Michael J. Behe's Blog, page 526

Jerry Coyne discovers the lack of intellectual freedom on campus

Now, Darwinian evolutionary biologist Jerry Coyne believes that the student he quotes at Why Evolution Is True genuinely believes what he is saying:

Conservative ideas do not deserve equal consideration to that afforded liberal and left ideas, because conservative ideas are not equal to liberal and left ideas. There is no legitimate argument for supporting Donald Trump and his allies, at least not one that holds up in any academic community worth its salt. Advocating nativism, sexism, government by oligarchic graft and anything else the president represents is not productive in a space meant to contribute ideas to the world.

We’ve already reached tacit agreement on this. We’re an overwhelmingly left-leaning student body—73 percent of respondents to the Student Life survey mentioned in the original WU: In Focus piece identified as “very” or “somewhat liberal,” compared with only 8 percent who reported being any degree of “conservative.” Instead of propping up fringe ideas out of some sense of “bipartisan” openness, we should embrace the fact that so many of our students are liberal. Instead of wasting our time and mental energy on some right-wing argument no one really believes, we should spend time having meaningful conversations. How can we guarantee everyone health coverage? What’s the best way to redistribute wealth? How can we mitigate climate change, a thing we all agree is a problem? Sean Lundergan, “It’s OK that conservatives don’t feel welcome” at Student Life

At least one of Jerry’s commenters suggests that this is a hoax. Somewhat like the hoax papers Peter Boghossian’s team used to send up social science journals that pretend to be some type of science.

The trouble is, using that example, if someone with a Ph.d. is claiming that humans enforce “heteronormativity” on dogs, why shouldn’t we think that the Ph.d. is serious, given what the social sciences have become? In the same way, why shouldn’t we think Lundergan is serious, given what university is becoming? For now, assume it’s true.

Coyne makes the obvious point in response that

Alas, Lundergan’s prescription—to adopt the liberal position, ignore conservatives, and then figure out how to implement liberal policy—neglects an important reason why conservatives (or anyone with unpopular ideas) should not only speak, but should be listened to. And that, as John Stuart Mill argued in On Liberty, is because without hearing the other side, how do you know your own ideas are well formed and rational? Have you considered the best version of the other side’s views before rejecting them? If not, then you are incompetent to hold your own opinions.

Further, shutting down conservative opinions means that each generation of students must, if they are to be rational advocates of their views, relearn conservative ideas on their own initiative, and not by hearing them from the conservatives who “aren’t welcome.” Jerry Coyne, “Student op-ed: We don’t need to hear conservative voices” at Why Evolution Is True

Right. Students will graduate ignorant, intellectually unable to meet challenges, and mad as stink that the world doesn’t care to hear from them. Easily manipulated, one expects. There’ll be consequences. Why alumni or taxpayers fund universities that haven’t signed the Chicago Statement is a mystery to some of us.

The reader who sent this in comments: It must be weird being in Coyne’s shoes, where your own side has gone full moon loon. (In Canada, we call it a “three-loon special.” – (O’Leary for News)

Note: In fairness, most of the comments I (O’Leary for News) was able to read at the Student Life page told KGB. where to get off. It may be a U (Washington U, St. Louis) but it’s not the Soviet Union, after all.

See also: Neurosurgeon Michael Egnor Has Become Darwinian Jerry Coyne’s “Archenemy”

and

Jerry Coyne Has Another Reason To Be Mad At Templeton

Follow UD News at Twitter!

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

What would a multiverse really be like?

A philosopher follows a chain of reasoning, for example:

The possibility of a Spatial or Quantum Multiverse may give you strong reason to doubt your memory and your scientific view of the world. If there are many copies of you being created all the time in all sorts of environments, then only a few of those copies have accurate memories of the world’s history and beliefs about its large-scale structure. The reason is that the majority of them will be created with false memories, even though (since they’re copies of you) they have the same memories you do. They have memories of having lived for years or decades already, but in reality, they popped into existence a few moments ago in a small “bubble” of stability in a chaotic whole. And “they” might be “us.” So a multiverse might force us to question our memories and scientific beliefs.Thomas Metcalf, “A Multiverse of Possibilities” at Arc

The multiverse is not a logical deduction from the state of our universe. It is an attempt to short circuit discussion of apparent fine-tuning by appealing to the idea that no conclusions can be drawn because there is an infinite series we do not know about.

