In Praise of Proteins

Biochemistry at the moment is trying to figure out the method by which proteins – the tiny molecules which make our body work – fold themselves into the precise three dimensional shape they take to carry out their function.

The well-known strings of DNA, at the top, contain four different bases, labelled CGAT, which form in pairs, always C and G, A and T.  The whole string can be unzipped by molecular motors, and because the original “ladder” has a spiral shape, the rotation of such motors is helpfully converted into forward thrust.

The designs for these proteins are coded with four different bases arranged so that in protein-coding areas, every set of three bases (a codon) specifies a certain amino acid. There is some redundancy, as 64 different codons only need to specify 20 amino acids.  There are also start and stop codons, making a perfect two-dimensional engineering spec.  Each amino acid has around 20 atoms – some more, some less.  To make a protein, they are all welded together in the specified order by a very very fast and accurate factory called the ribosome, of which thousands are contained inside every human cell.

Recently a simulation was carried out to observe the folding tenency of the protein villin, a comparatively manageable collection of 140 amino acids – and it took 200,000 networked PCs in the fold-at-home project, working a total of over one million hours to work out all the animation.  This is where physics, chemistry and three-dimensional design considerations merge – it is the most complicated engineering challenge imaginable.

Ribosomes: protein factories read DNA and assemble proteins – step 1 in biology.   But where are the designs kept for the ribosome structure, and what could assemble them?

No human being can manage these parameters mentally.  The equations governing the forces of attraction and repulsion of the tiny atoms are staggering – they cover pages and pages – and the activities are astonishingly quick.  It is quite literally a huge, smooth vertical wall standing in front of the intellect at the moment, whose top is hidden in clouds far above. When you hear “hotly debated topic” and “need for further research” you know some very clever people are struggling, and with good reason: the kind of mind which could understand this complexity in real time – to give you an example, within a cell, proteins can collide with 500,000 other molecules in a single second – would already be a super-mind and unrecognisable as a human being.  But attempting it is a tribute to human ingenuity and ambition, and this is indeed what scientists are working towards; to the best of my ability as a layman, here is something of what I learned from reading about their work.

The proteins are pretty solid when they’re assembled: apparently they can be three times more difficult to compress than water, and some of their components are arranged as moving subcomponents – for example, able to make 180 degree flips back and forth – anywhere from 100 times a second to (get ready) 10 million times a second.  These proteins are called “enzymes” and act as catalysts – like little sanders wearing down organic material, in the mouth or stomach for example.  There are 4,000 known enzyme reactions, all different: the time taken to break some materials down has been calculated at 78 million years without these enzymes – but with them, 18 milliseconds.  These are extraordinary tools to have flowing freely in your body.

Papain, an enzyme within the papaya fruit, specifically attacks fibrin, the protective protein found around cancer cells and which also attaches tumours to bones, internal organs etc.  Scientists recently discovered papain has a restraining effect on cancer, for obvious reasons; where papaya is commonly eaten, tumour rates are low.  The older generations in Thailand, for example, had a low incidence of cancer while younger generations, abandoning traditional diets in favour of western chemically-produced fast “food”, adopt cancer at the standard western rate.  The remarkable thing about these enzymes is that each can attract, lock, slice, and eject as many as 30,000 proteins in a second, meaning they behave like highly focused chainsaws.  Natural technology is presently far beyond what we can achieve.

Hemoglobin molecule: the only possible engineering solution for transporting oxygen uniformly through a fluid to all parts of the body, with the dual design of carrying carbon dioxide away

These engineering challenges are never as simple as we, eager to trivialise the problem and by extension, the solution, make them out to be.  When a well meaning member of an audience asked Richard Dawkins to explain why he did not consider the blood clotting mechanism, an ingenious solution of many co-ordinated stages, to be a complex process, Dawkins erupted, “that is a creationist lie!”  In fact, all engineering solutions at this level require co-ordinated solutions, which is why at the moment we can hardlyfigure out how they work.  ENCODE results were not universally greeted with acclaim: many evolutionists claimed ENCODE told them nothing of any use, perhaps stinging from the new public perception of “junk DNA”, much touted by Dawkins, to be nonsense after all.

Take the hemoglobin molecule, which has four iron platforms, angled away from each other in an incrementally sprung mechanism, to collect up to four oxygen molecules from the lungs and deliver them to the cells.  The obvious solution is to make it easy for oxygen to stick to these little machines.  But if this were the case, it would mean that after dropping oxygen molecules off to the body’s cells, another passing hemoglobin could immediately snatch them back again.  So the hemoglobin is put together in rather a cunning way: the first oxygen molecule can only attach if it is forced under high pressure, due to the surrounding atomic forces within the alpha and beta chains.  But once attached, it starts to open up the hemolgobin’s sprung structure, making the second oxygen molecule much easier to attach.  And likewise, the third becomes even quicker to attach, and the fourth, instantaneous.

The binding of oxygen is shown here up close, in two internal structures within human hemoglobin.  On the left, hemoglobin with no oxygen bound to it. The heme is seen edge-on with the iron atom colored in gold. You can see the key histidine underneath attached to the iron atom. On the right, oxygen has bound to the iron, pulling it upwards. This in turn, pulls on the histidine below, which then shifts the location of the entire protein chain. These changes are transmitted throughout the protein, causing the shift in shape which changes the binding strength of the neighboring sites. (rcsb.org “molecule of the month”.  Seriously!)

After dropping the first oxygen molecule off, the shape of the protein changes yet again, and the second, third and fourth oxygen molecules are released even more easily.  So in conditions of high oxygen pressure, this fantastic little machine works extremely quickly, but in low pressure – passing by lots of oxygen molecules attached to cells – it doesn’t work at all.  Except, with a fantastic dual purpose mechanism it does collect carbon dioxide waste from the cell, under conditions of infitesimally small pressure – scavenging this rubbish wherever it can find it, and taking it back to the lungs for release – to be breathed out.  Any other design would be totally useless.

So essential is this process that in cases of carbon monoxide poisoning, the hemoglobin, are saturated with a molecule that is extraordinarily hard to shift, become carboxyhemoglobin – dangerous for cell tissues.  Hours are required for them to begin to return to normal function.  The need is for continual, perfected and comprehensive engineering solutions at all levels.  The hemoglbin are only part of such a solution: the red blood cells are shaped to fold into any corner of the circulatory system, and the lungs must allow the storage of air and the expulsion of waste; the muscles must completely engage the lungs and work by an automated system in sleep.  The protective ribs must allow expansion, and the whole system must react to the need for more oxygen, while the air intakes must have reactive mechanisms for dealing with obstructions, mucus mechanisms for grit and particles, and so on.  All these mechanisms demand coded proteins and mechanical engineering for their storage in the 2-d DNA.  So while on every level we see an essential solution, with protective safeguards built in, we imagine that it arrived by a series of errors!

Myosin is the molecule responsible for all the movements in your body – whether blinking or tunning, myosin is the tiny motor which does the work.  It is configured in such a way as to bind with actin: it breaks off the phosphate from a molecule of ATP, releasing a large amount of energy, and then performing a “power stroke”: a rotating and grabbing motion, moving the muscles it is attached to

But the hemoglobin needs to be folded in a precise shape, as you can see – it must have a recepticle for the iron atom, the right electrical charges all around each platform, and the right “spring” hinges to allow each binding operation to nudge the other components into a new state, from which they must return when their job is done.

DNA Gyrase from E.Coli is an enzyme belonging to the class of Topoisomerases, which allows the organism to modify the topology of its DNA. In other words it helps untangle, un-knot and relax supercoils in its DNA genome. It does so by binding to a strand of DNA, cutting both strands and then, while keeping hold of both cut ends, passing another piece of double stranded DNA through the gap. It then reseals the double stranded break. Essentially it allows portions of the large circular bacterial genome to pass through itself, such as to prevent knotting and entanglement. A number of antibiotics (e.g. Simocyclinone D8) target this enzyme, since it is essential to the organism’s survival. Humans also have a form of this enzyme but it’s construction is different and we are thus not affected by the antibiotics. (http://beautifulproteins.blogspot.com/)

This machine can’t arrive incrementally: it either works, or the organism dies straight away.  Slight variations in hemoglobin exist in the fetus, where oxygen conditions are different, and in various animals.  Horse hemoglobin differs from the human type by more amino acids than does the chimpanzee’s, for example, but in all cases the unique design is stable and fixed – and even minuscule changes of a single amino acid, or a single wrong placement, both errors involving perhaps 19 atoms – cause horrific disorders.

I love this technical drawing – this is part of a skeletal muscle attached to the heart, forming a very sophisticated mechanical and regulating device.  Multiple proteins include  T-Cap, a capping protein at the end of the titin molecules, Filamin – a capping protein at the end of the thin filament, and CARP which extends away from the Z-disc; other proteins include ALP, calcineurin, calsarcin, mink, myopadin, myopalladin, MLP, and ZASP/Cypher/LDB3. Some are thought to form part of the cardiac stretch-sensing mechanism. The core of the organization is α-actinin.  (e-heart.org)

Consider the problem: an amino acid is comprised of an average of 19 atoms.  A typical protein might have 541 amino acids in the case of hemoglobin, or in one case, titin, the component of muscle tissue, as many as 27,000 all joined together end to end.  A string of these amino acids is useless on its own – the string must be folded into a precise shape.  The amazing thing is this shape is determined completely by the precise order in which these chains of atoms are joined together.  Therefore the DNA, carrying this organised string of instructions, must have all its elements – 3 letters for each amino acid, in exactly the right order.  Hemoglobin would need 1,623 letters, and titin, 80,000 plus.  This is a requirement for massive precision.

