Man vs. Molecule!

“Faith is the great cop-out, the great excuse to evade the need to think and evaluate evidence. Faith is the belief in spite of, even perhaps because of, the lack of evidence.”

..Richard Dawkins

In reality, faith is an element of intelligent thought: faith in the cohesiveness and integrity of the mechanism one is investigating, faith in the world itself being a cohesive whole, faith in humanity, or if one has cancer, a healthy faith in the ability to understand the illness, and get better.  It is not faith, but despair which is the great cop-out, the great excuse to evade the need to think.

Evolution and Darwinism are not one and the same.  While genomic evolution is beyond doubt, and the mechanisms even observable in the laboratory, the first practical difficulty with Darwinism’s theory – random, solitary changes to nucleotides being the source of all biological enginering – is that it is nonsense. The second difficulty, almost as great, is that all experimental evidence flatly contradicts it.

The impossibilities saturate every evolutionary stage:

  • a random, simple beginning which nevertheless requires all the complex machinery for survival, and duplication
  • machinery whose sole function is to root out and eliminate the tiniest error, which has itself been composed only of errors
  • a wasteland of failure the size of a planet with barely a pinprick of successful permutations
  • the final products: purposeful, rational beings so convinced that life’s machinery is a product of laws that they devote their life to unravelling them

Why would anyone believe a system based on aimless chaos is at the same time law-bound right to the core, and liable to the analysis of science?

  • fear that interest in religious metaphors (ancient assumptions about higher intelligences) would immmediately wipe out motorways and the internet, and return us to the caves
  • the “argument from personal incredulity” – if we can’t imagine a mind titanic enough to conceive of living matter, there can’t possibly be one
  • the average mind does not continually re-think its worldview, which would be a daily effort and source of instability.  An authoritative, eloquent personality is trusted to have done the work.  The crowd simply dons their confidence, catchphrases, and even personality, as if their own
  • if “the wider community” rejects an idea, the member feels it must be a reasonable position. This is given momentum by their exclusion of him if he demurs – a frightening thought

Darwinism’s intellectual vacuum is covered up somewhat with the partly credible veil of natural selection.  This ornately embroidered cloth looks good from a distance, but the slightest touch causes it to be sucked into the void, because as  Dutch mutation theorist Hugo de Vries said, it may account for the survival of a species, but never its arrival.

In this jovial essay I try to show the combined engineering of man has, so far, been massively outclassed by that of the humble cell, in an evironment so much more difficult that one scientist likened progress in it to “swimming in molasses”.

An equation dictating the creative success of a (null creative power) x (thousand mutations) x (million procreations) x (billion generations) must produce the value zero, even if the experiment continued until the end of time.  Nevertheless, I hope you enjoy a scenic walk through these engineering triumphs of man and molecule.

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Father Christmas

kinesinWe all know Santa is a metaphor for selfless generosity.  Santa is a healthy concept for young minds to express gratitude, and emulate in the giving of presents (generating valuable oxytocin in the process) – and especially useful today since there seems no comparable human role model anywhere on the planet.

The concept of Father Christmas also stretches the imagination of young children; they consider their eventual discovery of his mythical status to be something of an achievement, vindication of their grown-up status.  And as Rebecca Watson points out, Dr Marjorie Taylor in Imaginary Companions and the Children Who Create Them, concludes:

pre-schoolers with imaginary friends are more creative, more social and more empathic.

But in character and dedication I’m afraid Santa comes a very distant second to the tireless kinesin motor deliverymen within the cell.

The kinesin illustrated above is from a Harvard animation and shows in correct proportion the transport of a sack of proteins from one place in the cell to another on one of the hundreds of thousands of highways which mysteriously build and unravel within every cell.  Kinesin actually walks, step over step, travelling exclusively outwards from the centre of the cell, in strides of 8 nanometres.  It can cope with obstacles in its path while holding onto its bag of goodies.

It covers 1 millimetre in 125,000 steps, making at most a few hundred steps in each journey, at a rate of 100 steps/second.  The 14 variant groups of these motor proteins have been the subject of ingenious research, some of which precisely measured their force in PicoNewtons while striding over nanometre bridges.  The graph is a straight line, meaning they’re as strong at the end of the journey as the beginning: given a surrounding supply of ATP they are literally tireless.

