From trash to treasure,no thanks to Darwinism

Junk No Mo: Scientists Turn Genetic Junk into Master Controller

Evolution News & Views May 8, 2015 2:45 PM 

You'll pardon two Aussies for their mixed metaphors. They represent the cutting edge of young scientists who have ditched the "junk DNA" label entirely. They now recognize the powerful regulatory role of micro-RNAs in the non-coding portions of the genome. Writing at The Conversation, Pamela Ajuyah (PhD student) and Nham Tran (lab head) at the University of Technology in Sydney begin their metaphors with a familiar irritation: junk mail.

Up until about two decades ago, one type of RNA, called microRNA, or just miRNA -- by virtue of them being very short, only 18-25 letters long -- were thought to be the junk mail of the genome, with no biological function. But today we know that these miRNA are actually not junk but play a very important role in regulating the activity of other parts of your DNA. [Emphasis added.]

After reviewing a little history about the Central Dogma and the Human Genome Project, they recount the surprise that only 2 percent of the human genome codes for proteins. "So the question is: what does the remaining 98 percent of our DNA actually do?" That's the spirit; seek function, and ye shall find. Biologists had made a big mistake by filtering the 98 percent into the spam folder.

For biologists, those important emails that slipped into the junk mail folder and were disregarded were miRNAs. That was until the first functional miRNA, lin-4, was officially discovered in 1993. Scientists were looking at the development of the nematode worm, Caenorhabditis elegans, and found that lin-4 inhibited protein synthesis of the lin-14 gene.

They subsequently found that miRNA can physically bind to mRNA and stop it creating proteins. Thus it effectively suppresses the activity of a gene. This discovery was thefirst evidence of miRNA negatively regulating RNA coding for proteins.

So, it turns out that the 98% of our genome that was regarded as "junk" might have a function after all.

After a little more history, catching up to the current count of 1,800 known functional miRNAs, they switch metaphors:

We now understand that miRNA control numerous genes and processes vital for cellular life such as metabolism, development and the immune system.

While two decades ago genes and proteins were seen as the most important players in what happens in our body, miRNAs are now recognised as the puppet masters, pulling the strings of various genes on the molecular biology stage.

Ajuyah and Tran appear genuinely excited about the prospects for discovering more function in the junk email (or more strings for the puppet master to pull). They talk about how cancerous tumors sometimes switch off the miRNAs that would otherwise activate anti-tumor proteins. This provides avenues for designing miRNAs to target tumors. Since miRNAs latch onto messenger RNAs promiscuously, it might allow miRNA-based drugs to target multiple genes simultaneously.

Back to the email analogy, they conclude:The interest in miRNA in the scientific community has increased exponentially in the last few years as researchers join in the race to develop a functional and effective miRNA-based therapeutic for cancer.

Far from being junk mail, miRNAs are the commands that redirect other messages, enabling some activities to go ahead and others to cease entirely. And now that biologists have updated their filters, they're now coming to grips with how powerful miRNAs can be.

We don't mind if the "puppet master" sets the "email filters" as long as everyone gets the message that the junk-DNA label belongs in the rear view mirror. (Mixing metaphors is addictive, isn't it?) What's going on here is one of the biggest paradigm reversals in decades: discovering that the junk is the master. Intelligent design theory expected that unknowns would prove functional. One only wonders how much further along genetics would be if the expectation of design had guided research two decades ago.

More Micro-RNA Function

A paper in Science, meanwhile, finds another function for miRNA: silencing the noisy genome. Hofman and Pilpel describe that discovery, then extend it into the search for additional functions of non-coding DNA:

And the story need not end with miRNAs. A most profound revolution in genomicsis the realization that there are many additional types of RNA. For instance,"antisense" RNAs may also act in noise filtration, especially when coregulated with their corresponding sense transcript. Perhaps some long noncoding RNAs, too, contribute to fine tuning of gene expression programs.

The Discarded Imagery

More evidence for the paradigm shift is seen in a review by Nathaniel Comfort in Nature of three new genetics books (including one, by Nessa Carey, reviewed by Casey Luskin here last week). His title is, "We are the 98 percent":

Today, junk DNA is at the heart of the most radical transformation of how we understand the genome since the information metaphor. Three books -- The Deeper Genome by John Parrington, Junk DNA by Nessa Carey, and Biocode by Dawn Field and Neil Davies -- present a vision of the twenty-first-century genome. Their relative success hinges on metaphor and imagery, both in how they conceive the genome and in the writing itself.