I don’t know what this is, but I want one

One titin molecule would have about half a million atoms.  To imagine this, think of each atom as a grain of sand, and each amino acid as a string of sand beads, totalling about 2cm length.  Titin would be more than half a kilometre in length.  Now imagine trying to fold that at 2cm intervals to get an exact shape, bearing in mind that each join between any two 2cm strings could fold in many different ways in three dimensions.  If anyone thinks this is a random procedure, they do not understand the number of possible ways it can go wrong!

Amongst the most intruiging protein folds, the propeller fold comes in a number of varieties. Shown here is a 7 bladed version, but they occur in 3 to 8 bladed varieties. Note that this fold is constructed from a single chain, rather than from 7 identical units, although this fold almost certainly arose from internal duplications of gene segments. Many hundreds of protein structures with this fold have been determined. In the case of enzymes the enzyme’s active site is often found in the cleft formed in the center of the propeller by loops connecting the successive four-sheet motifs. Examples include the the influenza virus protein neuraminidase – one of two proteins present in the viral envelope. It catalyzes the cleavage of sialic acid moieties from cell-membrane proteins to aid in the targeting of newly produced virions to previously uninfected cells. (http://beautifulproteins.blogspot.com/)

The time required to explore every possible folding possibility, needless to say, would be enormous, and even at a million possibilities per second, longer by far than the entire 14 billion years of the Universe.  But how long does such a molecule take to form, inside the chaotic conditions of the cell?  A few milliseconds.

Chaperonin helper module: top and side view. The hole i the centre opens up whehn parts of this little machine twist, to allow the protein in and form itself in safety

Amazingly, if the protein is having trouble forming, perhaps because of unusually chaotic conditions in the cell (a protein can bump into another molecule 500,000 times in one second) there are helper units called chaperonins: these resemble thermos flasks which, if they sense a protein is stuck to another one, or having trouble forming, they open their lid to allow the protein inside, where it can form away from the bustle of the cell.  When it’s formed, the thermos flask lid untwists, and the protein is released.  Time taken: a few thousandths of a second.

What if Dawkins is right – and it IS all random?

Lots of people have been known to ask Richard Dawkins when he claims all life arises from random mutations, and the Universe lacks an intelligent aspect of any sort: “What if you’re wrong?”

Well, it’s a certainly a good question – but there’s another question nobody has ever yet considered: what if he were right?!

People usually can’t imagine exponential rates of growth.  The legend goes of inventor of the game of chess being offered any reward by the Chinese emperor.  The man looked at the chess board and said, “there are sixty four squares.  All I ask for is a grain of rice for the first square, two for the second, then four for the third and so on, until the board is full.”  The emperor thought this a foolish request – he was prepared to give this man anything!  But trying to suppress his glee, he ordered his staff to carry it out.

The photo taken on March 29, 2006 shows the huge statues of emperors Yan and Huang under construction in Zhengzhou, capital of Henan Province. Emperors Yan and Huang, legendary chiefs of tribes in the Yellow River valley are seen as the founders of the Chinese nation.  I think the chess incident was quietly brushed aside

Of course, by the 15th square, there were now nearly 33 thousand grains of rice piled on the board.  By the 30th square, the reserves of the emperor’s castle were exhausted.  By the 37th square, every farm for miles around had to be raised for their stocks of rice, and by the 50th square, the total would have been 1,125 trillion grains of rice – more rice than existed on the whole planet.

This is exactly how it happened.  Interestingly, rice has more genes in its DNA than humans have in theirs!

I’m a programmer and I design my own database systems.  I confess I do it because it’s so easy – if it were frustratingly difficult I would find something else to do.   Well, about twenty years ago I was installing at a new client, when the MD asked if his old address database could be de-duplicated and loaded into mine.  I took a look and said, sure.  Just then their own head of IT, an excitable Chinese fellow, stepped forward and said, no, he would do it.  Are you sure, I asked him – it won’t take me long?  No, no, he insisted – it was his job.

He went away and wrote his program and later that day started to run it.  There were about 100,000 addresses to check, and each with six fields plus a post code.  After some hours it was six pm, and he was looking a bit tense – his system had managed to check only two addresses.  I waited until he casually sauntered over.  “Explain the logic,” I asked.  “Well,” he said, “I just take each line in one address, and compare it to each line of every other address, and if I find a duplicate, I delete that record.”   How he became a head of IT I will never understand.  “Ok, leave it with me.”

Badly in need of de-duplication

What he had asked this computer to do was, for each address, to take six separate lines of an address, one by one, and compare each with every one of the other lines in all the other addresses.  A total of 600,000 other fields – so each address had to make 3.6 million checks, meaning a total of 360 billion disk accesses.  I worked out it would have taken more than twenty years to run!  That is slow even by Accenture’s standards.  I didn’t tell him that, of course.  One of the reservations clerks was an intuitive guy who knew nothing about computers but who had somehow seen through this IT wizard, and he pleaded with me to tell him how long the process would have taken – I confess, I did.. I can’t stand professionals who are incompetent.

The problem with big numbers is that they are so hard to imagine, since the brain is used to manageable figures of fives and tens.  The digit 1 followed by 80 zeroes is assumed to be quite a large number, because, wow, imagine all those zeros!  But there again, zeros are not actual amounts, and 80 isn’t such a big number, so surely 80 of anything can’t be all that large?  In fact this number is about how many atoms there are in the Universe!

And as for lengths of time, 3 followed by 9 zeroes sounds trivial.  But it’s the number of seconds in one hundred years: let’s say you have another 25 years of life remaining – that’s 788 million seconds – and only about 525 million waking seconds.

Yes, yes, but this is boring.  What about those proteins?

A protein with a paltry 30 amino acid components – a level at which it might not even be considered a protein – could have those amino acids ordered in 20 to the power 30 (20 x 20 x 20…  thirty times) different ways, only one of which would result by chance in the aminos being in the right order to fold into a perfectly functional device (with four-fold symmetry in the case of hemoglobin).  Experimenting at one million different ways per second – all failures – would take 634 million billion years.  That’s the age of the Universe, multiplied by 45 million.

A larger molecule like titin would take – and this is going to be a big number – 20 to the power 27000, with no guarantee of success.   Who can imagine a number with more than 30 thousand zeros?  Just wait – I’ve done some calculations! If it were a random process, how much scrap titin would you have before you had one working molecule?

The 14 billion light year wide Universe. If Richard Dawkins had his way, the whole thing would be filled with failed molecules. And you thought parking was a problem now!

The calculations are below if you want to read them.  But the answer is, after getting only one four hundredth of the way through, the waste molecules – each too small to be seen with the naked eye – tightly packed top to bottom, end to end would fill the visible Universe up – a sphere 14bn light years in diameter.  To get a chance of one working titin molecule, using the Richard Dawkins method would be impossible in a finite Universe, and would take pretty well forever in an infinite Universe.

And what kind of powerful natural force could possibly create all these failed attempts?  How could the result be an island of highly structured order surrounded by an endless ocean of chaos?  There would actually be no room for anything else.  And yet there are roughly the same number of hemoglobin in your body as there are stars in the universe – 7 followed by 21 zeroes: each formed in a twinkling of an eye… and they all seem to be working perfectly.

Another turkey

The boring calculations:

The Universe is imagined to be 14bn light years across, so assuming it has a spherical shape for the sake of argument gives a volume of 4/3 * pi * the radius cubed.  That works out to 410 billion trillion cubic light years.  Now a line one light year long is about 9.46 × 1012 kilometres.  So a cubic light year is 836 × 1039 cubic kilometres.  On a nano scale, the titin protein is about 950 nanometres (nm) long (one million nm = 1 millimetre.. they are really, really small!) and let’s say 100 nm thick. and 20 nm wide.  Incorrectly formed molecules would be a lot longer and a lot thinner, but in terms of mass they’d all be the same.  This means in a cubic km you have just over 1 billion molecules end to end, 10 billion vertically and 50 billion side by side.  That gives a surprisingly manageable number of titin molecules in one cubic km of 500 with 27 zeroes after it.

So the total number of titin molecules to fill the whole Universe – leaving not a single scrap of space for anything else, would be

500 with 27 zeros  after it multiplied by 836 followed by 39 zeros multiplied by 410 followed by 21 zeros.

This number, if anyone is still reading, is just over 171 followed by 482 zeros.  But the number of failures required using the Dawkins method would have at least 30,000 zeros.  It’s the most absurd number you can imagine, and makes the Universe look like a very, very tightly limited place for random, exponential chaos.  I can’t work the figure out exactly because my computer gives up after 190 zeros.. which seems fair enough!

And this is only one protein in the human body.  The human body contains around 20,000 different kinds of proteins – each needing to be exactly, specifically, precisely configured and pre-aligned in the DNA before it jumps into life.  These are vast impossibilities in a disordered state.  There is no room whatever for random chaos in this system, and there never could have been.  This intuitive understanding is what gave birth to religion, for an individual to try and find the life most in accordance with a machine whose complexity we can never completely fathom.