Kinesin’s fuel efficiency is nearly 50% – much more than a gasoline engine, and scaled up, exerts an incredible amount of torque.  It requires no supernatural intervention: in vitro it behaves exactly as in the cell, given ATP, simply due to the arrangement of the amino acid components.  Its step is precisely calibrated to the microtubule segments; the two components are part of one system.

Therefore the distance walked by one of these little Santas in a day is 69 million nanometres, or 6.9 centimetres – small wonder you need your own body weight in ATP each day. Scale him up to our size so his stride is 80 cm rather than 8 Nm with a factor of 100m and he could be covering 4,200 miles in a day.

With perhaps 100,000 at work in a single cell, and with 100 trillion cells, that’s a total distance travelled per day of just under 7 metres per cell, 691 billion km all told.  Even if they only worked half the elapsed time, and then, only for one night – that’s easily enough to visit every house on the planet.

As for the elves, hammering away – clearly a metaphor for the ribosomes!  And Rudolph..  well, perhaps his nose is a phosphate molecule.

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Interplanetary Landers

lunar module and bacteriophage

When NASA went to the moon, they needed a craft landable at almost any angle on an unpredictable, undulating surface.  When Neil Armstrong piloted the capsule in search of a suitable site, confounded by the presence of large boulders and with only a tiny amount of remaining fuel, he propelled the capsule sideways at full tilt to clear the hurdles and land in a safe place – the Sea of Tranquillity.  In the Moscow, his success was closely watched by the CCCP Air Force brass, who spontaneously broke into applause.  They understood the nature of the challenge.

But the design was remarkably similar to the bacteriophage, an impressive piece of nanotech which lands on a host bacteria cell, bringing its tail into contact with the surface and injecting a tightly wound genome through the cell wall.  This is seized by ribosomes within the cell, and more bacteriphages manufactured, which self assemble, as the parts are machined in a certain order.  The DNA is repackaged into the head and fleets of bacteriophages have now infected the cell, and will search for greener pastures.

The study shows that DNA packaging motor is comprised of three primary parts: an elongated prohead that serves as the virus shell, a doughnut-shaped connector that is positioned at the entrance to the virus shell and feeds DNA into the shell, and a novel ribonucleic acid (RNA)-enzyme complex that converts chemical energy to mechanical energy needed for packaging.

The scientists analyzed the structure of the connector – the core of the phi29 DNA packaging motor – to a resolution of 3.2 angstroms, or 3.2 hundred-millionths of a centimeter.

Their findings show that the connector is made up of 12 protein subunits that may serve as “cylinders” in the motor system to pull long chains of DNA through the center of the doughnut-shaped system.

Five identical enzymes, called ATPases, are positioned around the connector, just outside the opening in the virus shell. The enzymes break down the cell’s chemical fuel, called ATP, to produce the energy needed to power the motor.

The researchers postulate that successive chemical reactions produced by the ATP cause the phi29 connector to oscillate and rotate, pulling the DNA into the shell two base pairs at a time.

Sources: Michael Rossmann, mgr@indiana.bio.purdue.edu

Dwight Anderson, dlander@tc.umn.edu

Writer: Susan Gaidos,  sgaidos@purdue.edu

Other source: Timothy Baker, tsb@bragg.bio.purdue.edu

http://www.purdue.edu/uns/mov/rossmann.motormovie.mov

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CNC Machining and One Ruthless Editor

L-R: Computer Numerical Control machine, Precision Engineering; J Jonah Jameson: Marvel Comics; Ribosome: Centre for Molecular Biology, UCal, Santa Cruz.  Parker, these photos are so good I can almost stand living in the same city as that menace, Spiderman. Get me some more! Whaddya waiting for, Parker?  Christmas?!

One machine common to all life on Earth is the ribosome.  Its strongly conserved nature, and the common sense observation that it makes everything else, indicates its central position in evolution.  The ribosome is not a single tool but a workshop split into two major parts, all created (using E. coli as an example) from around 7,400 amino acids, and around 250,000 atoms, all primed to use the strongest possible codon-amino acid mapping out of a practically endless range of possibilities.

Ribosomes can be so numerous as to make up 25% of the cell mass of E. coli. A striking feature of the ribosome is that, even given the large assorted collection of subunits, it self-assembles in vitro!

The core of the ribosome is RNA, supporting the idea that early forms of life relied on RNA rather than DNA.  But if such a workshop is necessary to create proteins, whether from templates of RNA or DNA – from where could the ribosome come from?  More vexing still for Darwinism is how editorial precision could arise in a system in which errors themselves were the key to prolific reproductive success at the start.  Why change a winning hand?

