Michael J. Behe's Blog, page 218

Minimal synthetic cell turns out to be an argument against naturalist origin of life, says biomedical engineer

The synthetic cell created in 2016 required some fixes:

Five years ago, scientists created a single-celled synthetic organism that, with only 473 genes, was the simplest living cell ever known. However, this bacteria-like organism behaved strangely when growing and dividing, producing cells with wildly different shapes and sizes. Now, scientists have identified seven genes that can be added to tame the cells’ unruly nature, causing them to neatly divide into uniform orbs.

BeauHD, “Scientists Create Simple Synthetic Cell That Grows and Divides Normally” at Slashdot

The function of five of the genes was unknown (wouldn;t they have been classified as “junk DNA”?):

“[The creators of JCVI-syn3.0] had thrown out all the parts of the genome that they thought were not essential for growth,” says Elizabeth Strychalski at the US National Institute of Standards and Technology. But their definition of what was necessary for growth turned out to be what was needed to make beautiful colonies growing on an agar plate, she says, rather than what was needed to produce cells that divide in a uniform and lifelike way.

By reintroducing various genes into these synthetic bacterial cells and then monitoring how the additions affected cell growth under a microscope, Strychalski and her team were able to pinpoint seven additional genes required to make the cells divide uniformly.

Laya Liverpool, “Artificial life made in lab can grow and divide like natural bacteria” at New Scientist

Rob Stadler, co-author with Change Laura Tan of Stairway to Life: An Origin-Of-Life Reality Check, writes to say,

This family of articles about JCVI-syn3 is quite a powerful argument against abiogenesis.

Abiogenesis [random origin of life] advocates claim that life started with “protocells” because extant life is far too complex to have started by natural processes.

But, all of our efforts to simplify extant life to produce a “protocell” have shown us that extant life is about as simple as it can be.

JVCI-syn3 has 473 genes, carefully paired down from the 1 million base pair genome of M. mycoides, and basically lives on life support.

JVCI-syn3A, the subject of this article, has an additional 19 genes (492 total) to make it a bit more robust, although still quite dependent on a coddled environment.

So, all available evidence tells us that “protocells” can’t be much simpler than extant life, but we all know that extant life is far, far too complex to have arrived from natural processes.
This should be the end of abiogenesis and rational atheism. But, we all know that these beliefs are not subject to lessons taught by actual evidence.

The paper is closed access.

See also: A zoologist on that microbe that copies its DNA in a way “unknown to science.” Tim Standish: Simpler systems do not necessarily come first because simple can be a lot harder to come up with than complex. Yes, that seems counterintuitive, but the history of technology bears that out. In some ways you could say the same about art.

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Rob Sheldon: Biologists’ use of the term “half-life” shows just how tenuous many of their propositions really are

Recently, our physics color commentator Rob Sheldon took issue with the use of the term “half-life” to describe the survival of DNA in fossils. He says the term has a specific meaning with respect to radioactive decay that just does not apply to other events in nature.

In the biology paper at issue, with “half-life” in the name, the authors explain and use the concept in connection with radiocarbon dating:

Abstract: Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10–6 per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.

Allentoft Morten E., Collins Matthew, Harker David, Haile James, Oskam Charlotte L., Hale Marie L., Campos Paula F., Samaniego Jose A., Gilbert M. Thomas P., Willerslev Eske, Zhang Guojie, Scofield R. Paul, Holdaway Richard N. and Bunce Michael 2012 The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils Proc. R. Soc. B.2794724–4733 http://doi.org/10.1098/rspb.2012.1745

But Sheldon points out,

The paper does explain the environmental conditions of 13.1C, ph=5.0 and 158 moa bone assemblage, which is the data needed to make sense of the claim. They even pointed out that this halflife=521 years was 400X slower than the test-tube numbers bandied about in the literature (which would have been 1.3 years?).

But after saying all that, they said the data had a correlation coefficient of R2 = 0.39, which is the lowest value I have ever read in the literature used to support a correlation. Normally if R2<0.5, the paper is rejected by the editors as not showing a correlation.