See also: The multiverse is science’s assisted suicide

and

What becomes of science when the evidence does not matter?

Follow UD News at Twitter!

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Researchers: Life didn’t just hang on but throve 3.5 billion years ago

 microbes that breath sulfate/ Guy Perkins and Mark Ellisman, National Center for Microscopy and Imaging Research

They argue that, if that;s true, life should be common in the universe. From ScienceDaily:

Scientists want to know how long life has existed on Earth. If it has been around for almost as long as the planet, this suggests it is easy for life to originate and life should be common in the Universe. If it takes a long time to originate, this suggests there were very special conditions that had to occur.

Actually, that doesn’t quite follow. There could have been very special conditions at the beginning. And, absent very special conditions, maybe life just would not originate at all.

This new study reveals a primary biological control step in microbial sulfur metabolism, and clarifies which cellular states lead to which types of sulfur isotope fractionation. This allows scientists to link metabolism to isotopes: by knowing how metabolism changes stable isotope ratios, scientists can predict the isotopic signature organisms should leave behind. This study provides some of the first information regarding how robustly ancient life was metabolizing. Microbial sulfate metabolism is recorded in over a three billion years of sulfur isotope ratios that are in line with this study’s predictions, which suggest life was in fact thriving in the ancient oceans. Paper. (open access) – Min Sub Sim, Hideaki Ogata, Wolfgang Lubitz, Jess F. Adkins, Alex L. Sessions, Victoria J. Orphan, Shawn E. McGlynn. Role of APS reductase in biogeochemical sulfur isotope fractionation. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-018-07878-4 More.

The question one is left with is, if life is 3.5 billion years old, why did it only become quite interesting about half a billion years ago (if that’s the story)? The microbes that metabolized practically anything just to stay alive didn’t appear to want to do much else. Yes, it’s an old question why they didn’t (couldn’t?) Or maybe they even did. But based on the history of the last half-billion years, there should be an answer.

See also: Photosynthesis Pushed Back Even Further. Time To Revisit The “Boring Billion” Claim

Earth’s “boring billion”now hot again (2015)

The “boring billion” years: New hypothesis suggests oxygen shortage stalled life (2014)

Why was there a “boring billion” years of single cell life? (2014)

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Life form’s environment so extreme is has never been cultivated in a laboratory

Deep diving robot/
Woods Hole, Andrew Fisher

From a a study of microbes (in this case, Archaea) that live in the hot, oxygen-free stream that flows through Earth’s crust, Hydrothermarchaeota, “this group of microbes lives in such an extreme environment that they have never been cultivated in a laboratory for study,” at ScienceDaily:

They found that Hydrothermarchaeota may obtain energy by processing carbon monoxide and sulfate, which is an overlooked metabolic strategy. The microbes use energy from this process to grow as a form of chemosynthesis. …

The researchers also found genetic evidence that Hydrothermarchaeota have the ability to move on their own. Motility offers a valuable survival strategy for the extreme environment they call home, which has a limited supply of nutrients essential to life.

“Studying these unique microbes can give us insights into both the history of Earth and the potential strategies of life on other planets,” said Stephanie Carr, first author on the paper and a former postdoctoral researcher with Orcutt who is now an assistant professor at Hartwick College. “Their survival strategies make them incredibly versatile, and they play an important, overlooked role in the subsurface environments where they live.”

Paper. (open access) – Stephanie A. Carr, Sean P. Jungbluth, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Tanja Woyke, Michael S. Rappé, Beth N. Orcutt. Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere. The ISME Journal, 2019; DOI: 10.1038/s41396-019-0352-9 More.