It's time for new metaphors, Comfort says; the encyclopedia image of the Central Dogma proved too static, the junk-DNA metaphor too limiting. He's not ready to believe all the non-coding regions are functional, but both metaphors (instruction book of life versus junk DNA) are outdated. "The old metaphor [instruction book] is not wrong; it is incomplete," he explains. "In theFinding apt imagery to replace the dead metaphor of the 'instruction book of life' could enable us to break free of the cliché of nature versus nurture. It could usher in a more democratic conception of life, in which all the world's a cell, and all the genes and genomes merely players.

That's a bit weird, but at least it's not dismissive of the genome as mostly junk. These are dynamic times as scientists revise old notions of the genome and try to visualize its complex functions. It appears that the concept of "junk DNA" itself is the thing most likely to end up on the junk pile. new genome, lines of static code have become a three-dimensional tangle of vital string, constantly folding and rearranging itself, responsive to outside input."

So what should be the new metaphor to describe a genome that is "more than a set of rules and parts descriptions"?

On Mathematics and darwinism.

Mathematicians and Evolution

As recently highlighted here, mathematics is an academic locale where scientific skepticism of Neo-Darwinism can survive the current political climate! Discovery Institute recently received an e-mail from someone commenting on the Scientific Dissent from Darwinism List where over 600 Ph.D. scientists from various fields agree that they are "skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life." This skeptic of evolutionary-skepticism e-mailer wrote "I'm a mathematician and certainly am NOT qualified to support such a statement. Only evolutionary biologists are qualified to respond here." While the Dissent from Darwinism list does contain individuals trained in evolutionary biology, the question remains "Is the objection valid?"

The truth is that mathematics has a strong tradition of giving cogent critique of evolutionary biology. After all, Darwin's theory of evolution by natural selection is fundamentally based upon an algorithm which uses a mathematically describable trial and error process to attempt to produce complexity. Population genetics is rife with mathematics. In fact, one criticism of the alleged transitional fossil sequences for whales is that they represent evolutionary change on too rapid a timescale to be mathematically feasible. It seems that there is no good reason why those trained in mathematics cannot comment on the ability of the Neo-Darwinian mutation-selection process to generate the complexity of life.

One of the best known mathematical forays into evolution was the 1966 Wistar Symposium, held in Philadelphia, where mathematicians and other scientists from related fields congregated to assess whether Neo-Darwinism is mathematically feasible. The conference was chaired by Nobel Laureate Sir Peter Medawar. The general consensus of many meeting participants was that Neo-Darwinism was simply not mathematically tenable.  

The proceedings of that conference, Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), reports various challenges to evolution presented by respected mathematicians and similar scholars at the conference. For example, the conference chair Sir Peter Medawar stated at the outset:

"[T]he immediate cause of this conference is a pretty widespread sense of dissatisfaction about what has come to be thought as the accepted evolutionary theory in the English-speaking world, the so-called neo-Darwinian Theory. ... There are objections made by fellow scientists who feel that, in the current theory, something is missing ... These objections to current neo-Darwinian theory are very widely held among biologists generally; and we must on no account, I think, make light of them. The very fact that we are having this conference is evidence that we are not making light of them."

(Sir Peter Medawar, "Remarks by the Chairman," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. xi, emphasis in original)

Various scientists, including some mathematicians, proceeded to comment about problems with Neo-Darwinism:

"[A]n opposite way to look at the genotype is as a generative algorithm and not as a blue-print; a sort of carefully spelled out and foolproof recipe for producing a living organism of the right kind if the environment in which it develops is a proper one. Assuming this to be so, the algorithm must be written in some abstract language. Molecular biology may well have provided us with the alphabet of this language, but it is a long step from the alphabet to understanding a language. Nevertheless a language has to have rules, and these are the strongest constraints on the set of possible messages. No currently existing formal language can tolerate random changes in the symbol sequences which express its sentences. Meaning is almost invariably destroyed. Any changes must be syntactically lawful ones. I would conjecture that what one might call "genetic grammaticality" has a deterministic explanation and does not owe its stability to selection pressure acting on random variation."

