viruses do not affect humans and may well have a positive , necessary role to play @ @ @ @ @ @ @ unaware.5 ( I would bet on it . )
From time to time a storm arises in the virosphere and affects humans .
But that ’ s no reason to think either that viruses weren ’ t designed or that the designer of viruses isn ’ t good .
• Wertheim , J. O. et al .
2013 .
A case for the ancient origin of coronaviruses .
Journal of Virology 87:7039-7045 .
• Simmonds , P. , Aiewsakun , P. and Katzourakis , A .
2019 .
Prisoners of war — host @ @ @ @ @ @ @ .
Nature Reviews Microbiology 17:321-328 .
• Cui , J. , Li , F. , and Shi , Z .
2019 .
Origin and evolution of pathogenic coronaviruses .
Nature Reviews Microbiology 17:181-192 .

I’ve been asked to comment on the coronavirus epidemic and evolution. Much of what I wrote six years ago during an outbreak of Ebola virus applies to the current predicament as well.1 The bottom line is that, while of course the virus is dangerous, the situation can be compared to a strong storm on the ocean. The waves may be huge and the surface roiling, but the deeper waters continue as they always have, essentially undisturbed. In a similar way, although superficially it changes very rapidly, some researchers think that the coronavirus2 and many other virus types3 have remained basically the same for tens of millions of years.
What Is a Virus?
Viruses are scraps of genetic material (some composed of DNA, some of RNA, usually wrapped in a protein coat) whose total genetic information ranges from about one ten-thousandth to about one millionth that of the human genome. A virus cannot reproduce by itself; rather, it has to hijack a host cell’s molecular machinery to do so. The immune system fights it every step of the way, but sometimes loses. When the virus wins, the replication and release of its progeny can trash a cell. If many cells are damaged by the multiplying particles, serious health consequences result.
In order to enter a cell, a protein on the surface of the virus particle must bind specifically to a “receptor” protein sticking out from the surface of the cell. It can be likened to a skeleton key that can fit a few kinds of locks, allowing a burglar to enter a home. Once inside, the burglar can use his standard tools to loot and pillage. But the key is key — unless the key fits, the home is safe. Viral mutations can change the shape of the skeleton key at random. Most of the time the process doesn’t work but, every once in a while, the virus hits the jackpot. In some cases, a viral key that had bound to a wild-animal protein mutates and becomes able to bind to a similar human protein. If a human is in close contact with the animal, the virus may be able to jump over. Then, like an invasive species in a new environment, the virus can multiply until the immune system learns to deal with it. Various common strains of coronavirus infect humans and cause the usually mild symptoms of the common cold. But when an animal coronavirus strain crosses over to humans (such as the SARS virus of the early 2000s, the MERS virus a decade later, and the current COVID-19), it can be much more virulent.4
Viral Design
So, do I think viruses were designed? Yes, I most certainly do! The viruses of which we are aware — including the coronaviruses, Ebola, and HIV — are exquisitely, purposively arranged, which is the clear signature of intelligent design. Well, then does that mean the designer is evil and wants people to suffer? No, not necessarily. I’m a biochemist, not a philosopher. Nonetheless, I see no reason why a designer even of such things as viruses should be classified as bad on that basis alone.
I started this post with an analogy of a storm on the ocean. Certainly, if we were on a ship in a powerful storm, we might be excused for thinking storms are bad. But in calmer moments we understand that on balance the ocean is very good and that, given an ocean and the laws of nature, storms will arise from time to time. What’s more, we just might get caught in one. In the same way, most viruses do not affect humans and may well have a positive, necessary role to play in nature of which we are currently unaware.5 (I would bet on it.) From time to time a storm arises in the virosphere and affects humans. But that’s no reason to think either that viruses weren’t designed or that the designer of viruses isn’t good.
References:
Behe, M. J. 2014. Evolution and the Ebola virus: Pacing a small cage. Evolution News https://evolutionnews.org/2014/10/evolution_and_t/ Wertheim, J. O. et al. 2013. A case for the ancient origin of coronaviruses. Journal of Virology 87:7039-7045. Simmonds, P., Aiewsakun, P. and Katzourakis, A. 2019. Prisoners of war — host adaptation and its constraints on virus evolution. Nature Reviews Microbiology 17:321-328. Cui, J., Li,F., and Shi, Z. 2019. Origin and evolution of pathogenic coronaviruses. Nature Reviews Microbiology 17:181-192. Roossinck, M. J. 2011. The good viruses: viral mutualistic symbioses. Nature Reviews Microbiology 9:99-108.
Photo: A coronavirus, by CDC/ Alissa Eckert, MS; Dan Higgins, MAM / Public domain.