The more we know, the more insights we can have, sure. But it’s not always clear what specific things truly extreme life forms can tell us about the more common ones. Maybe the message is more general, that life forms try their hardest to survive every circumstance. But what is it they have that rocks don’t?

See also: New Life Form More Different From Others “Than Animals Are From Fungi”

Organisms Found That Hover Indefinitely Between Life And Death

Light-loving cyanobacteria found, improbably, nearly 2,000 feet underground

and

Life form found at abyssal depths

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Sponges really are older than comb jellies, researchers say

Researchers’ data favors sponges as sister group to all existing animal lineages/Professor Gert Wörheide, LMU

There’s been a bit of a jostle recently between claims made for sponges vs claims made for comb jellies as the first significant complex life. Both types of life forms are at least 500 million years old. Using a bigger data set, this group of researchers favors the sponges. From ScienceDaily:

Of particular interest among these animal phyla are the sponges (Porifera) and the comb jellies (Ctenophora), as it remains unclear which of these groups represents the sister group to all other animals. “Irrespective of whether we include paralogs or not, our results are consistent with the classical view of animal phylogeny in that the sponges are the sister group to all other extant animal lineages,” says Wörheide. Analysis of the ortholog gene content on its own places the comb jellies as the sister group of Placozoa, Cnidaria and Bilateria (this last group accounts for 95% of extant animal species). Including homologous gene family content data, however, identifies ctenophores as the sister group of the Cnidaria. This result agrees with a proposal drawn from morphological studies — the Coelenterata hypothesis — that dates back to the mid-19th century, a view which had gone out of favor in recent years.

“We conclude from our results that the anomalous placement of some highly divergent lineages, such as the comb jellies, reflects a fundamental limitation in the ability of conventional sequence-based methods — which rely on data for orthologs alone — to resolve the branching patterns of very ancient lineages,” says Wörheide. Paper. (paywall) – Walker Pett, Marcin Adamski, Maja Adamska, Warren R Francis, Michael Eitel, Davide Pisani, Gert Wörheide. The role of homology and orthology in the phylogenomic analysis of metazoan gene content. Molecular Biology and Evolution, 2019; DOI: 10.1093/molbev/msz013 More.

For various views, see

Researchers: Sponges Definitely Oldest Animals, Not “Anatomically Complex” Comb Jellies

Our physics color commentator Rob Sheldon offers an analysis:

Problem. Square peg. Round hole.

Solution. Bigger hammer.

Who says evolution has unsolved problems?

So let’s wait and see what the other side says. Chances are we haven’t heard the last of it.

Sponges vs. jellies: Comb jellies still the “oldest” complex life form, researchers say

Sponges back in the ring with comb jellies for “oldest” title fight

Comb jelly files: Complex features do not each emerge once

Comb jelly DNA sequence offers “unintuitive facts” about evolution…

and

Researchers: The sponge is the oldest animal phylum after all (2015)

and

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Researchers: How the immune system “thinks”

structure of an animal cell/royroydeb (CC BY-SA 4.0)

From ScienceDaily:

During infection, T-cells of the immune system synthesize acetylcholine, explains Dr. Mak. In the brain, acetylcholine functions as a neurotransmitter and controls learning and memory. In the immune system, T-cells making this classical brain chemical are able to jump out of the blood circulation and take action in the tissues to fight infection.

First author Maureen Cox summarizes the study findings this way: “The neurotransmitter acetylcholine is produced by T-cells during viral infection to facilitate their entry into tissues under attack, where these cells then kill the virus-infected cells.”

The discovery was made when the lab team genetically engineered a mouse lacking the ability to produce the neurotransmitter in T-cells and observed that the immune cells could not control chronic virus infections in its absence.