Biology is machinery, plain and simple.  It requires the gene reading equipment, a renewable fuel source, little motors to crank out the fuel all day every day, seamless error checking methods and duplication equipment, plus you have to pack about two metres of DNA into every one of 100 trillion cells of the body.  And the whole thing has to work seamlessly for eighty or ninety years without stopping once.  Understand how all this works and you will be looking into the mind of the most superb programmer in the Universe.

Random mutations behind tightly engineered biological machinery?  No, definitely not.

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.
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55 Responses to In Praise of Proteins

  1. Charlie ******** says:

    Hi Iain
    I’ve just come across your site, very informative, lots of interesting topics.

    With regards to protein folding, the biologist Steve Jones said on BBC radio 4, ‘In Our Time’ episode on natural selection, ” the analogy is like taking a roll of sticky tape, unrolling it scrunching it up and every time you do that you get the same scrunched pattern, we simply do not understand how that happens.

    But in the same series on the episode on genetic mutation, he said, “evolution is a series of successful mistakes.” and “Its thanks to mutation that we’re not all still in the primeval soup”.

    In not sure how he manages to make these statements without feeling the conflict that must be going on in his thoughts. The information you have supplied speaks for itself.

    The ‘In Our Time’ podcasts can be found at – http://www.bbc.co.uk/podcasts/series/iots/all

    Thanks for the great site, I look forward to having a closer look.

    • Many thanks for that – I was afraid I was going to get flamed for a minute there!

      I spent some time on Richard Dawkins’ site last November in an effort to find what the current knowledge was on protein folding, stable DNA patterns and so on. He was very open about his uncertainty which I found refreshing. I recall he said in reply to one of my questions that he had presented some arguments for genetic stability in The Ancestor’s Tale “although without any great conviction”.

      I feel certain that if people are really looking for truth, and not just something to hit the spiritual-minded over the head with, biology will lead to the discovery of layers of intelligence. What those forms take and how they can be used to better our knowledge is anyone’s guess. Even the Dalai Lama is saying we need to look beyond religion towards other ways of expressing our affinity to natural intelligences. But before we get that far I would like to see religion honoured for the intuitive gems and the sustenance it has offered mankind over the years.

      I hope that it happens in my lifetime but I am not overly optimistic. Meantime I will keep having fun!

  2. What a great article on proteins! I learned a lot here!

    If someone asked me to debate it, I would address the random question this way: Part of the process of randomness is that not all possible permutations need to be performed before the correct selection is made. If asked to pick a card at random from a deck until I get the 2 of hearts, I probably won’t need to pick all 52 cards before getting to it. In fact, I might even get it on the first pick. Arguing that there are 52 permutations is a smokescreen that obscures the simple fact that once you pick the right card, you can stop filling up the universe with the other choices.

    But I’m throwing that out there so you can tear it down. You know I don’t buy the “evolution is random” theory either. But neither do I buy the theory that some magical sky wizard who needs us to worship him figured out all this stuff either. I like that you are getting at a main point that there must be some underlying structure to the universe we have not yet formally comprehended, and that this structure has something to do with concepts our primitive brains understand as information and intelligence. You have also earned major respect from me by not promoting any specific deity as the responsible party. I don’t mind when people argue for the existence of some kind of super-intelligence. But as soon as they tell me they know which one it is, and that their ancient text revealed all we need to know about him (or her, or it) then I write them off as hopeless.

    You are often write about two different aspects of religion. One is religion as a cosmological understanding: we don’t know what’s going on but we can commune with the mystery to a certain extent. The other is religion as a sociological phenomenon: there may not be any objectively verifiable theology, but we can clearly see positive social benefits from a philosophy that promotes altruism and kindness and solidarity.

    But religion, historically, has been the enemy of these two positive outlooks just as often (if not more often) as science. Sometimes it seems you equate religion with positive cosmology and positive sociology. Any study of history suggests otherwise. These two positive outlooks are the realm of philosophy, perhaps. They do not belong exclusively to either science or religion. Instead, they are the axes along which any pro-human science or religion should align, or the criteria by which they must be judged. Science and religion are both tools for attaining these philosophical ends. Like any tool, they can both be used for much more sinister purposes.

    I truly believe the work you are doing here is very, very important. You are paving the way for a new thinking that combines the best of science and religion in a truly humane conception of the universe, an over-philosophy that synthesizes what each of these branches of thought fails to achieve on its own.

  3. Thanks!

    I think limiting the permutations in one construction doesn’t help! Even if proteins spring forth in one leap – you still have to find 20,000 different designs, all functioning in a specific way, and all the production machinery too. But proteins themselves do not behave in a random way. Their function is not random. Their error checking is not random. Their enzyme actions are not renadom. The places they are sent to are not random. The assembly-helper chaperonins are not random. Their copy mechanisms are not random – or else you couldn’t have a trillion identical ones being produced – the finest assembly lines in the universe. Nothing about them is random. Not a single thing. There are “attack” proteins with little scissors in them – they just found one in the AIDS virus! It cuts its way into the DNA to splice in new pieces – what?! Little burglar proteins! That’s unbelievable! To attribute their origin to randomness makes no sense on any level. Ths mad urge to attribute everything to randomness, somehow, in any way, maybe this way? maybe that way! What about if this is random? maybe then everything is random? Please, find randomness! It seems a kind of, I don’t know, desperation.

    Dawkins dismisses “why” as a silly question. But when applied, “why” completely wipes his arguments. Why would any set of atoms combine to make machines which act with a purpose? When you say “evolution” you may as well say, “um, it happened, therefore – look! It happened. Therefore, it’s evolution!” This isn’t a scientific argument. It’s not even an argument, and not even a theory, it’s just a tautology: “if it happened, it happened – if it didn’t happen, it didn’t happen”. Even hard core researchers have to continually fight against the instinctive idea that these machines are designed for a purpose. They have to suppress this feeling all the time! You read research papers and they use phrases like “the protein’s task…” “somehow the protein’s design allows it to..” “the protein’s sole purpose is to work with..” “the specific function of this protein is at last clear..” “After much research we at last we understand how this protein achieves its purpose..” “Somehow it happened” is not an argument of any kind!

    I think religion is often used as a ring-fenced area into which all the antipathy towards universal intelligence is dumped. Well, forget religion then. You don’t have to look at religion at all: every element of society with a lasting influence must arise from a deeper source, since they are a product of group intelligence. Why have a society which bands together to work towards a purpose? Why have children, when they undermine your own chances of survival? Why even draw breath? Why blink? Why find a mate, when you can see how slim the chances of a successful union are? These are all natural instincts; the intellect has nothing whatever to do with any of them. Even the idea that we should have laws, and name them, and reward those who abide by them, and punish those who don’t, must have a reflection in universal truth. The idea of a leader. The idea of one who we try to emulate, or defer to their mentality. It shows a pattern of order to which all subscribe. Otherwise, why does every society organise laws? It would be simpler for each person to wander off and do their own thing. “Ah, it’s evolution!” But this natural group instinct exists, and nobody argues against it just because they can’t write the equations for it.

    Even Dawkins, when asked, “why do you feel some behaviour is worthwhile and other behaviour should be discouraged, if the universe is random?” replied that he didn’t know, that it just seemed right but he couldn’t explain it. Where are the equations? Where is his proof? If a religious person were to use that argument, Dawkins shouts them down. “I despise faith,” he says. How can life work completely apart from natural intuition? It can’t, and religion has sprung up to reflect this.

    The idea of laws – magnetism, gravity, genetics, heredity – do not occur to the animal; they have no way of calculating or measuring them. But with a little more cortex, science proved the universe is founded on laws. On order. Animals know nothing about the equations behind aerodynamics, digestion, diet, polarised light, radar, sonar, camoflage, molecular forces or chemical signalling, and yet they use all these complicated principles far better than man and without any written storage or communication. Their offspring grasp these things intuitively when given an example. So natural intelligence proves superior to our intellect. Yes, we can describe the processes somewhat. But can we fly by polarised light, like bees? Or swoop blindly using sonar, to within millimetres of accuracy, or detect ultraviolet vole droppings from a quarter mile up in the air? Of course not, we have no matching snesory organs. It would be stupid to deny this. A 737 is an impressive aircraft but the bird, with its incredible acrobatics, global navigation systems, precise homing instincts, beautiful plumage, cheerful song, and self sustaining energy sources are superior in every possible way. And they never crash!

    We will never make a machine as agile as a bird, or even as beautiful as a flower, or as complex as an ant. Or even of a bacterium, with its high compression DNA injection pod. We can’t even replace our existing senses or limbs if they fail. Death is proof of this. Have you seen a kidney dialysis machine? It is the size of a wardrobe. Our technology is still hopelessly crude. All the talk about artificial limbs is nonsense. Lose a finger and the surgeons will give you a plastic stick, or offer to cut off a toe and stick it on instead.