New discoveries are being made about the ribosome all the time.  Relevant to Darwinism, in 2009 Nature published some new discoveries by Johns Hopkins researchers concerning the remarkable actions of the ribosome’s ruthless quality control editor; if you think I tend to anthropomorphise molecules, note how the researchers detail –

..a new “proofreading step” during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a “delete” button.

It turns out.. ..that the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products which, as workhorses of the cell, carry out the very business of life.

“What we now know is that in the event of miscoding, the ribosome cuts the bond and aborts the protein-in-progress, end of story,” says Rachel Green, a Howard Hughes Medical Institute investigator and professor of molecular biology and genetics in the Johns Hopkins University School of Medicine. “There’s no second chance.”

“We thought that once the mistake was made, it would have just gone on to make the next bond and the next,” Green says. “But instead, we noticed that one mistake on the ribosomal assembly line begets another, and it’s this compounding of errors that leads to the partially finished protein being tossed into the cellular trash.”

To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction Green says is “shocking” and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.

http://phys.org/news150559493.html#jCp

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Electric Motors

flagellar motor oldest motor on earth

(L-R: electric motor patent schematic, electric fan motor (top view), SEM photos of flagellar motor

The earliest forms of life, dating back perhaps three and a half billion years, are assumed to be bacteria, and as far as we observe, every cell comes from a cell. Under episodes of cell stress or genome shock, as Shapiro points out in Evolution, a cell “activates the molecular systems that restructure genomes” (ref. Jorgensen).  This intense scurry for novelty in response to an external threat, and the coding of solutions into DNA which is passed sideways to their peers, is an observed method of evolutionary progress, and as antibiotic researchers will tell you, it is very effective indeed.

These bacteria are some of the most complicated and smartest critters on the planet – the proof being their survival over eons and their central role even in the biology of human beings: you might not want to live with them, but you can’t live without ’em.

A method of their locomotion so strongly conserved that it still exists today is the flagellar motor.  This cunning device rotates between 20,000 and 100,000 RPM, five times the speed of an F1 engine, and due to the high surrounding pressure at molecular levels (a severe difficulty in nanotech engineering) can stop immediately.  When you assemble these motors, they work automatically in response to signals from within the bacteria – there is no need to invoke the supernatural any more than there is to keep track of your electric fan.

The combination of molecules is so precise, and once correctly assembled, they are so sturdy and incapable of misperforming that they only require the context of the cell with its switches, endless supplies of recyclable fuel, and regulatory systems, to perform their specialised task.

Proton or sodium driven, they are equipped with rotor, clutch, bushings, washers, gearing, and even a tiny printed maintenance schematic:

Osaka Graduate School of Frontier Sciences  (bacteria don’t really have a printed manual. Who could read it anyway, below the wavelength of visible light?)

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Multiple Electric Motors

One motor is fine, thanks, but how about seven, all hooked up in parallel? The MO-1 bacteria has a sheathed stack of seven flagella, interspersed with counter-rotating elements which reduce friction.  This system was analysed by Osaka University in 2012 (see below).  With this multiple motor, it swims at a rate of 300 micron/sec, slightly more than one metre/hour. A grain of talcum powder is about 10 micron in diameter.

The seven filaments are enveloped with 24 fibrils in the sheath, and their basal bodies are arranged in an intertwined hexagonal array.. ..this strongly suggests that the fibrils counter- rotate between flagella in direct contact to minimize the friction of high-speed rotation of individual flagella in the tight bundle within the sheath to enable MO-1 cells to swim at about 300 μm/s.

..http://www.osaka-u.ac.jp/en/news/ResearchRelease/2012/11/20121127_1

These bacteria are about 225 nanometres wide, slightly less than a quarter of a micron – 44 side by side would be no wider than a grain of talcum powder – so if  scaled up to the size of a small speedboat, perhaps 3 metres long, its proportional speed would be in excess of 14,000 kph – about ten times the speed of sound.

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Solar Panels

solar cell and photosynthesis

(L-R: Solar cell roof; photosynthesis process; photosystem i. The photosystem, which the researchers crystallized in its trimeric form, contains 12 different proteins in each monomer, along with 96 chlorophylls and more than 30 other cofactors.The photosystem contains 12 different proteins in each monomer, along with 96 chlorophylls and more than 30 other cofactors. For the first time, the structure allows them to begin to figure out how these molecules work together as a system to gather solar energy and then transfer that energy to the center of the complex, where electron-transfer reactions convert it to the chemical energy that drives almost all life on Earth.