(Murray Eden, "Inadequacies as a Scientific Theory," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. 11)

"[I]t seems to require many thousands, perhaps millions, of successive mutations to produce even the easiest complexity we see in life now. It appears, naively at least, that no matter how large the probability of a single mutation is, should it be even as great as one-half, you would get this probability raised to a millionth power, which is so very close to zero that the chances of such a chain seem to be practically non-existent."

(Stanislaw M. Ulam, "How to Formulate Mathematically Problems of Rate of Evolution," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. 21)

"We do not know any general principle which would explain how to match blueprints viewed as typographic objects and the things they are supposed to control. The only example we have of such a situation (apart from the evolution of life itself) is the attempt to build self-adapting programs by workers in the field of artificial intelligence. Their experience is quite conclusive to most of the observers: without some built-in matching, nothing interesting can occur. Thus, to conclude, we believe that there is a considerable gap in the neo-Darwinian theory of evolution, and we believe this gap to be of such a nature that it cannot be bridged within the current conception of biology."

(Marcel Schutzenberger, "Algorithms and Neo-Darwinian Theory," in Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (Wistar Institute Press, 1966, No. 5), pg. 75)

These are potent arguments from academics qualified to assess the mathematical ability of a random / selective process to produce complexity. While evolutionary biologists and other types of biologists can yield many insights into evolutionary biology, scientists other than biologists, such as mathematicians, are most certainly qualified to comment on the feasibility of Neo-Darwinian evolution.

On Darwinian hagiography

Scientific Consensus? You've Got to Be Kidding, Right?

Evolution News & Views May 4, 2015 3:51 AM | 

We are often told that "nothing in biology makes sense except in the light of evolution." The statement was first made in 1973 by neo-Darwinist Theodosius Dobzhansky. (Neo-Darwinism is the view that evolution is due to the natural selection of variations that originate as gene mutations.) Dobzhansky's statement is false. Nevertheless, it has become the majority opinion ("consensus") of the scientific establishment. Sometimes, it is carried to absurd extremes.

For example, in a blog post last week defending that reliability of "scientific consensus," theoretical astrophysicist Ethan Siegel wrote:

[E]volution was the consensus position that led to the discovery of genetics...

What a hoot! The truth is that Gregor Mendel discovered genetics with no help from evolution. Mendel published his theory about the same time that Charles Darwin published The Origin of Species, but Mendel did not accept Darwin's theory, and Darwin's followers ignored Mendel's theory for decades.

Here's an excerpt from a chapter titled "You'd Think Darwin Invented the Internet" in Jonathan Wells's book, The Politically Incorrect Guide to Darwinism and Intelligent Design:

Augustinian monk Gregor Mendel found Darwin's theoryunpersuasive. The data he collected led him to conclude that heredity involves the transmission of stable factors that determine an organism's traits. Although the factors can be mixed and matched during reproduction, they remain discrete and unchanging from one generation to the next. Darwin's view of heredity was quite different. He believed that every cell in an organism produces "gemmules" that transmit characteristics to the next generation in a blending process he called "pangenesis." The advantage of Darwin's view was that gemmules could be changed by external conditions, or by use and disuse, and thus account for evolutionary change. The disadvantage of Darwin's view was that it was false.

Mendel's theory of stable factors contradicted Darwin's theory of changeable gemmules. Thus, although Mendel's work was published in 1866, Darwinists totally ignored it for more than three decades. William Bateson, one of the scientists who "rediscovered" Mendelian genetics at the turn of the century, wrote that the cause for this lack of interest was "unquestionably to be found in that neglect of the experimental study of the problem of Species which supervened on the general acceptance of the Darwinian doctrines... The question, it was imagined, had been answered and the debate ended."

Even after 1900, Darwinists had little use for Mendel's theory. By the 1930s, however, the evidence had corroborated Mendelian genetics. Darwinists abandoned pangenesis and subsumed Mendelism in a "neo-Darwinian synthesis" that still dominates evolutionary biology.

In 1999, Darwinist Bruce Alberts claimed that Darwinism is "at the core of genetics." Yet Mendel had no need for Darwin's hypothesis. How can Darwinism, which contributed nothing to the origin of genetics and resisted it for half a century, now be at its core? It is Darwinism that needs genetics, not genetics that needs Darwinism.