That is to say, even after correcting for pH, temperature, species, type of bone, location, (burial to remove cosmic rays), and chromosomal variation—they still had a variable half-life of (my eyeballing their plot), somewhere between 100 – 2000 years. In the body of the paper they bandy about correction factors of 5 and 73 for things like temperature and pH. So indeed, 1.2 million year mammoth DNA is quite reasonable if we plug in -5C and ph<7.5. But then the use of “half-life” as a some sort of constant number is meaningless.

So I stand by my statement. Biologists should use this paper as a warning about the uselessness of a half-life number for DNA, especially for predicting DNA preservation or dating artifacts. You would be better served by casting lots.

Rob Sheldon is the author of Genesis: The Long Ascent and The Long Ascent, Volume II.

See also: Does DNA really have a “half life”? Physicist Rob Sheldon is sceptical. Sheldon: “As a physicist, I would like to point out that biologists are misusing the word “half-life”. DNA does NOT have a half-life of 521 years. Radioisotopes have a half-life, because the nucleus is unstable to natural decay through the weak force (for isotopes of interest).” He goes on to say that the weak force of the universe “is unaffected by temperature, pressure, time, or chemicals.” Not so for DNA.

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A zoologist on that microbe that copies its DNA in a way “unknown to science”

Timothy Standish offers us some thoughts on that microbe (a protist, Carpediemonas membranifera) that, without being a parasite, lacks most of the molecular equipment needed to kickstart DNA replication (and no one understands how it does that):

It occurs to me that if I was a Darwinist, I’d be all over this, saying things like, “Look, we can see that organisms survive perfectly well without all the stuff you ID types think is essential. This shows that organisms can evolve from much simpler forms.” It surprises me that I’ve not seen anything like that, but often enough complexity comes first followed by simplicity made possible by further advances.

Turbine engines are a great example. Internal combustion reciprocating engines got progressively more complex before the quantum leap to jet engines, but this didn’t really happen in one huge jump, it was the combination of steam turbine engines, internal combustion and a whole lot of fancy metallurgy that everyone forgets that came together in the mind of Frank Whittle and some others. But what a huge leap going from basically thousands of moving parts to a single moving part that produces more power for less weight.

Note that while some may see this as a kind of evolutionary process, the huge leap took a brilliant mind. I suspect the same principle is true in living things. Simpler systems do not necessarily come first because simple can be a lot harder to come up with than complex. Yes, that seems counterintuitive, but the history of technology bears that out. In some ways you could say the same about art.

Before getting too carried away down this track, one should also keep in mind that organisms as they exist are amazingly robust. Humans can survive after the removal of quite a few important organs ranging from the thymus gland to the spleen. This isn’t an indicator that these organs lack function, it is an indicator of just how robustly organisms are designed.

The mechanism that is being used to begin DNA replication in this microbe may not be what we have come to expect from other living things that have been studied, but DNA must replicate, so an initiation mechanism must exist. If it isn’t the mechanism used by other organisms, it may call into question the logic that says shared mechanisms are evidence of shared ancestry. Or maybe there is some backup mechanism we are unaware of and this is an example of the devolution that Mike Behe has pointed out as a major mechanism of adaptation.

Whatever the explanation, the most important quote in the article came from Dayana Salas-Leiva, “I was astonished.”

So was I!

See also: At New Scientist: “single-celled organism that lacks most of the molecular equipment needed to kick-start DNA replication” It’s a protist? “Protists are a group of loosely connected, mostly unicellular eukaryotic organisms that are not plants, animals or fungi. There is no single feature such as evolutionary history or morphology common to all these organisms and they are unofficially placed under a separate kingdom called Protista.” In short, just the sort of life form that might be doing something really different. Because nature is full of intelligence, there are probably many alternative programs out there. It all didn’t just somehow happen randomly once.

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From Philip Cunningham: The human eye, like the human brain, is a wonder

(Which allegedly required no actual design) With references, courtesy Philip Cunningham:

The human eye consists of over two million working parts making it second only to the brain in complexity (1).