The most basic requirement of plants is the ability to convert sunshine into energy, presumably dating back three billion years, and remaining essential today.  Without this ability leaves are left with only a decorative function.  All the work, as usual, is carried out in the cell.  But what a cell!

The mechanisms and processes are so interdependent one wonders how they could ever work at all. Graham R Fleming, a chemistry professor at the University of California, Berkeley, and director of the Physical Biosciences Division of Lawrence Berkeley National Laboratory, leading the reasearch team which took ten years of work to finalise the structure of Photosystem I (the large machine to the right) called it “an absolutely spectacular piece of work.”

Mankind recently came up with sloar panels, which are relatively simple by comparison.  Even still, they took some working out.  The idea that plants could have been a self-assembling early form of life is because we see them growing from nothing but dirt and sunshine.  We all assume photosynthesis is a simple process, because this is how it’s first explained:

But this is how it really is:

image002

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Garbage Grinders

waste disposal

Once proteins are formed in the cell, there are circumstances in which they need to be destroyed, for example, if incorrectly formed or of no further use.  The cells have their own aggressive TSA agents who spot and stamp such proteins with a ubiquitin molecule which alerts other transport systems that the protein needs to be scrapped.  A proteosome is shown to the right (illus: David Goodsell).  This shredder has a twist-open lid which is activated by the unique combination of three destruction tags added to the errant protein.

In the first step, a ubiquitin-activating enzyme (known as E1) hydrolyzes ATP and adenylylates a ubiquitin molecule. This is then transferred to E1’s active-site cysteine residue in concert with the adenylylation of a second ubiquitin.[34] This adenylylated ubiquitin is then transferred to a cysteine of a second enzyme, ubiquitin-conjugating enzyme (E2).

scanners

Could even an aggressive TSA agent, armed with handcuffs, a skull cracking baton, crippling taser and loaded weapon, find a threatening person in under a second?

In the last step, a member of a highly diverse class of enzymes known as ubiquitin ligases (E3) recognizes the specific protein to be ubiquitinated and catalyzes the transfer of ubiquitin from E2 to this target protein. A target protein must be labeled with at least four ubiquitin monomers (in the form of a polyubiquitin chain) before it is recognized by the proteasome lid.[35]

pat_down

“I said, business or pleasure? Don’t mess with me, dawg!”

It is therefore the E3 that confers substrate specificity to this system.[36] The number of E1, E2, and E3 proteins expressed depends on the organism and cell type, but there are many different E3 enzymes present in humans, indicating that there is a huge number of targets for the ubiquitin proteasome system.

http://en.wikipedia.org/wiki/Proteasome

tribunalsservice

Proteins are destroyed only after judgement by a tribunal, but also, cell death is instituted by another three-stage process. If all levels signify their assent, the cell commits suicide, by disassembling itself into components harmless to processes external to the now defunct cell

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Anti Freeze

antifreeze

Cells have developed antifreeze proteins in response to severe cold.  Failure to have done this in time would, of course, have stopped them in their tracks permanently.  The antifreeze molecules lower the freezing point of water contained within the cell, disrupting the freezing process by limiting the growth of water-hungry ice crystals.  Various kinds are shown above (illus: David S. Goodsell)

When water begins to freeze, many small crystals form, but then a few small crystals dominate and grow larger and larger, stealing water molecules from the surrounding small crystals. Antifreeze proteins counteract this recrystallization effect. They bind to the surface of the small ice crystals and slow or prevent the growth into larger dangerous crystals.

Antifreeze proteins lower the freezing point of water by a few degrees, but surprisingly, they don’t change the melting point. This process of depressing the freezing point while not affecting the melting point is termed thermal hysteresis. The most effective antifreeze proteins are made by insects, which lower the freezing point by about 6 degrees. However, antifreeze proteins, even the ones from plants and bacteria that have smaller effects on freezing point, are useful in another way. They are placed outside cells where they control the size of ice crystals and prevent catastrophic ice crystal formation when the temperature drops below the (lowered) freezing point.

http://www.rcsb.org/pdb/101/motm.do?momID=12

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Gearboxes

audi 6 gear box

Motors and gearboxes abound in the molecular world. How else would things get done? Especially interesting is the ingenious viral packaging motor, requiring a self-adjusting gear system to avoid breakage of DNA when being packed into the capsule at the highest rate of speed, and a pressure of 47 atmospheres.