“We now have absolute genetic proof that immune cells need this brain chemical,” says Dr. Mak. “We believe it’s an entirely new lens though which to look at numerous diseases including cancer, viral infections and autoimmune conditions.” Paper. (paywall) – M. Rosas-Ballina, P. S. Olofsson, M. Ochani, S. I. Valdes-Ferrer, Y. A. Levine, C. Reardon, M. W. Tusche, V. A. Pavlov, U. Andersson, S. Chavan, T. W. Mak, K. J. Tracey. Acetylcholine-Synthesizing T Cells Relay Neural Signals in a Vagus Nerve Circuit. Science, 2011; 334 (6052): 98 DOI: 10.1126/science.1209985 More.

Researchers can say that “thinks” is “just an image” if they like. But at what point does it become clear that somehow something must have been doing something that we would normally describe as thinking or else this wouldn’t be happening.

See also: Researcher: Mathematics Sheds Light On “Unfathomably Complex” Cellular Thinking

How do cells in the body know where they are supposed to be?

Researchers A Kill Cancer Code Is Embedded in Every Cell

How Do Cells Interpret The “Dizzying” Communications Pathways In Multicellular Life Forms?

and

Cell atlases reveal extreme complexity at biology’s frontiers

Follow UD News at Twitter!

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Endangered languages: Efforts to save them sometimes involve questionable claims

The many, probably doomed, efforts to save minority languages are sparking new interest in the origin of language: Also in making statements about language that are well-meaning but questionable:

And sadly, just because the linguistic community has only recently identified a language does not mean it’s invulnerable. Recently identified languages can disappear just as easily as those recognized for decades. Koro Aka, for instance, may already be at risk of slipping away, since there are few Koro Aka speakers under the age of 20. “A process of language shift is underway,” Harrison says. “Younger generations are using it only sporadically. It’s definitely in decline.” Even so, he reports, a small group of young Koro Aka speakers is putting up a valiant fight to save the language. Some even appeared on the National Mall in Washington, D.C., recently to share the Koro Aka language and culture with visitors around the world. The youthful Koro Aka speakers on the mall may have grasped something many of us do not: the rewards of keeping a rare language alive even if a more common tongue would suffice. Languages supply the very framework on which our thoughts coalesce—a framework that is completely distinct in each language and gives rise to distinctive modes of thinking and expression.Elizabeth Svoboda, “Where Do “New” Languages Come From?” at Sapiens

“Distinct modes of thinking”? This reminds me of a story I once did for a Canadian magazine on translating the Bible into Inuit, an official language of the Canadian Territory of Nunavut:

I remember once being introduced to three Inuit clergy — two Inuit priests and their bishop. They were engaged in a process called “back translation” of passages from the Bible into English from Inuktitut. To ensure that the meaning of the text is preserved, the translated text is then translated back into English by third parties (in this case, themselves), and later checked by the original translator.

I happened to overhear one of the priests turn to his bishop and say, “It’s hard sometimes to work with this text. It feels alive.”

Compared to the latest missives from a northern government bureau, I’m sure it certainly does feel alive. I was tempted to shout into the room, “Yes, because the person who wrote it WAS once alive, and meant what he said.” More.

On major human issues, there are many personal histories and philosophies but no distinct rational mode of thinking that absolutely evades conversion to another language.

Reality check: A current factoid is that more than 40% of the world’s estimated 6000 languages are endangered. But languages are like species; where the line is drawn usually involves political, social, and economic considerations. And saving minority languages is bound to be a source of clean, government-funded jobs in remote places. One hesitates to argue with that. And it also offers opportunities for software (cue software developers). Expect the number of newly discovered threatened languages to grow, irrespective of the tide of other events.

The main reason minority languages die out (think Cornish, Welsh, and Irish, for example) is that language is the business end of consciousness. People gravitate toward majority languages because they offer the maximum number of opportunities (usually those with the largest number of speakers).

Take medicine as an example: If only 6000 people speak a language, the speakers can have a physician or two who grew up speaking it but not necessarily an endocrine specialist. And knowledge of endocrine systems is not typically transmitted in languages with only 6000 speakers. Spread over many areas of life, this process gradually marginalizes the minority language further and further, without anyone intending to create that effect.