Of course, the "scientific consensus" now holds that Darwinian evolution is true, and the main point of Siegel's blog post is to argue for the trustworthiness of the "scientific consensus." But Siegel makes it clear that most people don't count as scientists:

In order to become and remain a scientist, you need a four-year degree with a major in your chosen scientific field, a four-to-six-year (on average) PhD degree, where you specialized in a particular sub-field of your science and demonstrated yourself capable of making original contributions, and continued to remain active in the field, staying abreast and even participating in many of the latest discoveries.

The skills you develop as a scientist are unique to scientists, and the ability to interpret results in the context of your sub-field and what's known about it is unique to scientists within that sub-field.

And finally -- and this is the most important part -- in order to obtain an accurate, nuanced, complete picture of a particular problem or set of problems, you need this incredible set of scientific knowledge and experience that is (in most cases) non-transferrable from one discipline to another.

Whoa! By these criteria, Siegel should stick to his own specialty, theoretical astrophysics. He should leave biology to biologists, such as Jonathan Wells(PhD in Molecular and Cell Biology, University of California at Berkeley).

But here's the catch: Jonathan Wells is not part of the "scientific consensus" in biology, because he doesn't accept Darwinian evolution. Of course, Gregor Mendel was not part of the "scientific consensus" in his day. In fact, not even Charles Darwin became part of the "scientific consensus" until his theory was propped up by Mendelian genetics almost half a century later.

So what are we to make of the "scientific consensus" about evolution? Probably no one can say it better than David Berlinski, who wrote in The Devil's Delusion:

Within the English-speaking world, Darwin's theory of evolution remains the only scientific theory to be widely championed by the scientific community and widely disbelieved by everyone else. No matter the effort made by biologists, the thing continues to elicit the same reaction it has always elicited: You've got to be kidding, right?

And now the good news.

THE WATCHTOWER MAY 2015

 COVER SUBJECT | IS THE END NEAR?

“The End”—What Does it Mean?

hen you hear the words “The end is near!” what comes to mind? Do you think of a wild-eyed preacher thundering from the pulpit and gesturing dramatically, Bible in hand? Or do you picture a bearded old man standing on a street corner, wearing a long robe tied at the waist with a rope, holding a sign bearing a doomsday message? Imagining such scenes may make some people feel concerned, while others may feel skeptical or even amused.

The Bible does state: “The end will come.” (Matthew 24:14) The same event is also called “the great day of God” and “Armageddon.” (Revelation 16:14, 16) True, there is much religious confusion on the subject and strange, gloomy notions abound. Nonetheless, the Bible itself is quite clear about the end—revealing what it is and what it is not. God’s Word also helps us to see clearly whether the end is near. Best of all, it teaches us how to survive! First, though, let us clear up some misconceptions and establish a definition. What does “the end” really mean according to the Bible?

 WHAT THE END IS NOT

1. THE END IS NOT AN EPIC, FLAMING DESTRUCTION OF THE EARTH.
   The Bible states: “[God] has established the earth on its foundations; it will not be moved from its place forever and ever.” (Psalm 104:5) That scripture and others assure us that God will neither destroy the earth nor allow it to be destroyed—ever!—Ecclesiastes 1:4; Isaiah 45:18.
2. THE END IS NOT A RANDOM, UNSCHEDULED EVENT.
   The Bible reveals that the end is scheduled—God has set a specific time for it. We read: “Concerning that day or the hour nobody knows, neither the angels in heaven nor the Son, but the Father. Keep looking, keep awake, for you do not know when the appointed time is.” (Mark 13:32, 33) Clearly, God (“the Father”) has scheduled the exact “appointed time” when he will initiate the end.
3. THE END IS NOT TRIGGERED BY HUMANS OR BY DEBRIS HURTLING THROUGH SPACE.
   What will bring about the end? Revelation 19:11 says: “I saw heaven opened, and look! a white horse. And the one seated on it is called Faithful and True.” Verse 19 continues: “And I saw the wild beast and the kings of the earth and their armies gathered together to wage war against the one seated on the horse and against his army.” (Revelation 19:11-21) Though much of the language here is symbolic, we can readily discern this much: God will send an army of angelic creatures to exterminate his enemies.