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Changing Rooms

chaperonin changing room

(L-R: Thiemo Sander Changing Room,whitezine.com; Chaperonin molecule by David Goodsell, stage diagram: rcsb.org)

The only thing that stops some proteins forming in the cell once they’ve been printed out of amino acids and welded together is the sheer level of activity around them.  Try getting dressed amidst a riotnig mob!  A molecule can bump into others half a million molecules in a single second. Proteins not only carry out a function, they also act as receptors for messenger molecules which change their conformation, and this difference in conformation is detected by other proteins which are designed to act accordingly.  They therefore act as senders and receivers of messages, in addition to performing their own strictly delineated tasks.

But all this bustle means sometimes privacy is needed to allow new proteins to fold themselves from a long string of amino acids to a final three dimensional structure, a function of the chemical and magnetic attractors and disulphide bridges pre-aligned in the amino acids arrangements, from the nosey and rambunctious behaviour of all the other molecules.  The folding of proteins is itself a puzzle.  If they were to take every possible route to folding, they could take thousands of years.  Instead they tend to snap together in milliseconds, forming disulphide bridges and becoming shapes which are three times harder to compress than water.

Special chaperonin molecules attach to flustered proteins that have got their undies in a twist on the way to the catwalk, and guide them to a special class of chaperonin changing rooms – flasks with twist open lids, and attractive carbon-walled spaces inside.  Ahh, peace at last!  Once the protein has got dressed and ready for work – achieving its tertiary structure – the flask opens and out it goes into the chaos of the working day.

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Shredders

chip crusher and proline enzyme

The enzymes created in the body and supplied by, say fruit, are the chainsaws and industrial shredders of the body.  One molecule of bromelain, the enzyme found in pienapples, particularly in the core, can locate, secure, chop, and expel 30,000 proteins in a single second.  This is why it’s so effective in digestion and reducing inflammation.

Papain from papaya fruit works at a similar rate, targeting fibrin – the tough material around cancer cells.  Natural chemo?  Draw your own conclusions!  The fastest enzymes that chemists have been able to create work at a rate of 2 per second.

Despite the fast-growing body of knowledge, there is an ongoing debate as to how enzymes such as ornithine decarboxylase achieve rate accelerations as high as 10 power 17 (that’s 100 thousand trillion) thus performing within milliseconds a reaction that in their absence takes millions of years (Table 1). Furthermore fundamental questions regarding the evolution of enzymes also remain open; for example, how their function is related to their fold and whether, in the formation of enzyme active sites, substrate binding precedes the catalytic chemistry or vice versa.

http://www.weizmann.ac.il/Biological_Chemistry/scientist/Tawfik/papers/Article5.pdf

The dismal failure is explained by the need for chemists to work in a truly Darwinian way, by trial and error combining pieces from a library of genetic strips.  No useful protein is made of less than about 40 amino acids, and the real action only begins at around 50.  The largest libraries created are nucleic acid repertoires containing about 10 power 15 molecules.

To give you an idea of the difficulty, remember these proteins are only measurable in angstroms.  The mass of a fully randomised 50 nucleotide library with 10 power 30 variants is over 25,000 tonnes.

Thus, in practice, the in vitro evolution of an active molecule reelies on the sampling of a neglible faction of the potential consequences.

(ibid)

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Insulated Cables

dupont cable and mylein sheathed nerve bundles

Left: Dupont cabling; right: nerve bundles indiidually sheathed with myelin, an insulation material which causes the signal to be accelerated by a factor of 50 times.  next time you touch something hot, the speed at which the signal reaches your brain is down to this marvellous dual function protective accelerant.  Essential for survival in a hostile environment.

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Cities and Highways

highways and kinesin deliveries

The transport routes and complexity inside every cell make the comparison to a modern city a fair one.  Activity within the cell proceeds at such a pace that a molecule may interact with others half a million times within the space of a second.  A system of walkways connects the various parts of the cell, and checkpoints abound, especially on the cell wall.  Above is a conceptual cartoon of various motor protein delivery units.

Below is a David Goodsell illustration of a small part of a cell, in which enzymes are shown in blue, with water molecules as small cyan heart shapes.  The level of activity within a cell is simply incredible.  As James Shapiro says in Evolution:

Proteins operate as conditional microprocessors in regulatory circuits.  They behave differently depending on their interaction with other proteins or molecules.