People want their kids to know languages in which they can get ahead, not ones in which they are trapped. Thus, saving minority languages is a fine cause if it doesn’t interfere with reality. Not if, for example, it means enforced schooling in a dying language.

The reality is that humans develop and discard languages all the time, as we do fashions. Preservation is worthwhile but it is the job of museums.

Children frequently make up (and discard) languages, if they have co-operative playmates. Here is the example that attracted the attention of the researchers noted above:

Where Do “New” Languages Come From?

See also: Can we talk? Language as the business end of consciousness

Follow UD News at Twitter!

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Hearing, the cochlea, the frequency domain and Fourier’s series

In recent weeks, we have seen repeated attempts to suggest that Mathematics is essentially a mind game we make up as an aspect of culture. There has been a very strong resistance to the idea that there are intelligible manifestations of structure and quantity embedded in the fabric of the world (and indeed in that of any possible world). And when test cases have been put on the table, they have been consistently brushed aside as cases where our mathematical modelling has been applied; that is it’s all in our heads.

So, it is appropriate to put on the table a test case that is quite literally in our heads, hearing and particularly how the cochlea works. Video:

We see here how there is a frequency domain transformation that makes use of the mechanical properties of the inner ear. That is, our hearing moves from the time to the frequency domain, sensing pitch; also, subtle timing differences between sound arrivals at our right and left ears help us to locate sound sources in the space around us. As was noted in a comment in the Fourier thread:

_____________

KF, 4: >>On how hearing creates a frequency domain transform of sound inputs, driving the onward processing, Wiki is a handy reference:

The stapes (stirrup) ossicle bone of the middle ear
transmits vibrations to the fenestra ovalis (oval window) on the outside
of the cochlea, which vibrates the perilymph in the vestibular duct
(upper chamber of the cochlea). The ossicles are essential for efficient
coupling of sound waves into the cochlea, since the cochlea environment
is a fluid–membrane system, and it takes more pressure to move sound
through fluid–membrane waves than it does through air; a pressure
increase is achieved by the area ratio of the tympanic membrane to the
oval window, resulting in a pressure gain of about 20× from the original
sound wave pressure in air. This gain is a form of impedance matching –
to match the soundwave travelling through air to that travelling in the
fluid–membrane system . . . .

The perilymph in the vestibular duct and the endolymph in the
cochlear duct act mechanically as a single duct, being kept apart only
by the very thin Reissner’s membrane. The vibrations of the endolymph in the cochlear duct displace the basilar membrane in a pattern that peaks a distance from the oval window depending upon the soundwave frequency.
The organ of Corti vibrates due to outer hair cells further amplifying
these vibrations. Inner hair cells are then displaced by the vibrations
in the fluid, and depolarise by an influx of K+ via their
tip-link-connected channels, and send their signals via neurotransmitter
to the primary auditory neurons of the spiral ganglion.

The hair cells in the organ of Corti are tuned to certain sound frequencies by way of their location in the cochlea,
due to the degree of stiffness in the basilar membrane.[3] This
stiffness is due to, among other things, the thickness and width of the
basilar membrane,[4] which along the length of the cochlea is stiffest
nearest its beginning at the oval window, where the stapes introduces
the vibrations coming from the eardrum. Since its stiffness is high
there, it allows only high-frequency vibrations to move the basilar
membrane, and thus the hair cells. The farther a wave travels towards
the cochlea’s apex (the helicotrema), the less stiff the basilar
membrane is; thus lower frequencies travel down the tube, and the
less-stiff membrane is moved most easily by them where the reduced
stiffness allows: that is, as the basilar membrane gets less and less
stiff, waves slow down and it responds better to lower frequencies.
In addition, in mammals, the cochlea is coiled, which has been shown to
enhance low-frequency vibrations as they travel through the fluid-filled
coil.[5] This spatial arrangement of sound reception is referred to as
tonotopy . . . . Not only does the cochlea “receive” sound, it generates
and amplifies sound when it is healthy. Where the organism needs a
mechanism to hear very faint sounds, the cochlea amplifies by the
reverse transduction of the OHCs, converting electrical signals back to
mechanical in a positive-feedback configuration. The OHCs have a protein
motor called prestin on their outer membranes; it generates additional
movement that couples back to the fluid–membrane wave. This “active
amplifier” is essential in the ear’s ability to amplify weak
sounds.[6][7]

The active amplifier also leads to the phenomenon of soundwave
vibrations being emitted from the cochlea back into the ear canal
through the middle ear (otoacoustic emissions) . . . .