The retina covers less than a square inch, and contains 137 million light-sensitive receptor cells. The retina possesses 7 million cones, which provide color information and sharpness of images, and 120 million rods which are extremely sensitive detectors of white light (2).

There are between seven to ten-million shades of color the human eye can detect (3).

The rod can detect a single photon. Any man-made detector would need to be cooled and isolated from noise to behave the same way (4).

On average, about a quarter of a billion photons enter our eyes each second (5).

For visible light, the energy carried by a single photon would be around a tiny 4 x 10-19 Joules; this energy is just sufficient to excite a single molecule in a photoreceptor cell of an eye (6).

The eye is so sensitive that it can, under normal circumstances, detect a candle 1.6 miles away (7),

But if you’re sitting on a mountain top on a clear, moonless night you can see a match struck 50 miles away (8).

It only takes a few trillionths of a second, (picoseconds), for the retina to absorb a photon in the visible range of the spectrum (9).

The inverted retina, far from being badly designed, is a design feature, not a design constraint. Müller cells in the ‘backwards’ retina span the thickness of the retina and act as living fiber optic cables to shepherd photons through to separate receivers, much like coins through a change sorting machine (10).

The eye is infinitely more complex than any man-made camera (11).

The eye can handle between 500,000 and 1.5 million messages simultaneously, and gathers 80% of all the knowledge absorbed by the brain (12).

The brain receives millions of simultaneous reports from the eyes. When its designated wavelength of light is present, each rod or cone triggers an electrical response to the brain, which then absorbs a composite set of yes-or-no messages from all the rods and cones (13).

There is a biological computer in the retina which compresses, and enhances the edges, of the information from all those millions of light sensitive cells before sending it to the visual cortex where the complex stream of information is then decompressed (14).

This data compression process has been referred to as “the best compression algorithm around,” (15 & 15a).

While today’s digital hardware is extremely impressive, it is clear that the human retina’s real-time performance goes unchallenged. To actually simulate 10 milliseconds of the complete processing of even a single nerve cell from the retina would require the solution of about 500 simultaneous nonlinear differential equations 100 times and would take at least several minutes of processing time on a Cray supercomputer. Keeping in mind that there are 10 million or more such cells interacting with each other in complex ways, it would take a minimum of 100 years of Cray time to simulate what takes place in your eye many times every second (16). (of note: the preceding comparison was made in 1985 when Cray supercomputers ruled the supercomputing world).

In an average day, the eye moves about 100,000 times, and our mind seems to prepare for our eye movements before they occur (17).

In terms of strength and endurance, eyes muscles are simply amazing. You’d have to walk 50 miles to give your legs the same workout as the muscles in one of your eyes get in a day (18).

The brain exploits a feedback system which produces phenomenally precise eye movements (19).

The human is the only species known to shed tears when they are sad (20).

Tears are not just saline. Tears have a similar structure to saliva and contain enzymes, lipids, metabolites and electrolytes (21).

And, tears contain a potent microbe-killer (lysozyme) which guards the eyes against bacterial infection (22).

The average eye blinks one to two times each minute for infants and ten times faster for adults.

This blinking adds up to nearly 500 million blinks over an average lifetime (23).

References:

– 20 Facts About the Amazing Eye – 2014An eye is composed of more than 2 million working parts…. 20: Eyes are the second most complex organ after the brain. – Susan DeRemer, CFRE – Discovery Eye FoundationVision and Light-Induced Molecular Changes

Excerpt : “The retina is lined with many millions of photoreceptor cells that consist of two types: 7 million cones provide color information and sharpness of images, and 120 million rods (Figure 3) are extremely sensitive detectors of white light to provide night vision.” – Rachel Casiday and Regina Frey Department of Chemistry, Washington University

– Number of Colors Distinguishable by the Human Eye – 2006 “Experts estimate that we can distinguish perhaps as many as 10 million colors.” – Wyszecki, Gunter. Color. Chicago: World Book Inc, 2006: 824…. “Our difference threshold for colors is so low that we can discriminate some 7 million different color variations (Geldard, 1972).” – Myers, David G. Psychology. Michigan: Worth Publishers, 1995: 165. From Number of Colors Distinguishable by the Human EyeStudy suggests humans can detect even the smallest units of light – July 21, 2016