The big problem with claiming the first forms of life were single celled creatures is that, as far as anyone knows, a cell comes only from a cell. last week I was told that there was a workable solution to the origin of life, and that was abiogenesis.  This was accompanied by the usual offhand comment, as a teacher to an errant pupil: “look it up”.

Well, abiogenesis simply means life arose from dead molecules.  It’s rather like the explanation HG Wells’ time traveller gave to his learned audience:  “You simply push this lever forwards to travel into the future, and backwards, to travel into the past.”  This is no explanation, but only a description which anyone could observe for themselves.  But if abiogeneis actually occurred it leaves the problem of where one draws the line between dead and living matter.  If dead matter is so close to living matter, and so prone to jump into life early on in a planet’s formation, then can any matter really be dead?  The development of the required complexity is answered with a word, while the problem remains unsolved.

In any case, a cell without the required components which protect it and yet allow sustenance to enter it, and the machinery to duplicate it, is no cell at all, and cannot even be called a distinct unit. The remarkable thing about life is that it exists in any form at all.

4939547762_5956f7cdd9

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People Carrying Stuff

people carrying things on their heads

Traffic in the cell is well controlled.  Kinesin motors walk outward from the centrosome to the cell wall, and Dynein motors walk the opposite way, their steps neatly matching the tubulin components.  Packages are collected, handed off to others, or delivered.

Above right is the cover of Cell magazine, V 141:2, April 16 2010, and inset, reversed animation still from Science magazine, 4 Mar 2011.  The neat division of directions mirrors our bi-directional motorways.

Interesting fact! Did you know the only pulic road in England where you can legally drive on the right is the entrance to the Savoy hotel, in Lonon’s Strand?  Apparently this was originally so ladies could alight from the carriages.  Since the renovation the restaurants and staff are as fantastic as always, but their new paintings – slightly less so.

Savoy Hotel London

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(Reversible) Fuel Generators

proton powered fuel generator

Left: proton powered fuel generator by directindustry.com – but it’s not reversible; right, ATP synthase
http://mcb.berkeley.edu/gallery2/main.php?g2_itemId=99

The fuel in the cell is created by ATP synthase, a stunning piece of design described in more detail elsewhere on this site.  Essentially it continually takes spare hydrogen ions from one side of the periplasm and pulls them into a device resembling a revolver barrel, which  rotates a few degrees around a stator with asymmetrical paddles that create, for every full turn, three adenosine triphosphate molecules, or ATP.  This is achieved by pulling in a similar molecule but in diphosphate form and adding one phosphate, then booting it out for use elsewhere in the cell.  It therefore converts an electrical gradient into a fuel surplus.

The cell’s machinery uses ATP by breaking off a phosphate, and releasing a burst of energy, creating a lone phosphate and ADP, making the fuel 100% recyclable.  And if you think that’s clever, consider this: if there’s a surplus of ATP but not enough electric gradient, it works backwards perfectly – pulling in ATP and breaking off a phosphate, spinning the unit in reverse, and throwing a hydrogen ion out the other side.  This is tantamount to a car engine sucking in exhaust, running backwards, and silling up your petrol tank.

Tens of thousands of these motors work in the nucleus of every cell, and they’re no slackers: they create your own body weight in recycled fuel molecules every day.

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Ribbon Data Cables

ribbon cabling in computers

The wiring in the brain was recently analysed by building a connectome of a monkey (right). Ribbon cables are very effective for organising data transfer, and, come to think of it, they probably add a great deal of flexible strength to the brain mass as well, which might raise the crisis threshold as far as possible in self-created compression instances, for example when a professional footballer is stopped in his headlong rush by an opposing team member.

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The Spiral Staircase

salter spiral stair dot com

Why not? A very elegant invention, to be sure! (right: Modern Topics in Biochemistry, 1966)

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Rail Handcars

handcar for converting vertical motion to rotational motion and the reverse

The rail handcar converts downward thrust provided by one or two passengers into rotary movement, generating forward thrust for the vehicle as a whole.  Devices which proceed along the endless stretches of DNA use ATP to generate circular motion, which generate forward thrust along the double helix.

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Screw Top Containers

screw top container

Sorry, but it’s a fact – twist lids are nothing new.  They arrived with the cell, and that’s a certainty

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Shoelace Ends

shoelaces telomerase and chromatin detail

The chromosomes need shoelace tips to stop from fraying. They’re even attached in a neat bow, and we use them in pairs!