Otoacoustic emissions are due to a wave exiting the cochlea via the
oval window, and propagating back through the middle ear to the eardrum,
and out the ear canal, where it can be picked up by a microphone.
Otoacoustic emissions are important in some types of tests for hearing
impairment, since they are present when the cochlea is working well, and
less so when it is suffering from loss of OHC activity . . . .

The coiled form of cochlea is unique to mammals. In birds and in
other non-mammalian vertebrates, the compartment containing the sensory
cells for hearing is occasionally also called “cochlea,” despite not
being coiled up. Instead, it forms a blind-ended tube, also called the
cochlear duct. This difference apparently evolved in parallel with the
differences in frequency range of hearing between mammals and
non-mammalian vertebrates. The superior frequency range in mammals is
partly due to their unique mechanism of pre-amplification of sound by
active cell-body vibrations of outer hair cells. Frequency resolution
is, however, not better in mammals than in most lizards and birds, but
the upper frequency limit is – sometimes much – higher. Most bird
species do not hear above 4–5 kHz, the currently known maximum being ~
11 kHz in the barn owl. Some marine mammals hear up to 200 kHz. A long
coiled compartment, rather than a short and straight one, provides more
space for additional octaves of hearing range, and has made possible
some of the highly derived behaviors involving mammalian hearing . . .

In short, sinusoidal frequency domain decomposition of sound waves is a key mechanical phenomenon exploited by our hearing system, leading to in effect a frequency domain transformation of the temporal pattern of compressions and rarefactions that we term sound. This is of course closely related to the patterns we explored and discovered using Fourier power series and integral analysis of oscillations and transient pulses.

Where, on the mechanical side, harmonic motion is tied to elastic and
inertial behaviour. Which in turn is directly connected to a rotating
vector analysis — leading straight to the complex exponential analysis
that draws out the full power of complex numbers, form Z = R*e^i*wt, w
being circular frequency 2* pi*f (in radians per second), f the cycle
per second frequency. All of this ties back to the fundamental frequency
cycles and integer-multiple frequency harmonic epicycles in the OP
above.

Again, Mathematical study turns out to reflect quantities, structures
and linked phenomena which are embedded in the fabric of our world.

KF

PS: Notice, not a few design subtleties?

PPS: The vocal tract, in effect a wind instrument, also exploits
fundamentals and harmonics to create auditory, frequency-based patterns
as well as transients.>>

______________

We see here yet another case where structure and quantity are embedded in the natural world and are exploited in the design of our bodily organs; here, those for hearing. Thus, literally in our heads. END

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Physicist Rob Sheldon on Paul Davies’ “life writes its own software” claim

Recently, we quoted Paul Davies writing on the information content of life forms in New Scientist, in connection with his new book, The Demon in the Machine, to the effect that the really tough question is how life’s hardware can write its own software.

Here’s pour physics color commentator Rob Sheldon’s response:

Davies is being vague, which helps if you are trying to get funding, or avoid being defunded. As I understand it, he is claiming that information can be increased by having information feed back on itself—improving the input and flow. I wrote a paper on this topic:

If you look at the paper, notice Figure 1, where a colleague and I argue that the information flow is growing exponentially. If information is a conserved quantity, then the ability to increase the information flow leads to faster and faster complexity. This is a property of feedback-enabled or “bootstrap” systems, as illustrated by the Intel/Microsoft “bootstrap” of a computer program that starts from a ROM chip on the motherboard.