The Bible’s message about the end is good news rather than bad

WHAT THE END IS

1. THE END OF FAILING HUMAN GOVERNMENTS.
   The Bible explains: “The God of heaven will set up a kingdom [government] that will never be destroyed. And this kingdom will not be passed  on to any other people. It will crush and put an end to all these kingdoms, and it alone will stand forever.” (Daniel 2:44) As was stated earlier, in point 3, there will be an extermination of “the kings of the earth and their armies,” who will have “gathered together to wage war against the one seated on the horse and against his army.”—Revelation 19:19.
2. THE END OF WAR, VIOLENCE, AND INJUSTICE.
   “[God] is bringing an end to wars throughout the earth.” (Psalm 46:9) “Only the upright will reside in the earth, and the blameless will remain in it. As for the wicked, they will be cut off from the earth, and the treacherous will be torn away from it.” (Proverbs 2:21, 22) “Look! I am making all things new.”—Revelation 21:4, 5.
3. THE END OF RELIGIONS THAT HAVE FAILED GOD AND HUMANS.
   “The prophets prophesy lies, and the priests dominate by their own authority. . . . But what will you do when the end comes?” (Jeremiah 5:31) “Many will say to me in that day: ‘Lord, Lord, did we not prophesy in your name, and expel demons in your name, and perform many powerful works in your name?’ And then I will declare to them: ‘I never knew you! Get away from me, you workers of lawlessness!’”—Matthew 7:21-23.
4. THE END OF PEOPLE WHO PERPETUATE AND SUPPORT THE CURRENT STATE OF AFFAIRS.
   Jesus Christ said: “Now this is the basis for judgment: that the light has come into the world, but men have loved the darkness rather than the light, for their works were wicked.” (John 3:19) The Bible describes an earlier worldwide destruction during the time of the faithful man Noah. “The world of that time suffered destruction when it was flooded with water. But by the same word the heavens and the earth that now exist are reserved for fire and are being kept until the day of judgment and of destruction of the ungodly people.”—2 Peter 3:5-7.

Note that the upcoming “day of judgment and of destruction” is compared with the destruction of “the world” of Noah’s time. What world was destroyed? Our planet survived; it was “the ungodly people”—God’s enemies—who “suffered destruction.” During God’s upcoming “day of judgment,” those who choose to be God’s enemies will likewise be destroyed. But God’s friends will be preserved, as were Noah and his family.—Matthew 24:37-42.

Imagine how splendid this earth will be after God eliminates all wicked influences! Clearly, the Bible’s message about the end is good news rather than bad. Still, you may wonder: ‘Does the Bible tell us when the end will come? Could it be near? How can I survive it?’

AFTER THE END

What will it be like after the end? Many scriptures describe that wonderful time. For example: “‘[God] will wipe out every tear from their eyes, and death will be no more, neither will mourning nor outcry nor pain be anymore. The former things have passed away.’ And the One seated on the throne said: ‘Look! I am making all things new.’” (Revelation 21:4, 5) The end does not have to mean the end of your life. God wants us to survive, and he tells us how.

It's design all the way down II

Developments from the Study of Cells and Molecular Machines

Evolution News & Views April 28, 2015 3:57 AM |

 

Intelligent design becomes increasingly apparent at the smallest scales of life as imaging improves and scientists get a closer look at the cell's inner workings.

Dynein

Scripps Institute seeks to reveal the "structural secrets of nature's little locomotive." (Emphasis added.) The dynein-dynactin complex has defied analysis because "the complex's large size, myriad subunits and high flexibility have until now restricted structural studies to small pieces of the whole." Finer details have shown "how dynein and dynactin fit together on a microtubule, how they recruit cargoes and how they manage to move those cargoes consistently in a single direction."

Myosin

Another locomotive protein, myosin-5, is like a tightrope walker on thin actin filaments. A news item from the University of Oxford says, "Remarkably, these proteins not only function like nano-scale lorries, they also look like a two-legged creature that takes very small steps."

Yet the stiff-legged motion seemed awkward at first -- something like a Monty Python "silly walk" sketch. But by filming the machines at 1000 frames per second, the Oxford scientists could see that the molecular machines' motion is anything but random or silly (see the animation above). "The movement resembles the twirling of a dividing compass used to measure distances on a map," chemist Philipp Kukura says. It's a bigger feat than first appears. "Think of it being rather like trying to walk a tightrope in a hurricane whilst being pelted with tennis balls."