    Man’s gift is his abstract mind, his mystical sense, his intellect, and his capacity for understanding and determining his fate. if we’re not going to use it, we’re doomed. The intellect is severely limited. People who discard their intuition and rely only on intellect are a danger to themselves. There is a sense that they are experts on a tiny island of knowledge, but floundering with the bigger challenge of living a well rounded life. This may even be the cause behind autism: the “Geek Syndrome” in Wired magazine’s article on Silicon Valley’s high autism rates. The intellect alone does not lead anywhere.

    Nature has proven too complex for the intellect to manage, in every direction: we run up against a wall. Try as we might, it is not possible to grasp a self-built enzyme performing its function ten million times per second, or the different possibilities of a hundred million such objects, all communicating and travelling to pre-determined points in a factory some nanometres wide. Design and purpose is everywhere. You can’t find any natural systems without a functioning design from the molecules, from the very atoms, right to the surface features! But then the tautology is invoked: “yawn.. evolution: if it happened, it happened. If it didn’t happen, it didn’t happen. what’s to know?” And the questioning mind is told, intuition is pointless – roll over and go back to sleep.

    This is the enemy of progress, not religion. Religion has no quarrel with science! None at all! It is science which is holding itself up! These scientists’ intuitive senses are screaming at them – it’s designed, you fool, it’s designed! And they just dismiss it. They dimiss their own sentiment. It’s incredible, just incredible that they try to study nature while ignoring their natural senses. They won’t trust their own feelings. Small wonder if they attach no significance to the sentiments of the religious. To them no sentiment ahs value. So how can they make progress, using only one leg, and only one arm? Words fail me. I am so tired of hearing people trying to explain away design. Let them design something equivalent then! Anything at all! But they never can- find me one design which was arrived at by chance. Just one, in any field. One book which was written by chance. A man who walked from one town to another, eyes shut, by chance. Even walked to his town centre, eyes shut, by chance. As you say, each step may be correct without having to try all steps. But the odds against are vast, vast, vast. And the odds against grow greater with every step, not less! All this random theory – it’s nonsense, it’s just silly. It immediately divorces a person from reality, from their own senses. What nanotech motor did we design, compared to the 30,000 atoms of the ATP synthase, a reversible electrical, chemical and rotational motor and generator combined? A crude flap on a crude stick with a massive battery attached. It’s just a joke.

    If we ask what other faculties man has, we find he has a mystical sense, whose results have been recorded and theories explored through religion. There is a certainty about the religious because these experiences arise from an intuitive understanding. Religions have been as different as languages, because they are aiming towards a concept that is vast in scope and using a different sense, a natural sense, one which seems to have been present from the beginning, and was even present in the Neandertal, a different species altogether.

    But you can’t dismiss people as hopeless just because they are certain about their idea of God! People are certain that their kids are the best, their parents were the best, their job is the best (for them), their hometown has the sweetest memeories, their partner is the best, their own face i s the one they feel most comfortable with, their own voice the one which they prefer.. this is a human thing, resulting from imprinting. None of these ideas have even the faintest truth behind them. How can everyone’s kids be the best, out of a billion children? We don’t want the best, or else we would all be trading kids. We want what is OURS. For you, your beliefs are the best! But I can’t just dismiss you as hopelss if they don’t align with mine. Someone yesterday wrote off 400,000 kids in Belarus and Ukraine as “a few chernobyl kids. the price worth paying for nuclear power”. Ok, he’s hopeless, let’s face it.. but I wouldn’t consider him a progressive part of the human race any more than the champions of eugenics. Alright, so some people are hopeless, but not because of their certainty – only due to their callous disregard for others. We can do without these creeps.

    Those who claim that mathematics can bring us to the truth of religion should look at the chemistry and electrical dynamics of proteins, or the mechanics of black holes and quasars, or of quantum physics, and explain – if we struggle to arrive at a solid foundation which can then explain all the successive phenomena arising from it, in any of these areas – why do they think we will somehow be able to fully explore an even more complex field of Universal intelligence, whose very nature, at the moment, nobody can even agree on, and some claim does not even exist! We still don’t understand gravity, but we rely on our instinct and our senses to negotiate it. We never dismiss these skills because they are not based on equations.

    If anything, this gives value to the idea that there must be some other, natural, sense in man capable to cut to the essential truth of things without going through the laborious route of the intellect. The natural world is already an example of this in all the other directions. If a bird tried to calculate all the aerodynamics of its actions it would never leave the ground! Some of the larger birds spend weeks trying to fly and seem fearful after many failures – but they never give up! The ant’s tiny brain is still able to produce a marvellous social order without poverty, suffering and inequality in its own society.

    If we are going to rely always on the intellect, which explores its curiosities and deals in speculations, and plans for a few weeks or months or at the most a year in advance, always in a laborious and incremental way, and often mnistaken, and always arguing, arguing, arguing its case – we are always going to be subject to unforeseen crises. We have to develop a more valuable sense in its infancy now, but there nevertheless. Otherwise, despite our improved brain and biology, we declare man to remain inferior to the natural world in every way and mroe liable to calamity now than even ten thousand years ago.

    Seeing the extreme order which is behind the natural world, of which we are part, how can it be that the most complex biological machinery is also the most useless, incapable and even self-destructive? It means nature rises to a certain point and then becomes a failure. I think this idea must arise from a mind which is somehow already divorced from its own nature, orphaned somehow genetically, and has already given up, and tries to make its own laws and do whatever it pleases, to ignore and spite a Universe for which it no longer feels any sympathy. This ignores all the intuitive knowledge, assembled as best as we have been able to do so far, in religion, which tries to remind man of a destiny more suited to his nature – a living being trying through fits and starts, to enlarge a divine spark within. I think no such person can ever be called hopeless..!

  4. shajanm says:

    Dear Iain, thanks for the great work you are doing here. Evolution of complexity through natural selection of random genetic changes is not a real scientific explanation. It is only a re-statement of known facts, packaged to look like an explanation. But I believe this is still an improvement from any explanation involving a supernatural designer. Unfortunately there is no third choice.

    I think even materialists (at least the more sensible among them) are frankly puzzled by complexity in nature and the absurdity of claiming all this emerged through cumulative random changes. But they are convinced by another fact: Such complexity has indeed evolved! It is real and observable – and it appears that any kind of explanation for this fact must involve randomness.

    What other explanation is conceivable? Where is the evidence for the Life force? If there is an intelligence what is its source and how does it operate?

    The answer may not come from the science lab, but from a correct understanding of the structure of our own thinking. Science of evolution is unique because it is the case of life studying itself. Questions such as ‘what exactly is scientific knowledge?’ need to be asked and answered in the light of the only certainty about life: Evolution.

  5. biochemist says:

    Ever heard of a process called “gene duplication”? This is one of the main driving forces of evolution (next to recombination and mutation). It explains for example why titin mostly consists of two types of domains (type I (fibronectin type III domain; 132 copies) and type II (immunoglobulin domain; 112 copies)) and why so many proteins with distinct functions have a high degree of similarity in their fold, amino acid sequence and DNA sequence. If every amino acid had to be randomly mutated, your calculations might make any sense, but this is not the only process involved. Furthermore, the whole point of evolution theory is that not every combination of mutations has to be made, but successful mutations are selected and spread through the population (because of survival of the fittest). If you’re still in doubt, consider that the most essential machinery for life (metabolic enzymes that convert sugar in to energy) are conserved from bacteria to mammals and that chimpanzees are for 99% genetically identical to humans…

    • Naturally, I’m aware of the standard theories, but these were thought up before the complexity of proteins became apparent, or thought up as imaginary devices to waft the real problems away. Titin is indeed a molecule of recurrent forms, but you have to remember that even tiny variations in the design lead to terrible, incapacitating conditions. It is strange to see the insurmountable complications of huge molecule size wafted away as mere duplications, but this is exactly the mental process needed to keep the original theory intact – random nonsense assembles itself into mighty, intricate machines (titin is over 3,000,000 daltons).

      The problem is really one of conception. The idea that a protein does a certain task and therefore must be a binary situation of success or failure completely fails to take into account the complexity required for it to function at all. It is all very well pointing to one or two elements in the finished product and retroactively imagining them as gradually arrived at or somehow multiplying themselves and leaving it at that, but this doesn’t work. It fails completely. You cannot assemble any working protein step by step unless the entire mechanism is taken into account. This is why the fundamental design of each one changes so little between species, and even then, changes due to specific, essential needs.

      It arrives, somehow, as a whole. The ribosome functions as a whole; it is even geared up for the existing codon mapping and it cannot partly function in incremental pieces. Every protein and every machine examined so far has the same weird characteristic: it functions as a whole or not at all. Little thermos flasks in which proteins can form, automated scissors for destroying unwanted components, checksum counters moving at terrific speeds, spring loaded injectors, folding magnets.. the wonders are endless. This irreducible nature is the whole cause of disease. There is no use having half of a component or a third or 80% or even 99% correct – each one functions as a whole or not at all. So the irreducible complexity which formerly was attached to, say the eye, is now with deeper knowledge attached to the proteins from which they are formed. And with still deeper knowledge, the machinery which forms the proteins.