Davies realizes that all these OOL projects (and he’s had a hand in several of them), focus on the hardware. But it is the software that is controlling the hardware, and it is the software that is growing in complexity. So if the software is managing the information flow and bootstrapping, then the focus needs to be on “laws of physics” that use feedback networks.

There aren’t very many institutions that fund that sort of research because physics almost always defines itself as a commitment to reductionism, leaving “networks” to the biologists and biochemists. So Davies is wistfully imagining that the study of “networks” will eventually reveal a reductionist “law”, and somehow we’ll arrive back at physics again. This was certainly the hope of the Sante Fe Institute in its early days, though after 40 years it appears to have given up.

Is it reasonable for Davies to hope for a “law” of information multiplication in physics?

I think it is a reasonable hope provided that we redefine what he means. The work that George Montañez has done on irreducible complexity suggests that we have a method of measuring information and complexity of biology. If Montañez adds self-reference to his definition, we would be well on our way to defining the information content in a cell.

Davies is suggesting that the way to pack more information into a smaller volume is effectively to make information hierarchical. It is as if we take a text, compress it with PKZIP, add some more zipped files, and then pack them all in a library file. When we need the information, we read the header in the library file, extract the file that we want, and then unzip it. This packing and zipping can be done again and again, putting libraries inside libraries inside libraries, as much as is needed, so that an incredible video game with great graphics displaying Terabytes of information can be shipped in a file of 1 Gbyte.

But what Davies perhaps doesn’t recognize is that the header files, the directories must be “above” the information level of the files. Nothing in the zipped file tells you how to extract it. Yes, there are “self-extracting” files, but those are more properly “programs.” And I guarantee that if you made one on Windows 10, it won’t work on my Linux 18.04, because it relies on “knowing” the operating system that reads it. The Department of Defense has some 40-year old computers in a bunker whose only job is running old software, should there be a need to cross-calibrate output. Which is to say, to preserve the information in those old programs, they also need to preserve the old hardware.

So if Davies believes that a hierarchy of information can pack more information in, and possibly explain the incredible information content of biology, then there must be something “outside” or “above” the biology that is responsible for the compression algorithm. That information cannot arise from inside the cell any more than a self-extracting program can exist without the operating system/hardware outside it.

The only thing Davies hasn’t done is name this attribute.

Should we suggest a name? How about … intelligent design?

See also: Paul Davies: The really tough question is how life’s hardware can write its own software Davies, author of The Demon in the Machine:How Hidden Webs of Information Are Finally Solving the Mystery of Life thinks we overlook the difficulty and offers a solution: Nature got there first.

Paul Davies And The “Struggle To Define Life”

and

Paul Davies: Life’s defining characteristics are better understood as information

Follow UD News at Twitter!

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana

Science Mag’s hit on Michael Behe’s new book Darwin Devolves avoids his main point

In American Association for the Advancement of Science’s magazine, Science,  we read,

In the grand scheme of evolution, mutations serve only to break structures and degrade functions, Behe argues. He allows that mutation and natural selection can explain species- and genus-level diversification, but only through the degradation of genes. Something else, he insists, is required for meaningful innovation. Here, Behe invokes a “purposeful design” by an “intelligent agent.”

There are indeed many examples of loss-of-function mutations that are advantageous, but Behe is selective in his examples. He dedicates the better part of chapter 7 to discussing a 65,000-generation Escherichia coli experiment, emphasizing the many mutations that arose that degraded function—an expected mode of adaptation to a simple laboratory environment, by the way—while dismissing improved functions and deriding one new one as a “sideshow” (1). (Full disclosure: The findings in question were published by coauthor Richard Lenski.) Nathan H. Lents , S. Joshua Swamidass , Richard E. Lenski, “A biochemist’s crusade to overturn evolution misrepresents theory and ignores evidence” at Science

Who are the reviewers? Readers may remember Nathan Lents from his book, Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes, which prompted the legitimate question, “Does Nathan Lents, author of a “bad design” book really teach biology? (A doctor looks at his claims about the human sinuses).” Pathologist and biomedical engineer Joshua Swamidass has long been associated with theistic evolution group Biologos, though maybe not so much now. Richard Lenski is a respected researcher and NAS member who runs multi-generation evolutionary experiments on bacteria.