Interesting fact: telomerase is generated in abundance in meditators, and telomerase extends the life of the cell by extending the telomerase at the end of the chromosomes.  Just saying!

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Television

television

The invention of television was certainly ingenious and changed the face of the Earth, and relied on a material called selenium, which converted photon stimulation to electrical signals.  The Russian, Nipkow,  experimented with it in the 1800’s but found it unworkable due to the weak signal and rapid decay.  It was Baird who in the 1920’s, with the advent of electrical amplifiers, realised that the signals all decayed at the same rate, and all that was required was a consistent amplification.  Refining the process was to take up the remainder of his life.

The eye uses a similar system in which retinal, a small molecule which fits into the binding site of a large protein called opsin, making up rhodopsin, is triggered into activity by the sensitivity of the opsin molecule to photon stimulation.  The following chain reaction of chemicals and eventual electrical signals, include feedback loops, timing mechanisms, amplifiers and interpretive mechanisms in the brain woudl fill a book.

Even modern television doesn’t improve on the devices contained within the retina, which are dealt with in greater detail elsewhere on this site.  The chain of events which give rise to sight are so important that the eyes use about 1/5th of the body’s energy; the eyes are constantly in vibratory motion, without which, the signals would cease to be forwarded to the brain.

The eyes include their own immune system, variable blood flow heat sinks behind the RPE controlled by the iris contraction, built in sunglasses, a recycling depot and separate circuits for motion, line detection and binocular perspective. And lastly, remember that all these components are smaller than the wavelength of visible light.  They transmit signals of light for us to use, but in their molecular world, they all work completely in the dark.

Priceless!

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Velcro

velcro2

How else can cells stick to each other?  Clever stuff.  Illustration (right) by David S Goodsell.

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Darwinism has, by virtue of powerful influences and some regrettable bunk, turned into a kind of cult.  Professor Dawkins believes

“religion is about turning untested belief into unshakable truth through the power of institutions and the passage of time.”

Well, he’s partly right: Darwinism claims science and logic as its own, while cheerfully rejecting whatever parts of both do not suit it.

Just as the wealthy extol the benefits of money, while keeping it all for themselves, some advocates of freethinking clearly feel free thought is not suited for the likes of us.

It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true.

They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.

..JBS Haldane, Possible Worlds

I now believe there is a God…I now think it [the evidence] does point to a creative Intelligence almost entirely because of the DNA investigations.

What I think the DNA material has done is that it has shown, by the almost unbelievable complexity of the arrangements which which are needed to produce life, that intelligence must have been involved in getting these extraordinarily diverse elements to work together.

..Antony Flew

About iain carstairs

I have a great interest in both scientific advances and the beauty of religion, and created www.scienceandreligion.com about 15 years ago with the aim of finding common ground between the scientist and the believer, and to encourage debate between the two sides.
This entry was posted in Amino Acids, Antibodies, Antony Flew, Aquired bacterial immunity to antibiotics, Atheism, ATP Synthase, Biology, Brain damage, Brain Hygiene, Brain wiring, Bromelaine, Cell duplication, Chaperonins, Charles Darwin, Connectin, David S Goodsell, DNA, Evolution, Evolution: View from the 21st Century, Fountain of Youth, Genome as Read/Write System, Gratitude, Horizontal genetic transfer, Human genome, Interstellar Molecules, James A Shapiro, Meditation, Nanotechnology, Natural Intelligence, Oxytocin, Proteins, Rhodopsin, Ribosome, Richard Dawkins, Telomerase, Telomeres, The Brain, The Machinery of Life and tagged , , , , . Bookmark the permalink.

5 Responses to Man vs. Molecule!

  1. Carstairs.samuel says:

    We (you) are amazing.

    Love Jane

    Sent from my iPad

  2. I wrote, coincidentally, an appreciation of the long period of the earliest bacterial cells this week under the title “Genesis for Non-Theists.” I’m astounded by the richness of your discussion of what cells are capable of, and it certainly confirms both my sense of awe and also why it may have required two billion years for the basics to come together (especially considering the conservative effects of an error-editor).

  3. Pingback: Cancer: Don’t Shoot the Messenger | ScienceAndReligion.com

  4. Pingback: Blame Where It’s Due Please, Mr Fry! | ScienceAndReligion.com

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