Excerpt: Research,, has shown that humans can detect the presence of a single photon, the smallest measurable unit of light. Previous studies had established that human subjects acclimated to the dark were capable only of reporting flashes of five to seven photons…

it is remarkable: a photon, the smallest physical entity with quantum properties of which light consists, is interacting with a biological system consisting of billions of cells, all in a warm and wet environment,” says Vaziri. “The response that the photon generates survives all the way to the level of our awareness despite the ubiquitous background noise. Any man-made detector would need to be cooled and isolated from noise to behave the same way.”…

The gathered data from more than 30,000 trials demonstrated that humans can indeed detect a single photon incident on their eye with a probability significantly above chance.

“What we want to know next is how does a biological system achieve such sensitivity? How does it achieve this in the presence of noise?

How many photons get into your eyes? – 2016

Excerpt : About half a billion photons reach the cornea of the eye every second, of which about half are absorbed by the ocular medium. The radiant flux that reaches the retina is therefore approx. 2*10^8 photons/s.

Photon Excerpt For visible light the energy carried by a single photon is around a tiny 4×10–19 joules; this energy is just sufficient to excite a single molecule in a photoreceptor cell of an eye, thus contributing to vision.[4]How Far Can We See and Why? Excerpt: “Detecting a candle flame: Researchers believe that without obstructions, a person with healthy but average vision could see a candle flame from as far as 1.6 miles.”An Eye for Exercise Your eye is a very active organ – December 28, 2001

(HealthDayNews) — The cells in the retina are so sensitive that if you’re sitting on a mountain top on a clear, moonless night you can see a match struck 50 miles away.

Vision and Light-Induced Molecular Changes

Excerpt: “Thus, when 11-cis-retinal absorbs a photon in the visible range of the spectrum, free rotation about the bond between carbon atom 11 and carbon atom 12 can occur and the all-trans-retinal can form. This isomerization occurs in a few picoseconds (10-12 s) or less.” – Rachel Casiday and Regina Frey, Department of Chemistry, Washington University

Fiber optic light pipes in the retina do much more than simple image transfer – Jul 21, 2014

Excerpt: Having the photoreceptors at the back of the retina is not a design constraint, it is a design feature. The idea that the vertebrate eye, like a traditional front-illuminated camera, might have been improved somehow if it had only been able to orient its wiring behind the photoreceptor layer, like a cephalopod, is folly. Indeed in simply engineered systems, like CMOS or CCD image sensors, a back-illuminated design manufactured by flipping the silicon wafer and thinning it so that light hits the photocathode without having to navigate the wiring layer can improve photon capture across a wide wavelength band. But real eyes are much more crafty than that.

A case in point are the Müller glia cells that span the thickness of the retina. These high refractive index cells spread an absorptive canopy across the retinal surface and then shepherd photons through a low-scattering cytoplasm to separate receivers, much like coins through a change sorting machine. A new paper in Nature Communications describes how these wavelength-dependent wave-guides can shuttle green-red light to cones while passing the blue-purples to adjacent rods. The idea that these Müller cells act as living fiber optic cables has been floated previously. It has even been convincingly demonstrated using a dual beam laser trap….

…In the retina, and indeed the larger light organ that is the eye, there is much more going on than just photons striking rhodopsin photopigments. As far as absorbers, there are all kinds of things going on in there—various carontenoids, lipofuscins and lipochromes, even cytochrome oxidases in mitochondria that get involved at the longer wavelegnths….

,,In considering not just the classical photoreceptors but the entire retina itself as a light-harvesting engine… that can completely refigure (its) fine structure within a few minutes to handle changing light levels, every synapse appears as an essential machine that percolates information as if at the Brownian scale, or even below….

The Wonder of Sight – April 15, 2020

Excerpt: The eye processes approximately 80% of the information received from the outside world. In fact, the eyes can handle 500,000 messages simultaneously. It happens all the time, and you don’t even have to think about it. Your eyes just do it! The eye is infinitely more complex than any man-made camera or telescope.

