More on politics ruining everything: Science edition.

Here’s What Happens When Science Goes Woke 

Denyse O'Leary 

Let’s look at some of the things that are happening. Darwinian evolutionary biologist Jerry Coyne puts the matter concisely when he says, 

The old saying goes that “all science is political”, a saying that is true only if you stretch the meaning of either “science” or “political”. I’m baffled, for instance, to understand how my work on the genetics of hybrid sterility in Drosophila is political. But don’t worry: the ideologues will find a way to make it so. “You’re doing your work in the milieu of a culture,” they’ll babble, “and decisions about what to fund and publish are explicitly political.” Blah blah blah.

JERRY COYNE, “SCIENTIFIC AMERICAN GOES DEFENSIVE; TRIES TO PRETEND THAT EVERY SOCIAL JUSTICE SCREED IS A “SCIENCE STORY”” AT WHY EVOLUTION IS TRUE (NOVEMBER 10, 2022) 

Okay, Here’s Another One

One of many: 

Consider this recent front-page New York Times story: “He’s an Outspoken Defender of Meat. Industry Funds His Research, Files Show.” The exposé targeted Dr. Frank Mitloehner, an air-quality specialist at the University of California, Davis. Never mind his position at a respected research institution and stellar publication record; the Times wants you to know that Mitloehner’s work is funded by “farming interests” trying to deflect blame for climate change:

“According to internal University of California documents reviewed by the New York Times, Dr. Mitloehner’s academic group, the Clear Center at UC Davis, receives almost all its funding from industry donations and coordinates with a major livestock lobby group on messaging campaigns.”

There’s no need to refute the story’s allegations; that’s already been done. The Clear Center has always disclosed its industry funding. Mitloehner has also responded to the story, explaining that his research team uses the grant money to devise solutions that help “reduce the environmental footprint of animal agriculture.” We’ve discussed some of this impressive work in recent articles. Other scientists have pointed out that none of the Clear Center’s work deviates from the scientific consensus on climate change. 

CAMERON ENGLISH, “NYT ATTACKS GREAT SCIENTIST, FURTHER TANKS ITS CREDIBILITY ” AT AMERICAN COUNCIL ON SCIENCE AND HEALTH(NOVEMBER 7, 2022) 

Industry funds most science research, as English goes on to point out. The alternative would be that government funds all science research and you pay for it via your taxes. 

Some Political Issues There? 

While we are here, emerging out of the COVID years, premier science journal Nature is now telling us that “Health policymakers need to cultivate social trust and plan effective communication strategies well before the next infectious disease goes global.”

Wait. What? More propaganda? Why not make correct information the next big priority instead? One that is not marred by professionals getting kicked off social media merely for a dissenting opinion?

Read the rest at Mind Matters News, published by Discovery Institute’s Bradley Center for Natural and Artificial Intelligence.

 

More intelligent than we thought?

Mitochondria Promoted to Information Processing Systems 

David Coppedge 

One way to infer the possibility of intelligent design is to judge whether an object grows more fascinating and inscrutable the more its details are revealed. Watch for the phrase, “more complex than thought” in scientific papers. One is sure to encounter that phrase often in biology, particularly in cell biology.

In a fascinating Perspective paper in Cell Metabolism, Martin Picard and Orian S. Shirihai tell about the “particularly exciting time for mitochondrial biology” going on right now. Figure 1 in their open-access paper illustrates historical landmarks in mitochondrial research on a chart, showing “the need for an integrative view of this multifaceted organelle.” It’s time to promote mitochondria to leadership positions. 

The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS).  

Mitochondria Are Beautiful 

How they integrate this new picture into evolutionary theory we will look at shortly. For now, notice their praise for the organelle that for so long was underappreciated. Mitochondria deserve better than to be dubbed “bean-shaped ATP-synthesizing chemiosmotic machines,” as marvelous as that description had been.  

In this perspective, we argue that as we move toward increasingly accurate mechanistic models of the role of mitochondria in human health, we need an understanding of mitochondrial behavior extending far beyond energetics. As echoed by others, the “powerhouse” analogy promotes an overly simplistic picture of this beautifully complex organelle. The outdated mechanical analogy is too unidimensional to guide integrative scientific thinking. The challenge ahead is to integrate current prevailing perspectives of mitochondria as inherited, dynamic, energy-transforming, signaling organelles whose influence extends to all cellular compartments, and to the whole organism. Here we propose that our existing knowledge of mitochondrial biology can be integrated under the common framework of mitochondrial signal transduction. Consequently, a more integrative and accurate analogy portrays mitochondria as the processor of the cell — or more precisely as the mitochondrial information processing system (MIPS). 