If you know a bit of the history of the debate, two things stand out from the review. As author Michael Behe observes,

In a few days I will offer a detailed rebuttal. But the overwhelmingly important point to notice right up front is that the reviewers (Lenski plus Josh Swamidass over at Peaceful Science and John Jay College biologist Nathan Lents) have absolutely no response to the very central argument of the book. The argument that I summarized as an epigraph on the first page of the book so no one could miss it. The one that I included in the title of a 2010 Quarterly Review of Biology article upon which the book is based. The one for which I chose the most in-your-face moniker that I could think of (consistent with the professional literature) to goad a response: The First Rule of Adaptive Evolution: Break or blunt any gene whose loss would increase the number of offspring. The rule summarizes the fact that the overwhelming tendency of random mutation is to degrade genes, and that very often is helpful. Thus natural selection itself acts as a powerful de-volutionary force, increasing helpful broken and degraded genes in the population. Michael Behe, “Woo-hoo! In Science Review of Darwin Devolves, Lenski Has No Response to My Main Argument” at Evolution News and Science Today

Odd indeed. Claims around reproductive fitness (increasing the number of offspring) form the bulk of the news we hear around Darwinism. It’s supposed to explain how you vote, shop, and tip at restaurants, never mind why the peacock has a spectacular but useless tail. So the audience for the review (and the book) is presumably familiar with the concept. Do the reviewers, peers in the field, not have a response? They comment on just about everything else Behe has done.

Second, overall, the language of the review reminded some of us of something we’d heard before and it was easily traced: Lents and Swamidass had been struggling in public on how to do a hit on Behe’s book. And they came up with some of these ideas, served up to Science as leftovers from a blog that took root in the ruins of a previous blog apparently founded in response to someone getting dumped as a commenter here at Uncommon Descent. (Look, we agree that the soap opera is dull; our notes are just for the record. Watch the ball instead.)

If the only purpose for accepting this review was to convince Science readers that Darwinism, the central dogma of evolution, is not simply collapsing, I believe that the review will succeed. Many researchers want nothing more than to get their grant and go through the approved motions to present the approved research, maybe get the desired positions. If information is in an approved paper, it will look like fact to them. Yes, that’s a racket, but what else is there?

On the other hand, if you are in a position that you can afford to know more of the bigger picture of why Darwinism isn’t working anymore, get Darwin Devolves and examine carefully Behe’s central point – the very one the Science reviewers chose to omit discussing: The First Rule of Adaptive Evolution: Break or blunt any gene whose loss would increase the number of offspring. Is it correct?

In these times, are you better off knowing the problems or innocently citing approved sources of misinformation as your reason for making decisions? You decide.

As we said earlier this week, “Hello? Darwin’s world is collapsing around us, snowflakes. See Suzan Mazur’s new book Darwin Overthrown: Hello Mechanobiology and the Dissent from Darwinism list now topping 1000 career scientists. And these are unrelated events we heard about just this week, never mind all the others of the last two decades.”

See also: Mike Behe’s New Book, Darwin Devolves: “Absolutely Convincing” Or “Omits Contrary Examples”

From our files:

Protein families are still improbably astonishing – retraction of Matlock and Swamidass paper in order?

Biologist Wayne Rossiter on Joshua Swamidass’s claim that entropy = information

Inference Review did not set out to make a fool of cosmologist Adam Becker

Copyright © 2019 Uncommon Descent . This Feed is for personal non-commercial use only. If you are not reading this material in your news aggregator, the site you are looking at is guilty of copyright infringement UNLESS EXPLICIT PERMISSION OTHERWISE HAS BEEN GIVEN. Please contact legal@uncommondescent.com so we can take legal action immediately.
Plugin by Taragana