'We've uncovered a very efficient way that a protein has found to do what it needs to do, that is move around and ferry cargos from A to B,' explains Philipp.... This study shows that if we want to build machines as efficient as those seen in naturethen we may need to consider a different approach.'

It seems that if you're designing tiny machines 'silly' walks may not be so silly after all.

DNA Repair Helicase

Scientists at the University of Illinois School of Engineering have, for the first time, "observed thestructure and correlated function of specific proteins critical in the repair of DNA," finding that one of the key proteins, UvrD, swivels between an open and closed state and back again. "As it turns out, the closed state unwinds the strands, using a torque wrench action. The open state allows the strands to zip together." When in the closed position, it acts as "a 'superhelicase'capable of unwinding double-stranded DNA over a great distance."

Chromatin

Intelligent design is evident in this headline from Princeton Journal Watch: "Decoding the Cell's Genetic Filing System." Codes? Filing systems? Indeed: five feet of DNA is packed into a tiny nucleus on tightly-wound spools of chromatin. "Access to these meticulously packed genes isregulated by post-translational modifications, chemical changes to the structure of histones that act as on-off signals for gene transcription," the article says. Experiments to try to modify chromatin helps the Princeton team get closer to "understanding nature's remarkable information indexing system."

RNA Polymerase

This machine is responsible for transcribing DNA. Again, it's a lot more sophisticated than it first appeared. Research at Harvard shows that a fairy tale about it was in the scientists' imagination, not the cell:

Once upon a time, scientists thought RNA polymerase -- the molecule that kicks off protein synthesis by transcribing DNA into RNA -- worked like a wind-up toy: Set it down at a start site in our DNA and it would whir steadily along, reeling off an RNA copy, until it reached the stop site.

Lately, they've realized they didn't give RNA polymerase enough credit.

"It's more like a high-performance sports car," said Stirling Churchman, assistant professor of genetics at Harvard Medical School. "It has to speed up, slow down and deal with obstacles in its path."

In a one-minute video clip, Churchman explains why she is excited about the research, bringing at least a little clarity to a situation that often leaves her "overwhelmed by how complex it is," yet still manages to do its job. Her team found "a lot going on" as the machine proceeds down the DNA strand. The "sports cars" even know how to slow down for "speed bumps" and avoid head-on collisions. "Ultimately, it emphasizes the simplicity of our current views of how transcription occurs," Churchman says.

Ribosome

Ribosomes process messenger RNA and translate it into protein. An article from CNRS (Institut de Génétique et de Biologie Moléculaire et Cellulaire) at the University of Strasbourg tells how French scientists mapped the complete human ribosome (all 220,000 atoms), including both subunits, at 3-angstrom resolution. The new model, much more detailed now than the simple animation in Illustra's 2002 documentary Unlocking the Mystery of Life, is bound to increase admiration of this "molecular nanomachine" so important to genetics. One finding so far: "after delivering the amino acids they are carrying, transfer RNA continue to interact with the ribosome at a specific site (the tRNA exit site)."

Incidentally, the April 24 issue of Science has a special section on "The delicate dance of translation and folding," with research papers about how the cell gets from messenger RNA to folded protein.

Lysosomes

Even the cleanup crew deserves our admiration. Current Biology produced a "Quick Guide" to lysosomes in the April 20 issue. Making up 5 percent of the cell's volume, lysosomes can break down a "wide variety of macromolecules" delivered to them by various pathways. Much more than "cell stomachs," though, these machines participate in the cell's signaling networks, membrane repair and defense against parasites. To maintain their acid requirement of pH < 5, they employ rotary machines similar to ATP synthase that pump protons into the interior. Lysosomes may also prove to be a fountain of youth: "Increased life span is the result of lysosomal production of the bioactive lipid oleoylethanolamide, which is translocated into the nucleus by a chaperoneprotein and affects the transcription of genes that regulate longevity."

Centrioles

Centrioles are involved in winching apart the chromosomes into the daughter cells. New findings announced by the Ecole Polytechnique Federale de Lausanne are of interest from an ID perspective: these molecular structures appear to be carriers of information outside of the genome. In the zygote, centrioles (which resemble the machines in cilia) are inherited from the father only. By tagging these paternal centrioles, the scientists found that they persist through at least ten cell divisions: "Even more intriguing are the implications the study has for biology at large, as it raises the possibility that centrioles, persisting across several cell cycles, could effectively be a non-genetic information carrier," the article says. "If this were confirmed, it could represent a paradigm shift in the way we think and understand the biology of an organellethat has been present across eukaryotic evolution."