Figure 2 in the paper shows how mitochondria do far more than deliver ATP molecules (which they do abundantly, rapidly, and efficiently). They signal. They network. They participate. In some ways, they direct the flow of information around the cell — and not only within the cell, but between cells. Their expertise extends to tissues, organs, and to the whole organism. 

What Signal Transduction Requires 

Picard and Shirihai argue that signal transduction is a more accurate analogy for mitochondria’s role. Intuitively, signal transduction implies information flow from inputs to outputs. The authors indicate three requirements for any signal transduction system: (1) sensing, (2) integration, and (3) signaling. For an illustration, consider those functions on a navy ship traveling through a mine field. Sailors tasked with sensing danger need the tools to read the inputs, such as sonar. They must transfer that information to the ship’s captain and advisors to select the best course of action. If a submarine was detected, the captain then signals the navigators to implement the course change. These requirements are readily understood for any adaptive signaling system, be it implemented in a football game, a mathematical model, or a rover on Mars. Sense an input; integrate the information; signal the output.

It also becomes obvious that such systems are irreducibly complex and imply foresight. If any one of the three requirements is not met, the ship could be blown up, the receiver gets into the wrong position for the catch, the model fails to reflect reality, or the rover drives off a cliff. The system design, to be successful, must be aware of the potential risks. This implies foresight by an intelligent designer. Clinching the case for design, each one of the requirements (sensing, integration, signaling) is usually irreducibly complex in itself.  

Requirements, Precisely Met 

In mitochondria, all three of these requirements are met with precision:

Sensing: The ability of mitochondria to detect metabolic and hormonal inputs, and to transform these inputs into morphological, biochemical, and functional mitochondrial states.

Integration: The pooling of multiple inputs into common effectors driven by the exchange of information among mitochondria and other organelles, and influenced by the current state of the mitochondrial network and of the cell.

Signaling: The production of mitochondrial outputs, or signals, that transmit information locally to direct metabolic pathway fluxes and influence other organelles, including nuclear gene expression, and systemically to regulate the physiology and organismal behavior.

Those interested in the details will marvel at how many parts mitochondria need carry out these roles. So equipped, they regulate gene transcription and energy production, they switch on responses to toxins, and they respond to stress. In extreme cases, they can even throw the switch for programmed cell death, or apoptosis. The details of these integrated organelles are staggering. 

The MIPS engages in functional interactions with the ER lysosomes, peroxisomes, lipid droplets, and likely other organelles… Mitochondrial metabolism is directly supported by surrounding organelles that provide various substrates, lipid intermediates, and ionic signals that not only supply substrates, but also communicate information about the overall state of the cell. In particular, input from the nucleus provides hundreds of proteins that sustain and confer mitochondria with both their molecular sensory machinery and the machinery for fusion/fission dynamics and motility that influence their propensity to adopt certain network configurations. 

Mitochondria can even fuse with one another without scrambling their parts or functions. They can migrate on the cytoskeletal highway and gather where they are needed. Of particular note is the finding that they can network with one another: “mitochondria are functionally linked and operate as ‘social’ collectives within the cell cytoplasm,” the authors say. Consider the far-reaching effects of mitochondria described in the authors’ summary: 

Mitochondria are equipped with a surprisingly wide variety of receptors and molecular features that give them the ability to sense hormonal, metabolic, ionic, genetic, and other inputs. With such sensitivity to a broad spectrum of inputs, the MIPS senses both the local biochemical conditions surrounding each organelle and systemic neuroendocrine signals produced in distant anatomical locations of the organism: by other cells, within other organs. 

A related paper in the EMBO Journal (open access), by Patron et al., tells how mitochondria use their proton gradient to regulate proteostasis. Sensing inputs from calcium ions and voltage from proton flow, mitochondria can switch a certain protease on or off “to reshape the mitochondrial proteome and adjust the cellular metabolism.” A preprint on bioRxiv adds that this calcium signaling is finely tuned. It’s title: “Goldilocks calcium and the mitochondrial respiratory chain: too much, too little, just right.” 

Don’t forget that these roles are all in addition to the mitochodrion’s already-celebrated function as a producer of ATP through a series of irreducibly complex machines. Want to ponder that role a little more? Another preprint on bioRxiv reveals new details from cryo-electron microscopy about Complex 1, the first of five intricate machines in the electron transport chain. This factory of machines feeds protons to the rotary engines (ATP synthase) that supply our energy needs each second. Incidentally, this study was done on fruit flies — you know, those nearly invisible flying machines? They also have mitochondrial information processing systems, like every other living thing! 