      The fractal nature of this continual irreducibility is lost when the mind analysing it can only visualise in small sections. The moment the mind appreciates the whole at any particular level the scale of the problems in design become overwhelming. Beyond all this, Jean Claude Perez, the HIV researcher, has shown in a peer-reviewed paper that the amino acids across the whole genome are arranged according to the golden ratio, which means they could never occur by chance. This occurs across different genomes, not only man’s. The consistency is better than one part in a thousand and acts as a checksum across the whole system: which is why Barbara McLintock was able to show that corn could regenerate entire sections of missing DNA. This was so unexpected that scientists ridiculed her but 20 years later after having been insulted for so long by science, she won the Nobel Prize for her work.

      The kind of minds dismissing “design” are so used to dealing in microcosms of microcosms and seem unable to take in a whole system which dwarfs in complexity and precision and speed anything man could even dream of assembling. The idea that all this unfolding order assembled itself out of disorder seems more bizarre by the day.

      As for the assembly of proteins, I have just been quoted $50,000 to get one model of a working hemoglobin molecule built over six months! And this is after already knowing the design! If this doesn’t show you the complexity of the electrical forces involved, and how it swamps the capacity of man’s incremental intellect, I don’t really know what will. The issue of protein design is so complex I am not convinced humans will ever really understand them. It seems like a wall of mighty engineering that can’t be surmounted.

  6. biochemist says:

    You don’t have to tell me about the complexity and multitude of functions of proteins, I’m a protein scientist myself. First of all, gene duplication and recombination aren’t “imagenary devices to waft the real problems away”. These are biochemical mechanisms already discovered in the 70ies of which the molecular details are nowadays very well characterized. For your example titin, the molecular function is a spring that holds the moving parts of muscles together. You can imagine that a fruitfly has different muscles that might not need as long springs as humans. Evolutionary advantage towards bigger muscles for bigger organisms likely gave an advantage to individuals with more domain copies in their titin gene. About your statement that it must function as a whole or not at all, how about the hundreds of other proteins that contain the same types of domains of which titin is made up for >95%? With completely different functions, like the antibodies in your blood? Proteins are quite reluctant to a lot of mutations, so your statement that a component has to function for 100% and not 60 or 80 or 90 is completely wrong. A lot of homologous proteins in different species have indeed more than 50% sequence divergence without losing their function and specificity. The SNP databank (single nucleotide polymorphisms) containing DNA mutations among humans already contained 52 million (!) SNPs in october 2011. With only 20.000 genes.

    Another thing about the space all the failed copies would need to fill; every organism (EVERY) on the planet can degrade proteins to its constituent amino acids for recycling purposes, so that’s maybe why we’re not living in seas of misfolded protein.

    For the ribosome, you may or may not know that this actually isn’t an enzyme, but a ribozyme (as the name suggests). This means its catalytic function is performed by the RNA molecules in the complex and not the proteins. Ribozymes have been shown to have other catalytic functions as well, leading to the RNA-world hypothesis (http://en.wikipedia.org/wiki/RNA_world_hypothesis). Proteins however had the evolutionary advantage of more diversity (4 vs. 20 building blocks), allowing a more diverge range of chemistry. This made protein synthesizing organisms able to live in different (more harsh) environments. Researchers have by random generation of RNA molecules even created ribozymes with entirely new catalytic functions (including the catalysis of their own synthesis). Remember, this is on a timescale of only years and without filling planets with failed copies. Another example is bacteria acquiring antibiotic resistance, also on a timescale of years or decades after the introduction of that (chemically often completely new) antibiotic. Or HIV building up resistance against all different sorts of treatments during an individuals life. Even tumorcells evolve by mutating normal membrane transporters to multidrug efflux pumps. Or a bacterium that by a single mutation in a common enzyme was able to degrade CFKs in a heavily polluted area, only a couple of years ago (vanneli et al., environmental microbiology, 1990). About the unsurmountability of protein engineering; in 2010 a completely new enzyme was built from scratch with a catalytic function that hasn’t been seen in any enzyme before (the Dies-Alders reaction if you’re interested, hence its name diels-aderase: Siegel et al., science, 2010). Even more, crowdsourcing via the protein folding game “foldit” resulted in modifications (designed by humans) that led to an 18-fold increase in catalytic activity (Eiben et al., nature biotechnology, 2012).

    Your arguments remind me of people claiming that something as complicated as an eye could never have formed by chance. Mathematical analysis showed that only a relatively small number of steps was needed to go from a bacterial light harvesting protein (bacteriorhodopsin) to the first light sensors in multicellular organisms, to primitive eyes in invertebrates and to the modern eyes we’re using at the moment. Just read the wikipedia on it if you’re interested (http://en.wikipedia.org/wiki/Evolution_of_the_eye). Evolution of proteins is even more imaginable since it actually happens in real-time in our labs, hospitals and bodies (drug resistance). Even a complex evolutionary step like the development of multicellularity has already been recreated in a lab (Ratcliff et al., PNAS 2012). A human being is likely genetically closer to a chimp than a chihuahua to a St. Bernard, though nobody seems to question the fact that they originate from the same ancestor. I think neglecting all the overwhelming evidence is ignorant and I hope you’re not surprised the scientific world disagrees with you.

    • I find all this circular logic very unconvincing, especially so when its aim is to wave away the problem of consciousness and make it into an unreliable, unplanned fluke. The idea that atoms would suddenly shape themselves into a very limited number of exceptional components, so disparate and so lacking in redundancy that they can be combined and recombined in endless ways, and that these noteworthy molecules would then assemble – absent any particular motive power – into functioning machinery, and that this functioning machinery would keep generating errors by mistake until they form superbly crafted engines and data storage mechanisms, is more incredible by far than anything I write.

      The idea of random mutations is clearly a nonsense, since complicated configurations can remain static of hundreds of milliosn of years, as I point out elsewhere. The wave-it-away argument is that “oh, well, they were successful so they didn’t need to adapt”. but the same applies to every living form, and those who are unsuccessful don’t magically transmute into better forms, they die out. Therefore the whole random mutations turning into successful organisms from less successful ones defeats itself from the world go. It’s a nonsense, and I’m susprised you’re willing to put your name it.

      The evidence that the cells use ubiquitin to mark and disassemble malformed proteins should alert you to the obvious fact – that some intelligence is behind this. Or perhaps they just jumped up and decided of their own accord?

      Beyond all this, the DNA is a code – a language with its own rules and syntax, and one which creates a measurable effect when interpreted by reading devices. Random forces never create codes. Can you name any language or code that was not created by intelligence? These principles are so simple a child can grasp them, but it is the convoluted hall of mirrors constructed by the randomised materialists in which life – their own included – is an illusion, which should generate more criticism than my humble observations!

      As for a light sensitive opsin molecule somehow arriving in tandem with nerve routes and decoding mechanisms in the nervous system, all I need to do is refer you to the history of the research on opsin molecules. How many years did it take dedicated brains with intelligence to unravel it? And if you look at the schematic which I included in The Willing Pupil, you will be hard pressed, I guarantee, to comprehend the gated switches, chemical signallers, photon detectors and circuit diagrams in their entirety. This awkward fact tells you that whatever kind of consciousness is behind life, it is nothing whatever like the human model, which is only a subset, working millions of times slower and in more primitive way. If not, then it could grasp – in real time – all the activity in biology at once. It is floundering because it has no chance of so doing! Simple facts, simple conclusion.

  7. biochemist says:

    Again, I studied biochemistry so you don’t have to tell me about chemical signaling, light sensors, nerves, cells or any molecular or cellular biology. If you can’t give any counterarguments for all my examples than this is not a discussion anymore (I don’t consider calling the most broadly accepted scientific theory on this topic a “convoluted hall of mirrors” an argument). You’re right that most people can’t imagine exponential growth, but did it occur to you that replication of organisms is an exponential process? With bacterial replication times of 20 minutes, I’m sure you can do the maths for how long it takes for a single more succesful bacterium (say a 19 minute replication time) to overgrow a population of millions. (I know you like numbers). If you deny random mutations occur, you might as well claim that the earth is flat. They are seen and exploited on a daily basis in thousands of labs around the world. If you deny that random mutations can’t lead to new functionalities of proteins, I would like to refer to the abovementioned citations. If bacteria can evolve to have entirely new functions (CFK or antibiotic degradation) in years and single-cells can evolve to multicellular organisms in months, compare that to estimated age of life and the answer you’ll get is the biodiversity we have nowadays. Sure, the beginning of life is hard to unravel because it happened so long ago, but if we can all have evolved out of single-cell organisms, is it so hard to imagine that this first single-cell organism has been the result of random events too?

    Code is just a human definition and the numerous fallacies in human DNA (transposons, old virus genomes, enormous regions of non-coding DNA) clearly indicate that it isn’t designed by a particularly intelligent being… If ubiquitin is your proof against evolution, please…: “No ubiquitin and ubiquitination machinery are known to exist in prokaryotes. However, ubiquitin is believed to have descended from prokaryotic proteins similar to ThiS[4] or MoaD.[5] These prokaryotic proteins, despite having little sequence identity (ThiS has 14% identity to ubiquitin), share the same protein fold. These proteins also share sulfur chemistry with ubiquitin. MoaD, which is involved in molybdenum cofactor biosynthesis, interacts with MoeB, which acts like an E1 ubiquitin-activating enzyme for MoaD, strengthening the link between these prokaryotic proteins and the ubiquitin system. A similar system exists for ThiS, with its E1-like enzyme ThiF. It is also believed that the Saccharomyces cerevisiae protein Urm-1, a ubiquitin-related modifier, is a “molecular fossil” that connects the evolutionary relation with the prokaryotic ubiquitin-like molecules and ubiquitin.” 2 mouseclicks away on wikipedia…

    The fact that something is hard to unravel has nothing to do with how hard it is to develop. Unlike for regular engineering, biochemistry happens at scales smaller than the wavelength of light so a lot of very indirect techniques are necessary to see what is happening, but once the structure of bacteriorhodopsin was elucidated, it already confirmed half of the hypotheses.