Walk By Faith – Now See Here, Touch & Smell to Discern Good & Evil – July 6, 2018

Excerpt: “I Am Joe’s Eye” (from the Reader’s Digest series) says “For concentrated complexities, no other organ in Joe’s body can equal me … I have tens of millions of electrical connections and can handle 1.5 million simultaneous messages. I gather 80 percent of all the knowledge Joe absorbs.”

Fearfully and Wonderfully Made – Philip Yancey, Paul Brand

Excerpt: The brain receives millions of simultaneous reports from the eyes. When its designated wavelength of light is present, each rod or cone triggers an electrical response to the brain, which then absorbs a composite set of yes-or-no messages from all the rods and cones.

Retina – Spatial encoding

Excerpt: When the retina sends neural impulses representing an image to the brain, it spatially encodes (compresses) those impulses to fit the limited capacity of the optic nerve. Compression is necessary because there are 100 times more photoreceptor cells than ganglion cells. This is done by “decorrelation”, which is carried out by the “centre–surround structures”, which are implemented by the bipolar and ganglion cells.

There are two types of centre–surround structures in the retina – on-centres and off-centres. On-centres have a positively weighted centre and a negatively weighted surround. Off-centres are just the opposite. Positive weighting is more commonly known as excitatory, and negative weighting as inhibitory.

These centre–surround structures are not physical apparent, in the sense that one cannot see them by staining samples of tissue and examining the retina’s anatomy. The centre–surround structures are logical (i.e., mathematically abstract) in the sense that they depend on the connection strengths between bipolar and ganglion cells. It is believed that the connection strength between cells is caused by the number and types of ion channels embedded in the synapses between the bipolar and ganglion cells.

The centre–surround structures are mathematically equivalent to the edge detection algorithms used by computer programmers to extract or enhance the edges in a digital photograph. Thus, the retina performs operations on the image-representing impulses to enhance the edges of objects within its visual field.

JPEG for the mind: How the brain compresses visual information – February 11, 2011

Excerpt “Computers can beat us at math and chess,” said Connor, “but they can’t match our ability to distinguish, recognize, understand, remember, and manipulate the objects that make up our world.” This core human ability depends in part on condensing visual information to a tractable level. For now, at least, the brain format seems to be the best compression algorithm around.

15a. Optimised Hardware Compression, The Eyes Have It. – 2011

Can Evolution Produce an Eye? Not a Chance! by Dr. David Menton on August 19, 2017

Excerpt: In an article in Byte magazine (April 1985), John Stevens compares the signal processing ability of the cells in the retina with that of the most sophisticated computer designed by man, the Cray supercomputer:

“While today’s digital hardware is extremely impressive, it is clear that the human retina’s real time performance goes unchallenged. Actually, to simulate 10 milliseconds (one hundredth of a second) of the complete processing of even a single nerve cell from the retina would require the solution of about 500 simultaneous nonlinear differential equations 100 times and would take at least several minutes of processing time on a Cray supercomputer. Keeping in mind that there are 10 million or more such cells interacting with each other in complex ways, it would take a minimum of 100 years of Cray time to simulate what takes place in your eye many times every second.”

Looking At What The Eyes See – February 25, 2011

Excerpt: We move our eyes three times a second, over 100,000 times each day. Why isn’t life blurrier? Reporting in Nature Neuroscience, psychologist Martin Rolfs and colleagues found that our mind seems to prepare for our eye movements before they occur, helping us keep track of objects in the visual field.

An Eye for Exercise Your eye is a very active organ – December 28, 2001 (HealthDayNews) — Did you know that you’d have to walk 50 miles to give your legs the same workout as the muscles in one of your eyes get in a day?How do our eyes move in perfect synchrony? By Benjamin Plackett – June 21, 2020

Excerpt: “You have a spare one in case you have an accident, and the second reason is depth perception, which we evolved to help us hunt,” said Dr. David Guyton, professor of ophthalmology at The Johns Hopkins University. But having two eyes would lead to double vision if they didn’t move together in perfect synchrony. So how does the body ensure our eyes always work together?