Can the MIPS be Darwinized? 

It is sad to see Picard and Shirihai, so well aware of the elaborate functional complexity in the Mitochondrial Information Processing System, attribute it to chance. They cling to Darwinian evolution and the myth of endosymbiosis. “Through evolution,” they dream with dogmatic snores, “the endosymbiotic incorporation of mitochondria marked the transition from a selfish unicellular world to a multicellular reality.” 

How can any sensible person believe such notions? One reason is that Darwinism grants materialists an unlimited research program with no requirement for understanding how chance pulled it off. 

The evolutionary co-opting of a variety of DNA-binding receptors, GPCRs, and transporters suggests that increasing the range of inputs that mitochondria were capable of sensing must have positively contributed to the organism’s adaptive capacity. As a result, the diverse mitochondrial sensing machinery has been evolutionarily selected and likely also enriched in mitochondrial membranes relative to other organelles. Defining the full spectrum of inputs directly sensed by the MIPS across different cell types is an outstanding research challenge. 

Selection without a selector. Co-option without an operator. Machinery without an engineer. Enriching without an investment advisor. Equipping without a trainer. A research challenge, indeed. 

Eli Cohen: a brief history.

 Eli Cohen

By The Editors of Encyclopaedia Britannica 

Eli Cohen, in full Eliahu ben Shaoul Cohen, also called Kamal Amin Thaabet, (born 1924, Alexandria, Egypt—died May 18, 1965, Damascus, Syria), Egyptian-born Israeli spy who infiltrated the highest ranks of the Syrian military and government by posing as a Syrian businessman. Between 1961 and 1965 Cohen passed Syrian secrets to the Israeli government in what is remembered as one of the most daring and productive intelligence-gathering 

Cohen grew up in Alexandria, Egypt, the son of Syrian Jewish parents. His fluency in Arabic, English, and French made him an attractive recruit for Israeli intelligence. He travelled to Israel for a brief espionage training course in 1955 and returned to Egypt the following year. Cohen, however, was expelled from Egypt along with other Zionist Jews in the aftermath of the Suez Crisis, and he settled in Israel in 1957. He worked as a translator and an accountant before once again being recruited by Israeli intelligence in 1960. 

After completing further training, Cohen was sent in 1961 to Buenos Aires, where he posed as an expatriate Syrian businessman. Using the alias Kamal Amin Thaabet, Cohen made numerous contacts in the Syrian expatriate community in Argentina and soon gained the trust of senior officials working in the Syrian embassy there. Those included the Syrian military attaché, Amin al-Hafez, who would later serve as president of Syria. Cohen made his desire to “return” to Syria well known to his new associates, and, when he moved to Damascus in 1962, his Syrian contacts helped him access the highest circles of power in Syria. He soon began to transmit information about Syrian military plans back to Israel.

Cohen’s espionage work took on even greater importance when a Baʿthist junta that included several of his associates from Argentina seized power in Syria in 1963. The coup’s leader, Amin al-Hafez, continued to favour Cohen, and he reportedly considered appointing him deputy minister of defense. Cohen received classified military briefings and was taken on tours of the Syrian fortifications in the Golan Heights.

Despite Cohen’s considerable talent for espionage, he displayed a tendency for carelessness, ignoring his Israeli handlers’ warnings against sending radio transmissions too frequently or always at the same time of day. That proved to be his downfall. In January 1965 Syrian counterintelligence identified his radio signal and apprehended him in the act of sending a transmission. Cohen was interrogated, convicted in a military trial, and publicly hanged in May 1965. 

Darwinism vs. the Science?

 Twelve “Shocking” Discoveries for Evolution 

Eric H. Anderson 

A correspondent preparing for a presentation asked if I “would care to chip in a few lines about what you see as truly remarkable or even shocking recent discoveries about genetics or epigenetics that provide additional support for the design inference. (Other than, that is, the famous work of ENCODE which seems to have deep-sixed the ‘junk DNA’ doctrine.)”

“Shocking recent discoveries”? Good question

Not So Surprising for Intelligent Design 

With two caveats, I’ll share a few from the past 15 years or so. The first caveat is that many discoveries trickle in slowly over time. So, we could perhaps point to earlier evidence for some of the items below from more than 15 years ago, but I would argue that the evidence has become much more apparent or more widely acknowledged since then. The second caveat is that some discoveries might be surprising or “shocking” from an evolutionary perspective, but not necessarily from a perspective of intelligent design.