    • Ok, in that case, please just build for me one working hemoglobin molecule, on any scale you like which is handle-able by human hands to show its activity, which can be used for a teaching aid – any colours, any rotational device you want. Build it in any way you like, but make it accurately reflect the component parts, its oxygenated and non-oxygenated states and show how CO2 is managed.

      You can take 6 months if you want, use any materials you like – the design is already precisely mapped out in the DNA, all the sequences of amino acids are known, all the charges of the atoms are known, all the rotational points are known and its incremental affinity for oxygen is understood. The design is there, please just build one so it works.

      So long as I have it by the end of October I will be delighted, as it will be given as a teaching aid for my late father’s hemotology laboratory in Toronto.

      I will of course make sure your name is engraved on the plinth and I will be happy to pay your reasonable expenses.

      Many thanks.

  8. biochemist says:

    Haha good one, if I would have been a craftsman I might have been able to help you. I could make you a recombinant one on the actual scale if you wanted, but that wouldn’t help you for teaching. If you’re really interested and happen to be on linked-in, there is a guy on the “structural biology group” that recently was talking about next-gen teaching tools like that. This however has nothing to do with the entire discussion before, again you fail to counterargument anything you say… But that’s ok because I can imagine it is quite hard to find arguments for intelligent design that match up against evolution.

    If your point is that it is all so perfectly functioning, consider that humans have been able to tweek DNA polymerase (another beautiful and seemingly perfect protein) to have 10x higher activity and 6x lower error rates as the ones found in nature (http://www.neb.com/nebecomm/products/productm0530.asp). And as I mentioned before, humans have been able to design a protein from scratch, only using basic chemical knowledge (not an already existing protein scaffold) to design an enzyme with a function that hasn’t been found in nature before (consider reading my suggested papers and links, you might learn something from it).

    • OK, all I want is one molecule.. only one. You don’t need to be a craftsman to build it, surely, or intelligence.. since neither was involved in its design or build so far.

      It’s a shame because I can see I’m going to have to do it myself. And once I do it, people will say how easy it must have been. But how strange.. a random product that takes no intelligence or craftsmanship to build at a rate of thousands per second, but which cannot be built by us in months without intelligence and craftsmanship!

      Anyone else with the smarts to finish this very easy task?

  9. Enthusiastic exchanges like these are why I stay subscribed to comment threads. Although some of the science here is beyond my immediate grasp, it sounds like the core disagreement is over randomness vs. design. In other words, “it just happened” versus “some intelligence made it happen.”

    Truth is, neither side has the complete answer. If it just happened randomly, and we don’t know why beyond that, then we can only speak with certainty about the results – not the cause. Randomness is a veil beyond which our mind can’t go. It just… IS. But if some intelligence made it happen, then we must wonder, “What designed the designer?” That takes the questions to the next logical level: what caused the cause? And what is the nature of that intelligence? Was it Zeus? Improbable. Was it Shiva? Unlikely. Or was it something completely indescribable? And we end up with another veil our human minds cannot assail.

    I don’t have the answer, but I suggest that attributing these developments to randomness or god are both equally indescribable solutions. Maybe randomness = god, since it is so beyond our comprehension that we can’t really say much about it other than “it makes things happen” – which sounds a lot like the theist position.

    As with most theist/atheist arguments, both sides make an inference from observation, and then stake out that inference as unassailable factual territory. It’s unfortunate, because we have two sides with so much intellect and insight to contribute to finding what I come back to this site for: the common ground between science and religion.

    Surely we all agree that we don’t know exactly how these marvelous forms came into being, and we all agree that it is a question worth exploring. Maybe we could work together as explorers of questions we all find interesting instead of dividng into groups which claim to have the answers already.

    Anyway, thank you again for providing a forum for these kinds of discussions! I hope we continue to get more perspectives on these questions, becuase they are always thought-provoking.

  10. Biochemist says:

    Very common symptons when engaged in a discussion you can’t win on the basis of arguments are changing subject, trying to reverse the burden of proof or asking something that a discussion partner can never provide. Just watch any FOX news discussion with a person that is smart but a bit too liberal for FOX’s taste. You show all the signs of someone that can’t win an argument based on reason. My suggestion is to remove all the fallacies from your article, like the calculations based on wrong premises and the total neglectance of the mechanisms of evolution. If not, you are indeed nothing better than pope Urban VIII or Bill O’Reilly, desperately holding to their believes and spreading propaganda against overwhelming scientific evidence.

    Why we can’t build chemical molecules (like proteins) with all their properties on a macro-scale: a lot of chemical properties like bond lengths, angles and dihedrals, as well as electrostatic interactions, are based on quantum mechanics, electrostatics and electrostodynamics. Forces are generally too high and non-linear to accurately simulate them with springs or magnets. This has nothing to do with how hard it is to design, those are just CHEMICAL properties, not even biological ones. We can simulate them in computers, what is indeed done all the time in science.

  11. If I may correct you, the word is beliefs and not believes, but if you can let me know where any assumptions are mathematically incorrect I would happily correct them.

    Also, as far as the hemoglobin molecule goes, the reason that a model is so difficult to build or even approximate is because we do not completely understand how it works. If we are looking at any situation and cannot understand how it works, how can we say we understand the mechanisms by which it has arisen? For your information, I have been quoted $50,000 for a post grad to build one molecule, over a six month period. The difficulty, they say, is because the device itself is so complicated and finely balanced. And, may I add, they say nobody yet fully understands exactlyhow it works.

    This rather contradicts the “wave it all away” approach. In fact you contradict it yourself: if the forces at that level are so complicated, how is it possible for any functioning machine to arise, especially when the machine requires so many components, and all those components require consistent manufacture, and those manufacturing machines require fuel, which itself requires assembly? We can’t solve these problems by waving them away. The design itself may be the hardest part, but that has already been done for us! And we still say it’s too difficult for us to understand! And if you think that a hemoglobin molecule is difficult, would you care to build a ribosome which assembles itself?

    It is all very well saying we have simulations on a computer, but computer animations are relatively easy to create because any difficulties can be programmed out. I can design a bridge which works upside down, on a computer, with cars racing along its underside, or even houses on roller skates, and send them flying through the CGI air, if I want, because I decide on the rules. In the real world, things are a lot more complicated, and in the molecular world, far more complex still: any molecular machine turning, spinning or travelling in the molecular world which suddenly loses its motive power, stops within a thousandth of a second. All these laws of physics are known to us. So where is the problem? I was not asking for a molecule to be built in real time or work in real time, but which simply snaps open and shut in the same way the actual molecule does.

    Moving anything in the molecular world is a hundred times more difficult than in our world, like walking in a hurricane, or swimming in a sea of molasses. And yet this molecular machinery has its own energy supply, its own repair mechanisms and even other machines which create the fuel required, and other machines which build those machines, and all of which are beset by the same adverse circumstances that we use to excuse ourselves from creating a duplicate!

    Each and every piece of machinery on the molecular scale acts apparently with a specific built-in purpose – that is, fulfilling a task that a highly intelligent human being cannot fulfil even if the problems were scaled up in size so that all the molecular difficulties of motion are eliminated, and slowed down by factors of millions of times so as to allow the human intellect to grasp the problems as they arise one by one. And these purposes are discreet: the chaperonin chamber has a swivelling lid which opens up to allow a protein string inside so it can form in peace.

    There are other molecules which actually decide if a cell should die, and once the deicsion is made – based on sound reasons, for example uncontrolled growth – release other machines which look like scissors and snip the DNA into tiny pieces working millions of times a second, targeting the DNA, not acting randomly – after first disassembling all the cell reproductive machinery. How can any sane person claim this all happens by accident? It’s the most highly organised, highly tuned and highly efficient set of systems known to man. Nothing man can design works anything like as well, nowhere near it. It’s completely off our scale of understanding.

    The inability of any engineer to build a single working molecule whose design is already known, should be adequate proof of this. But when common sense naturally concludes the pieces have been expertly configured, you hear the following well thought out rebuttal: . You’ll pardon me for saying so, but that is the most unscientific approach I have ever seen in my life. It’s a scandal that this wave-away approach passes for knowledge. It’s a disgrace, I would say, especially when natural selection – that tired one-liner which is supposed to explain every question under the sun – has already been proven, by a study of gene sweeps in Oct 2010 SciAm, to only act in cases where a single environmental pressure has remained constant for tens of thousands of years. “A rare occurrence,” as the researchers sheepishly admit. It is not a creative process of any structure at all, but only a fine sanding after the fact.

    As for scientific evidence, if you can let me know where anything I have said contradicts scientific evidence, as I attempt to draw all my information from scientific sources, I will happily correct it.