evolutionnewsandviews--2020-03-16--Counterprogramming for Cosmos 3.0: Two New Videos from Science Historian Mike Keas

Unless it ’ s put on lockdown , too , the third season of Cosmos ( “ Possible Worlds ” ) will release its third and fourth episodes tonight on National Geographic and Fox , at 8 pm and 9 pm respectively .
Luckily we have some very timely counterprogramming , in the form of videos by Discovery Institute science historian Mike Keas .
See the review here from Evolution News of the new Cosmos 3.0 series so far , noting that “ Maybe the producers are content to settle for low viewership on its release , reasoning that it @ @ @ @ @ @ @ anyway.
” Yes , I bet even now some teacher out there , with classes at home and learning remotely , has come up with the bright idea of watching Cosmos as an assignment for his students .
This has probably occurred to more than one teacher .
The series , as hosted originally by Carl Sagan and now by Neil deGrasse Tyson , has two notable priorities .
One is to instruct viewers about the incompatibility of science and religious faith .
The other is to promote what Tyson calls the “ @ @ @ @ @ @ @ spiritual , even redemptive ; but not religious , ” and emphasizes the unremarkable place of Earth and mankind in the cosmos .
Professor Keas , author of Unbelievable : 7 Myths About the History and Future of Science and Religion , takes on that perspective in these two excellent 15-minute videos .
He explains , “ There is a false idea circulating out there that science grows only when guided by godless thinking.
” On the contrary , modern science from its inception was a project guided by religious thinking , the @ @ @ @ @ @ @ two “ books , ” both revealing God ’ s thoughts though written in different languages ( mathematics , or Hebrew and Greek , respectively ) .
Cosmos takes aim at the Christian religion in particular , but this reflects a historical amnesia on the part of its producers .
As Dr. Keas demonstrates , Christianity contributed “ ideas , methods , and institutions ” without which science and scientists would have been significantly handicapped .
While mythmakers like Neil Tyson labor to persuade students and adults alike that religion and science are @ @ @ @ @ @ @ is true .
Keas puts it this way : “ We can comprehend a set of natural laws , imposed by God , that unify the heavens and the earth .
We can understand this because we are made in His image , and we can know the world.
” The truth is that watching Cosmos really is helpful for the curious mind , so long as it ’ s balanced by a better-informed view like the one offered here by Mike Keas .
Please share with your friends and family ( while @ @ @ @ @ @ @ .

Unless it’s put on lockdown, too, the third season of Cosmos (“Possible Worlds”) will release its third and fourth episodes tonight on National Geographic and Fox, at 8 pm and 9 pm respectively. Luckily we have some very timely counterprogramming, in the form of videos by Discovery Institute science historian Mike Keas.
See the review here from Evolution News of the new Cosmos 3.0 series so far, noting that “Maybe the producers are content to settle for low viewership on its release, reasoning that it will go straight into the public schools anyway.” Yes, I bet even now some teacher out there, with classes at home and learning remotely, has come up with the bright idea of watching Cosmos as an assignment for his students. This has probably occurred to more than one teacher.
Two Notable Priorities
The series, as hosted originally by Carl Sagan and now by Neil deGrasse Tyson, has two notable priorities. One is to instruct viewers about the incompatibility of science and religious faith. The other is to promote what Tyson calls the “Cosmic Perspective” — which is “spiritual, even redemptive; but not religious,” and emphasizes the unremarkable place of Earth and mankind in the cosmos.
Professor Keas, author of Unbelievable: 7 Myths About the History and Future of Science and Religion, takes on that perspective in these two excellent 15-minute videos. He explains, “There is a false idea circulating out there that science grows only when guided by godless thinking.” On the contrary, modern science from its inception was a project guided by religious thinking, the idea that Nature and the Bible form two “books,” both revealing God’s thoughts though written in different languages (mathematics, or Hebrew and Greek, respectively). Cosmos takes aim at the Christian religion in particular, but this reflects a historical amnesia on the part of its producers. As Dr. Keas demonstrates, Christianity contributed “ideas, methods, and institutions” without which science and scientists would have been significantly handicapped.
While mythmakers like Neil Tyson labor to persuade students and adults alike that religion and science are at war, in fact the opposite is true. Keas puts it this way: “We can comprehend a set of natural laws, imposed by God, that unify the heavens and the earth. We can understand this because we are made in His image, and we can know the world.”
The truth is that watching Cosmos really is helpful for the curious mind, so long as it’s balanced by a better-informed view like the one offered here by Mike Keas. Please share with your friends and family (while practicing proper social-distancing, of course).