Well, maybe not evolution. Since they have not evolved in all that time, we can think and understand them better as products of intelligence. That certainly makes sense of all these amazing molecular machines. If machines look better designed the closer you look, ID must be on the right track.

A line in the sand XI

May free speech R.I.P.:Pros and Cons

To be or not to be?Pros and Cons.

  

  

Building on quicksand?

PNAS Paper Admits Understanding the Origin of Cellular Features Is a "Glaring Gap" in Evolutionary Biology

Casey Luskin December 10, 2014 1:48 PM 

In 2001, biochemist Franklin Harold wrote in an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations." Last month, a new paper in Proceedings of the National Academy of Sciences, "Evolutionary cell biology: Two origins, one objective," admitted much the same thing. The article states (emphasis added):

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. ... Because all evolutionary change ultimately requires modifications at the cellular level, questioning and understanding how cellular features arise and diversify should be a central research venue in evolutionary biology. However, if there is one glaring gap in this field, it is the absence of widespread cell-biological thinking. Despite the surge of interest at the molecular, genomic, and developmental levels, much of today's study of evolution is only moderately concerned with cellular features, perhaps due to lack of appreciation for their wide variation among taxa. However, a full mechanistic understanding of evolutionary processes will never be achieved without an elucidation of how cellular features become established and modified.

Co-authored by some leading evolutionary biologists who are also critics of the standard neo-Darwinian paradigm, the article suggests that evolutionary and cellular biologists need to focus on "bridging the gap" between their two fields. However, though the authors aren't necessarily neo-Darwinians, they retain the evolutionary materialist view that biological processes produce clumsy features, evidence of an absence of design. They want to understand how "historical contingency" and the "opportunistic process of 'descent with modification'" have produced living systems. Thus, they take an efficient molecular machine like the ATP synthase and consider the possibility that it's a poor solution to the problem of generating ATP:

One remarkable example of how history continues to influence today's cell biology is the near universal use of ATP synthase as a mechanism for energy generation. Embedded in the surface membranes of bacteria and organellar membranes of eukaryotes, this complex molecular machine uses the potential energy of a proton gradient to generate a rotational force that converts ADP to ATP, much like a turbine converts the potential energy of a water gradient into electricity. However, the proton gradient does not come for free: cells first use energy derived from metabolism to pump protons out of membrane-bound compartments, creating the gradient necessary for reentry through ATP synthase. Even assuming that ATP production is an essential requirement for the origin of life, it is by no means clear that the path chosen for ADP-to-ATP conversion is the only possibility.

However, they acknowledge that selection can't explain everything:

A commonly held but incorrect stance is that essentially all of evolution is a simple consequence of natural selection. Leaving no room for doubt on the process, this narrow view leaves the impression that the only unknowns in evolutionary biology are the identities of the selective agents operating on specific traits. However, population-genetic models make clear that the power of natural selection to promote beneficial mutations and to remove deleterious mutations is strongly influenced by other factors. Most notable among these factors is random genetic drift, which imposes noise in the evolutionary process owing to the finite numbers of individuals and chromosome architecture.

Where selection fails, they propose forces like neutral drift. Yet as I explained here, under random genetic drift, features arise entirely due to random factors. At least natural selection offers some explanation as to how beneficial features are preserved. If selection has trouble building complex features, random drift would seem even more inadequate. Thus, incredibly, the paper argues that complex molecular machines evolved despite the fact that they may not have yielded a benefit:

Certainly, today's cells cannot survive without such molecular machines. However, the existence of complex cellular features need not imply that each of the myriad of changes that sculpted such structures over evolutionary time was adaptive at the time of establishment.

It seems doubtful that we can explain the origin of some of life's most complex, fundamental, and efficient machine-like features by appealing to random factors like random genetic drift, random recombination, and random mutation. This is hardly different from saying that molecular machines arose for no reason at all.

Be that as it may, their admission that explaining the origin of cellular features is a "glaring gap" shows that this remains a major problem for evolutionary thinking, whether under an adaptationist or a neutralist model. Though they don't put it quite as bluntly as Franklin Harold, this paper's message is no less potent: modern evolutionary biology lacks explanations for the origin of molecular machines.