  12. Biochemist says:

    Excuse me if I make language mistakes, I’m not a native English speaker. The point I already made before is that you assume in your calculations that all possible combinations of mutations have to be tried. The whole point of evolution is that this is not how it works. Succesful mutations are accumulated, resulting in new enzyme functionalities and bacterial strains with antibiotic resistance on timescales of years (antibiotics only approved in 2000 are now already starting to become obsolete because of new resistance mechanisms “evolving”). If you accumulate succesful mutations, the mathematics get completely different. Then there are the mechanisms of recombination and gene duplication I also mentioned before, making evolution even more complicated and fast. The wave-it-all-away approach you despise, you are using yourself. The argument that we can’t remake things (on a completely different scale) doesn’t go, because it doesn’t relate to how hard it is to evolve proteins to acquire certain functions. Again, single mutations can lead to new protein functionalities, which will be kept if they are succesful. As I said before, it is indeed still not clear how the first life on earth came to be and developed, but that’s what science is trying to figure out. I gave you examples of how it isn’t so hard to imagine, with ribozymes that catalyze their own synthesis and also performing other reactions, or the evolution of multicellularity from single cellular microorganisms. These even already started having differentiated cells with specific functions, performing appoptosis (programmed cell death) if this was advantageous for the newly evolved organism. Apoptosis doesn’t have any benefit for single cell organisms, so it is quite remarkable how seemingly complex systems can evolve on very fast timescales. If you follow phylogenetic trees you see more complex machinery coming up in more complex organisms. The protein complexes involved in transcriptional regulation for example have many more components in humans than in yeast, but organisms of different complexity in between also have complexes with homologs that seem to come up 1 by 1 as the organisms get more complex. Bacterial ribosomes are smaller and have a completely different molecular architecture as those in humans, showing that something as complicated as the ribosome might even have evolved twice (or has differentiated in a very eary stadium). At the same time, enzymes in the glycolytic pathways are conserved even from prokaryotes to humans, showing how early in evolution these complexes evolved, being essential for energy supply. Ion channels in bacteria look the same as in human nerves, even though they serve a completely different purpose in the context of the organism. This is yet another layer of complexity for evolution, proteins serving different functions in the context of the organism. I completely agree with you if you say that the beginning of evolution is still unclear and riddling, but the quasi-scientific calculations you’re making are just completely wrong and I think you’re intelligent enough to see that. It is a matter of opinion whether you think the vast amount of genetic data and knowledge about molecular biology supports or disproves evolution, but I would prefer the former. The fact that the same protein domains are present in all different sorts of proteins and complexes with completely different functionalities for example, doesn’t disprove evolution in my opinion but rather supports it (having mechanisms like gene duplication and recombination in mind).

  13. I do understand the idea about accumulating successes. The problem is that this idea was first presented in the mid 19th century, when it was assumed that the core elements of biology only had a few possible states and therefore any given state was reasonably easy to arrive at.

    The scale of the problem became apparent when it turned out that the roots of biology – proteins, cells, DNA, and all the mechanisms we’ve covered in detail elsewhere – were paradoxically far, far more complicated, and working millions of times quicker, than the life forms which they were constructing! The human intellect, for example, reacts in 1/8th of a second, but these machines can work at a rate of ten million times per second – that’s a difference of 1.25 million times, but when you realise there are trillions of such devices in the body, all of which interact, you understand it is impossible to conceive the activity in real time or anything like it. This is why the drugs companies are having such problems now with their research, especially into the brain. If you understand the implications of a single process and then have to follow it through to its final conclusion by considering, one by one, all the other processes which follow on – or which could potentially follow on from it – it would take, in terms of human time, thousands of years! It’s an absurd differential to try and get around by reasoning that it really isn’t all that complicated.

    The first theories about protein formations were a mess because it was realised that to try every possible folding state would take longer than the age of the universe, when in fact these proteins were folding in hundredths or even thousandths of a second. It was then proposed that the order of the amino acids determined an automatic folding process which was already perfectly aligned to achieve maximum stability – but this in turn meant that the designs stored in the DNA were even more remarkable. How could they possibly have arrived at this precise, exclusive arrangement out of an unimaginably large set of possibilities, in tandem with every other 2-d design within the DNA?

    As for the evolution of bacteria, of course, it’s obvious that this has taken place. What is never explained is why the organisms we are using to innoculate do not evolve to become more successful and more powerful than before! Why is it that evolution always reaches greater levels of efficiency, in some cases, even changing the entire design to suit conditions? There must be something we don’t understand, or we would just force our tools to evolve at the same rate – or at a greater rate, since we are controlling the laboratories. Instead, people say it is a problem we don’t know how to overcome. So evolution is not something which just happens on its own – something else is involved, and we don’t know what it its, or else we could take advantage of it.

    The puzzle gets more complicated when we try and evoke mutations. Hundreds of thousands of generations of fruitflies have been mutated deliberately, and nothing is ever achieved other than sickly, quick dying, or less robust models. More importantly, accelerated mutations never make a fruitfly anything other than a fruitfly. Breeding of dogs for thousands of years only ever creates dogs. We never see one species turn into another, because we don’t understand how it happens. What underlying design considerations allow bacteria to actually change their mode of attack, making the new machinery and components, to overrule defences which worked perfectly only a decade or two ago? Clearly another force is at work, but we can’t find it, because nobody is looking for it.

    As I again say, if my quasi calculations are wrong, show me, and I’ll correct them. But the argument of irreducible complexity, which used to be applied to organisms as a whole, now seems to apply to the proteins, the engines, the fuel sources, the transporters, the error correctors, the assemblers and disassemblers, the sentinels, the repair mechanisms and so on. It applies at every level of creation from atoms to amino acids, amino acids to proteins, and even proteins to living beings. Because if you put all the proteins in one place, a human being does not automatically form! The information about how cells become specialised is not known. The storage areas for essential machines like the ribosome are not known.

    And of all this mechanical stuff, none of it works unless it is all aligned: just because the first sequence of say 10 amino acids is precisely right in the large hemoglobin, it does not follow that these can evolve apart from the later ones, because due to protein folding, these first ten have to match exactly with other ones much further on down each of the four chains of molecules which make up the whole machine. Like an origami swan, in which you can’t just fold randomly and keep the good looking folds because they only have meaning in relation to later ones, even the final ones. You can’t start out with a gearbox, and say it is successful apart from the rest of the machinery which has to be added on top, or start with an engine which you keep because it’s such a great one, before you have the fuel and the spark plugs and the transmission, which all depend on the nature of the final vehicle, not the other way around. Each component is subservient to the overall design, and this is standard in all successful engineering. Any designer will agree, you must start with the overall design and work down to the components it needs. But in the field of biology, all of these principles are abandoned, in a medium which needs them more than any other.

    All of which means that the accumulation of successes must be done in jumps – and the mathematical improbability of any of these single jumps happening by chance is what I try to show, by maths which anyone can follow if they want, but which, as I say, may be incorrect in some regard, in which case, I am keen to know where, so I can fix them!

    I do appreciate your comments, but biologists tend to criticise the overall approach of an essay – maybe my style or images or a particular calculation – without ever once dealing with the fundamental point, which is, that all these incremental steps in biology are discrete, complete, and highly, highly specialised, and highly interdependent on other steps which are all equally improbable in their own way, and all highly specialised as well. Yes, they happened, clearly they did: but “evolution” has come to mean “it just happened by fluke – get over it”. Now, that may have been good enough 150 years ago, but to my mind, that isn’t good enough today.

  14. Biochemist says:

    For your question about bacteria, the answer almost literally is natural selection. If one bacterium has a mutation that allows it to survive a new antibiotic, all the others will die and the resistant one will multiplicate and soon the whole population is resistance. That is not even taking into account horizontal gene transfer, which even speeds up evolution for bacteria. The answer to my riddle before is by the way less than 3 days, before a single bacterium outgrows a population of 1 million if it has a mutation that causes it to have a 19 minute replication time instead of 20 (solve 2^(x/19)=1000.000*2^(x/20) for the amount of minutes). When evolutionary pressures get higher, like with antibiotics, it will be even faster because unsuccesful bacteria will be wiped out.

    Why we haven’t created a sort of superfruitfly is also quite obvious; the genetic analyses of these flies mainly aims to elucidate gene function by knocking out genes. This obviously often leads to miserable fruitflies, like the wingless ones after which WNT signaling is named. It is quite hard to improve an organism by removing functionalities instead of adding.

    Your calculations are wrong because they are based on the wrong assumptions. For the third time, evolution doesn’t work by systematically screening all possibilities but other mechanisms are at work speeding up the process, I think I have mentioned them often enough now. Therefore, the calculation itself doesn’t relate to the problem (the pace at which evolution could occur).

    Hemoglobin performs exactly the same function in humans, chimps, dogs, in all vertebrates in fact. However, if you look at their amino acid sequences, there is still a lot of variation, indicating that your argument is wrong. Just try performing a BLAST search of the hemoglobin sequence and allign the results, you’ll see what I mean. Funny thing is that the top hits are all apes and monkeys. Coincidence? Not likely, this goes for pretty much every human protein that you will BLAST search. Maybe that’s why I don’t know any creationist in the biochemistry department I’m in now (we do BLAST searches quite often). Even in human hemoglobin 155 natural variants are already annotated in the alpha subunit, whilst it only has 142 amino acids. (http://www.uniprot.org/uniprot/P69905) This means that almost every residue can be mutated and is mutated in different parts of the world, and this is yet only for the genomes that are already sequenced. Co-evolution of complexes is also a well documented phenomenon, seen in many protein complexes and homologues.