To prevent double vision, the brain exploits a feedback system, which it uses to finely tune the lengths of the muscles controlling the eyes. This produces phenomenally precise eye movements, Guyton said.

Each eye has six muscles regulating its movement in different directions, and each one of those muscles must be triggered simultaneously in both eyes for them to move in unison, according to a 2005 review in the Canadian Medical Association Journal. “It’s actually quite amazing when you think about it,” Guyton told Live Science. “The brain has a neurological system that is fantastically organized because the brain learns over time how much stimulation to send to each of the 12 muscles for every desired direction of gaze.”

Why Only Humans Shed Emotional Tears – 2018

Abstract Producing emotional tears is a universal and uniquely human behavior…

Facts About Tears – Dec. 21, 2018 Excerpt Tears Have Layers

Tears are not just saline. They have a similar structure to saliva and contain enzymes, lipids, metabolites and electrolytes. Each tear has three layers:

An inner mucus layer that keeps the whole tear fastened to the eye.

A watery middle layer (the thickest layer) to keep the eye hydrated, repel bacteria and protect the cornea.

An outer oily layer to keep the surface of the tear smooth for the eye to see through, and to prevent the other layers from evaporating.

Lacrimal glands above each eye produce your tears…

How Tears Go ‘Pac-Man’ To Beat Bacteria – January 20, 2012

Excerpt: In 1922, a few years before he won the Nobel Prize for his discovery of penicillin, bacteriologist Alexander Fleming discovered in human tears a germ-fighting enzyme which he named lysozyme. He collected and crystallized lysozyme from his own tears, then wowed contemporaries at Britain’s Royal Society by demonstrating its miraculous power to dissolve bacteria before their very eyes.

“That’s a seriously bodacious experiment”…

Eyelids—Intermittent Wipers – Dr. Don DeYoung – October 20, 2013

Excerpt: The blinking of our eyes is automatic and essential. Its saline washer fluid moistens and protects the outer cornea of the eye while removing dust. Other protective features include our eyebrow “umbrellas” and recessed eyeball sockets.

The average eye blinks one to two times each minute for infants and ten times faster for adults. This blinking adds up to nearly 500 million blinks over an average lifetime. The actual mechanism, however, is not well understood. It may involve a “blinking center” in the brain.

Today billions of windshield wipers duplicate the eye’s intermittent blinking. Yet none last as long or work as efficiently as our God-given eyelids.

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Does DNA really have a “half life”? Physicist Rob Sheldon is skeptical

It’s exciting how much DNA we are finding from how far back:

In 2013, a 700,000-year-old horse fossil frozen in permafrost became the oldest DNA ever sequenced. Before that, the oldest sequenced genome was from the remains of an 80,000-year-old Denisovan.

Then, earlier this year, scientists announced they’d sequenced DNA from a 1.2-million-year-old mammoth tooth – which currently holds the record for the oldest recovered and sequenced DNA.

Jacinta Bowler, “The Trouble With Dinosaur Bones” at ScienceAlert

We are told not to expect too many more DNA windows into time:

DNA has a half-life of 521 years, meaning that after 521 years, half of the bonds in its molecular backbone break. After 1,042 years, half of that remainder would be gone, too.

Jacinta Bowler, “The Trouble With Dinosaur Bones” at ScienceAlert

After a million years, they say, forget it. But our physics color commentator Rob Sheldon paused at the term “half life” and commented,

As a physicist, I would like to point out that biologists are misusing the word “half-life”. DNA does NOT have a half-life of 521 years. Radioisotopes have a half-life, because the nucleus is unstable to natural decay through the weak force (for isotopes of interest).

The weak force is unaffected by temperature, pressure, time, or chemicals, so it is accurate to say that “after X time, 1/2 the material will have decayed, making X=half-life.” Now of course, if the nucleus itself is bombarded with electrons or neutrons, the decay can be accelerated, but at this point we are entering the realm of atom smashers, and one shouldn’t call this “natural decay” any longer.