So with those caveats: 

Here Are Twelve; Likely There Are More 

1.Growing appreciation for frameshifting encoding.

2. Growing appreciation for bi-directional encoding.

3. Early evidence that some “neutral” mutations may not in fact be neutral.

4. Massive and extensive role for RNAs in cellular processes. Yes, this relates to ENCODE, but deserves to be mentioned in its own right, as there is rapidly growing experimental evidence for functional roles of specific RNAs.

5. The need for regular maintenance and care of DNA, such as the critical role of topoisomerase that Joe Deweese studies. By the way, if you’re speaking about this to an audience, a great object lesson is to show the supercoiling problem with a two-stranded piece of yarn. From personal experience, I’d recommend practicing at home beforehand. But once you get it down, it is a fantastic visual aid and very memorable. 

6. The growing list of alternative genetic codes.

7. Directly contrary to the evolutionary prediction, with more genomes in the database, the number of lineage-specific or taxonomically restricted genes. Not here and there, but extensive and pervasive. This is an absolutely massive problem for evolutionary theory.

8. Many functional roles have been identified for the inappropriately named “pseudogenes.” This counters one of the most loudly proclaimed evidences for blind undirected evolution.

9. Growing evidence for functional roles for some so-called “endogenous retroviruses.” There’s less information here so far, but it appears to be trending in the same direction as pseudogenes and other “junk DNA” claims generally.

10. Clear genetic-based evidence that several of the most loudly touted examples of evolution are in fact degradative. There is Michael Behe’s work of course, as well as Scott Minnich’s lab work and analysis of Lenski’s long term evolutionary experiment. The importance of this cannot be overstated. It is one of the few areas where we have real experimental data, as opposed to ideas, conjectures, and hand-waving claims about what evolution is supposed to be able to accomplish. And the evidence is extremely clear. 

11. Related to taxonomically restricted genes, but this needs to be mentioned in its own right: The grand hope of comparative genomic studies was to produce a coherent tree that would show the true evolutionary history. Exactly the opposite has happened. It is an absolute mess, with contradictions at every turn and nothing even approaching a unified evolutionary history. It’s reached the point where even prominent evolutionists have started abandoning the tree model altogether, reposing their hope in convergent evolution, HGT, some as-yet-undiscovered process, etc.

12. Less directly related, but perhaps worth mentioning:

(a) Growing recognition that protein folding requires careful control in many cases, not just an automatic fold. And, no, AlphaFold has not “solved” the problem from first principles. See Paul Nelson’s Evolution News article from a few weeks ago. Also listen to my podcast discussion with Paul.

(b) Growing support for the idea of protein rarity, and isolated regions in search space. This is exactly what we see in designed systems, and the opposite of what’s predicted by evolutionary theory. See the additional work of Douglas Axe and Brian Miller.

There are probably several others I’m forgetting right now.

Now the multiverse ruins everything?

 Meyer and Klavan: How the Multiverse Ruins Science…and Storytelling 

David Klinghoffer

Stephen Meyer had a fascinating conversation with podcaster Andrew Klavan and his son Spencer Klavan. The topic: how the multiverse theory destroys not only science (as Meyer explains in Return of the God Hypothesis) but storytelling. The younger Klavan is Associate Editor at the Claremont Review of Books and an Oxford PhD in classics. Impressive guy. He wrote an essay there analyzing the Marvel Cinematic Universe (MCU), of which “the multiverse has become the central governing concept.” 

Klavan nails it in his essay:

“In the infinite multiverse there’s a cure for every illness. A solution to every problem,” says the Scarlet Witch (Elizabeth Olsen) in Doctor Strange and the Multiverse of Madness. She’s exactly right, and that’s exactly the issue: two and a half hours of pointless carnage will end us right back where we started if the dead shall be raised as soon as the credits roll. The multiversal MCU is a world without narrative stakes, moral meaning, or tragedy, because it is a world without consequences. 

Now that is something I had not thought of. In a multiverse where no possibility is excluded and everything does and does not happen, every which way, any story we can tell is deflated by the realization that in another universe the tale has turned out differently. For example, if we suppose there is another version of Anna Karenina, taking place in a parallel reality in which the freight train stops just in time, that would drain a considerable amount of the interest from Tolstoy’s novel.

Read the rest of “Worlds Without End” at the Claremont Review of Books.