This is definitely NOT true of DNA. DNA can be destroyed by heat. Otherwise why do we boil baby bottles or put hospital sheets in an autoclave? And heat is a statistical process, (hot molecules are not all moving at the same speed), so what takes 1 minute at 100C might take 20 minutes at 80C or 1000 minutes at 60C.

Accordingly DNA has a half-life depending on temperature. It also depends on pH, on free-radicals, on UV light and presence of water. In other words, it depends on everything in the environment. This completely destroys what physicists mean by “half-life”, and makes hash of the word.

Mammoth DNA from the frozen tundra of Siberia has been resurrected after 1.2 Million years. Denisovan DNA over 60,000 years ago was recovered from a cool cave in Eurasia. In the tropics, no DNA is recoverable after a mere 1000 years or so.

So please, don’t use the word “half-life” with regard to biological molecules unless you are very carefully specifying the environmental conditions as well.

But the very term “half-life” makes it all sound so much more scientific. Who could resist?

Genesis: The Long Ascent and The Long Ascent, Volume II

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At New Scientist: “single-celled organism that lacks most of the molecular equipment needed to kick-start DNA replication”

And it is a free-living protist, not a parasite:

“I was astonished,” says Dayana Salas-Leiva at Dalhousie University in Halifax, Canada. The microbe, Carpediemonas membranifera, must have a mechanism for copying its DNA that is unknown to science.

Michael Marshall, “Microbe somehow survives without key proteins for replicating its DNA” at New Scientist

It’s a protist? “Protists are a group of loosely connected, mostly unicellular eukaryotic organisms that are not plants, animals or fungi. There is no single feature such as evolutionary history or morphology common to all these organisms and they are unofficially placed under a separate kingdom called Protista.” In short, just the sort of life form that might be doing something really different.

Because nature is full of intelligence, there are probably many alternative programs out there. It all didn’t just somehow happen randomly once.

The paper is open access.

and

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Discovery of useful “junk DNA” “has outstripped the discovery of protein-coding genes by a factor of five…

… and shows no signs of slowing.”

Yes, more from that commentary at Nature on the 20th anniversary of the Human Genome Project:

[I]t is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression

With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.

Alexander J. Gates, Deisy Morselli Gysi, Manolis Kellis & Albert-László Barabási, “A wealth of discovery built on the Human Genome Project — by the numbers” at Nature

To see how significant a change this is, consider a blast from the past:

[…The late] Dr. Susumu Ohno [1928 – 2000], writing in the Brookhaven Symposium on Biology in 1972 in the article “So Much ‘Junk DNA’ in our Genome” is credited with originating the term. As anyone can read below, he tried to (mistakenly) construct a scientific argument that the human genome can not sustain more than a very limited number of “genes” and argued for “the importance of doing nothing” for the rest. Though his misnomer was doubted from the outset (see the first question after his presentation calling his arguments “suspect”), the misnomer lived for a generation, in spite of ample evidence that it was false. The reason is, that “facts don’t kill theories, only theories that exceed obsolete dogma can kill old theories. “The Principle of Recursive Genome Function”, heretofore the only concise interpretation how directly amino-acid-coding regions (formerly called “genes”) work together with intronic and intergenic sequences, carrying much auxiliary information that is perused in fractal recursive iteration, only appeared in 2008. There may be other mathematical algorithmic theories for genome function explaining why and how “Junk DNA” is anything but “Junk” – this author will be pleased to list them – Pellionisz_at_JunkDNA.com

It’s a good thing for the Darwinians that they have always been able to afford top spin doctors via the tax dollars of people who are sceptical. It’ll be interesting to see what they come up with to front this one.

See also: Did beliefs about junk DNA hinder the Human Genome Project? But wasn’t a vast pile of junk DNA supposed to be one of the Great Proofs of Darwinism in the DNA? Funny, no one suggests that the constant diminution of the pile is evidence against the theory that its presence was supposed to be evidence for. Now why do you think that might be?

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Gregory Chaitin on why human creativity is not computable

There is a paradox involved with computers and human creativity, something like Gödel’s Incompleteness Theorems or the Smallest Uninteresting Number:

Gregory Chaitin: So there is a paradoxical aspect to creativity. You could have a mathematical theory of creativity that enables you to prove theorems about creativity, but is not implemented in software. That doesn’t give you an algorithm for being creative. Because if it’s an algorithm, it’s not creative, right? But you might be able to prove theorems about creativity.

Like I can prove theorems that most numbers are random or unstructured. I can’t produce individual examples that I’m certain are. So it might be that you could prove theorems about creativity. But the theory wouldn’t give you a formula, a recipe, for being creative. Because once it does that, then it’s not creative. You see? There’s this paradox.

Robert J. Marks: Yeah. And also, those theorems that you’re talking about are kind of meta. You’re using creativity to write theorems about creativity. And one of the important things is to define creativity.

News, “Why human creativity is not computable” at Mind Matters News

Summary: Creativity is what we don’t know. Once it is reduced to a formula a computer can use, it is not creative any more, by definition.

The paradox of the smallest uninteresting number. Robert J. Marks sometimes uses the paradox of the smallest “uninteresting” number to illustrate proof by contradiction — that is, by creating paradoxes. Gregory Chaitin: You can sort of go step by step from the paradox of the smallest “uninteresting” number to a proof very similar to mine.

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Math paradoxes show us that the world we live in is not and cannot be purely naturalist

Robert J. Marks sometimes uses the paradox of the smallest “uninteresting” number to illustrate proof by contradiction — that is, by creating paradoxes:

By way of illustrating the concept of proof by contradiction, Dr. Marks then offered his proof by contradiction that “all positive integers — numbers like 6 or 129, or 10 100 — are interesting.” If [some positive integers] are not interesting, there is a smallest, non-interesting number. But hey, that’s interesting! That’s the proof by contradiction.

Gregory Chaitin: An uninteresting number would be one whose numerical value is irreducible. And that’s exactly the proof… That’s a very good explanation, because then the next step from that to my incompleteness theorem is to say, “Well, what does ‘interesting’ mean?”

And one good definition of “interesting” is: An interesting number is one that stands out because there is a more concise definition of it or, more precisely, a program that is substantially smaller than its numerical value that calculates it… that’s some way it stands out from the run-of-the-mill numbers. And the run-of-the-mill numbers are ones whose numerical value is an incompressible or irreducible string of bits. So you can sort of go step by step from that paradox about the smallest uninteresting number, which is, ipso facto, interesting, to a proof very similar to mine.

News, “The paradox of the smallest uninteresting number” at Mind Matters News

Don’t miss the stories and links from the previous podcasts:

From Podcast 4:

Why the unknowable number exists but is uncomputable. Sensing that a computer program is “elegant” requires discernment. Proving mathematically that it is elegant is, Chaitin shows, impossible. Gregory Chaitin walks readers through his proof of unknowability, which is based on the Law of Non-Contradiction.

Getting to know the unknowable number (more or less). Only an infinite mind could calculate each bit. Gregory Chaitin’s unknowable number, the “halting probability omega,” shows why, in general, we can’t prove that programs are “elegant.”

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Did beliefs about junk DNA hinder the Human Genome Project?

Consider this thought from a commentary at Nature:

A great debate pre-dated the start of the HGP: was it worth mapping the vast non-coding regions of genome that were called junk DNA, or the dark matter of the genome? Thanks in large part to the HGP, it is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression.

With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set (1900 to 2017; see SI, Fig. S3a). For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.

Alexander J. Gates, Deisy Morselli Gysi, Manolis Kellis & Albert-László Barabási, “A wealth of discovery built on the Human Genome Project — by the numbers” at Nature

But wasn’t a vast pile of junk DNA supposed to be one of the Great Proofs of Darwinism in the DNA? Funny, no one suggests that the constant diminution of the pile is evidence against the theory that its presence was supposed to be evidence for. Now why do you think that might be?

See also: Junk DNA regulates regeneration of tissues and organs.

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