    The definition of a species is that it can have fertile offspring (horses and donkeys can have offspring, but those are infertile). When two species evolve away from each other too much, the discrepancies in their molecular machineries are too big to have (fertile) offspring. I would be surprised if a St. Bernhard and a Chihuahua can have fertile offspring, even when using IVF.

    Since a big part of the molecular machinery present in humans is already present in single cellular yeast, I think a lot of evolution happened on this level where it is much faster. After multicellularity was achieved, organisms didn’t need to evolve any of the basic molecular machinery needed to keep a cell alive, but evolution happened more on a specialization of cell-types level, using epigenetic mechanisms as another level at which evolution can occur. Exceptions are ofcourse things like different keratin genes that give rise to white hairs in polar bears and brown in grizzlies.

    I would really urge you to read this very recent (free) paper in Plos One: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035454 It gives some hints about how the very first stages of life may have evolved, if you’re interested.

    Whilst the amount of hints, clues and evidences for evolution are too much to summarize here, the only real argument for intelligent design is that it is all so complicated and seemingly perfect. This doesn’t compete with evolution theory, but mainly shows that it is just hard to comprehend the timescales at which evolution is happening.

    • the simple way, then, to evolve a fruitfly to a super fruitfly must be to subject it to damaging environments and accelerate its evolution. And this is where something strange happens: when fruitflies were exposed to DDT, the result was that in only a few generations – I don’t recall how many – strongly directional changes occurred that did not occur during other fruitfly research.

      The result was that they very quickly produced 400% more of a chemical which conferred resistance to DDT. Nobody could explain how this could happen in such a directed way. As Charles Darwin himself said, it would not be scientific to ascribe it to chance, because evolution always moves upward to greater complexity, whereas chance never moves in a single direction. In the mad rush to reduce everything to molecules and desperately strip meaning from their world, scientists have jettisoned even this one small last fragment of common sense. yes, hemoglobin varies between species – there is even an inexplicable change in fetal hemoglobin which compensates for the difference in oxygen intake; this variation is eliminated only when the child is born. How? “Oh, it was just random, natural selection, nothing more to learn”. There are differences in hemoglobin between species, but you will see that the basic design does not change. The basic purpose does not change: distribute oxygen in a liquid, by gaining it only under high pressure: but release it easily, carrying CO2 away in exchange. You still have spring loaded iron platforms which magnetise oxygen, and which carry Co2 as a waste product. The idea is always the same.

      How is it that with all these random mutations, hemoglobin doesn’t one day do something completely different, like, become a scaffolding protein, or a lipid? Because it isn’t designed that way. It carries out a specific purpose. The same princple holds true for each and every biological machine; you can’t get round it. If this were not true, there would be no point in studying biology at all, because there would be nothing to study! Nothing would be fixed, and no rules would apply, other than, “what happens, happens.. no reason, nothing to learn.” The expectation of finding natural laws which govern these systems is behind all biological research; with it, there would be no point in studying it other than idle curiosity or filling in empty time.

      If you are going to build a theory on chance alone – which is what natural selection is – dressed up of course as a purposeful engine, but in fact being nothing more than the result of random mutations as the engine of change – then you must also accept the mathematics of chance. You can’t simply take the final layer of logic – a successful change – and call it proof. Proof of what? proof that it happened? Of course, but is that all the theory is? Whatever happened, surely happened? That’s an utterly pointless philosophy. You have to start with the problem. Here is a fruitfly with perhaps 14,000 genes, and 165m base pairs. Why should a specific mechanism suddenly vary to suit the environment, when the variation is supposedly completely independent of the environment – being purely chance, retained only through survival – and when all others stay the same? If you are going to assign random causes, which modern biology demands, then you can easily work out the chances of a specific gene or collection of genes which manufacture this protective chemical wandering in the way you want. But it simply doesn’t work; the figures are absurdly unlikely. And yet they happen. Dressing it up in a lab coat doesn’t help: there is nothing behind this theory, nothing at all.

      But, seeing the rapid changes, and desiring to fit the crime to the suspect, scientists simply say, “you see? we were right!” When the result means nothing of the sort. Take a machine with 165m possible components, each of which according to theory can change at any time in 3 ways, and you firstly have nearly 500m different changes every generation, but to get a dozen or so in succession which all collaborate, the odds are fantastic; and yet it happens in the lab. To get such the vast number of changes required means that the whole mechanism must be inherently unstable, but biology relies on consistency. Where are the 400% variations in wings? Where are the 400% variations in numbers of legs? Where is the 400% variation in age, or in number of eyes, or antennae length? There weren’t any.

      Which is why long term species such as insects, which remain equipped and armed in much the same way as 400m years ago – that is, they remain what they were, more or less – disprove the idly wandering gene theory. Unless you are proposing that an ant should be able to turn into a leopard or an elephant, given enough time. But this is nonsense, completely unscientific. This fatuous superstition has crimped science, shut it into a box, and made it inapplicable to far more challenging areas such as consciousness; it’s time people saw it for what it is – it’s a fraud, it’s unsound, and unscientific. It is backwards and reductionist, when it should be advancing in complexity along with other mental concepts.

      But I don’t have a lab coat or a degree – I am simply armed with common sense. So of course, it is easy to dismiss my reasoning as the product of a lack of awareness of spans of time. In fact, the universe is quite a manageable age in seconds, something like 10 to the power 17 altogether – even a trivial number when compared to the exponentially complex mutations of biology.

      It would be better to argue with those who spent their whole lives wrestling with these problems – the scientists themselves. Here are their opinions:

      “Scientists don’t have a clue how life began.. geologists, chemists, astronomers and biologists are as stumped as ever by the riddle of life.”

      (..Science journalist John Horgan, February 28, 2011 (former senior writer at Scientific American) after the Origins Project Conference, Arizona State University.)

      “We have no evidence at all that the tree of life is a reality”

      (..Eric Bapteste, evolutionary biologist, Pierre and Marie Curie University, Paris)

      “The tree-of-life concept was absolutely central to Darwin’s thinking, equal in importance to natural selection. Without it the theory of evolution would never have happened.”

      (..W. Ford Doolittle, biologist, Dalhousie University, Halifax)

      “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. It is clear that the Darwinian tree is no longer an adequate description of how evolution in general works.”

      (..Biologist Michael Syvanen of the University of California)

      “The tree of life is politely buried, we all know that. What’s less accepted is that our whole fundamental view of biology needs to change.. biology is vastly more complex than we thought.”

      (..Michael Rose, evolutionary biologist, University of California, Irvine)

  15. biochemist says:

    To get back to your questions about hemoglobin, there are indeed proteins with different functions that seem to have evolved from the same ancestor as hemoglobin. Myoglobin is the oxygen-binding protein in muscle and doesn’t have the cooperative binding mechanism hemoglobin has because it is monomeric. It doesn’t need it since it isn’t in the blood flow where different levels of oxygen/CO2 saturation in different parts of the body exist. It shines a light on how hemoglobin might have evolved to become multimeric by acquiring mutations in the multimerization-surface, leading to the cooperative binding by allosteric effects, which would have been advantageous when organisms started becoming bigger and depending more on their circulatory system. But still, myoglobin is an oxygen-binder with a heme group, you might argue. What about phycocyanin, a pigment-protein complex from the light-harvesting phycobiliprotein family. Also a globin fold, but clearly with a different function, that is already present in the evolutionary ancient cyanobacteria. The point is, your reasoning goes the wrong way. You shouldn’t ask yourself why the function is everywhere (in vertebrates at least) the same and not changing. The answer is that if you loose hemoglobin functionality because of a mutation, you won’t be born alive. The question you should ask is: where did it come from? This is the question phylogenetic scientists ask themselves and for the majority of protein machinery, there is explanations how they might have evolved from machinery that is already present in single-cellular organisms. They again evolve at a much faster pace than vertebrates, so on that level, it is indeed not so strange that complicated machinery may have evolved relatively fast. So indeed, what happens, happens (I don’t think anyone can deny such a statement, just like grass is grass). But we DO need to learn how it all came to be, if we really want to understand (molecular) biology, evolution or the mechanisms of how bacteria acquire antibiotic resistance.

    Indeed, evolution theory is built on statistics. So is quantum mechanics, thermodynamics and pretty much all social and behavioral science. I wouldn’t call economy science, but governments base their policy on statistical models of the economy. This is how science works. You might not know, but there is a whole field involved in the mathematics and statistics of evolution: mathematical/theoretical biology. You can read a very accessible introduction about it on wikipedia: http://en.wikipedia.org/wiki/Biomathematics

    Your fly example is also explained directly by evolutionary theory. If you’re asking why there aren’t any variants with more eyes or bigger wings, it is because the applied evolutionary preasure was that of the harmful DDT, so organisms with an advantage against that would be more succesful, more fit if you will. Because in other fruitfly research this evolutionary preasure was absent, it wasn’t advantageous to have better resistance against DDT. Wingsize and number of eyes had already been optimized by millenia of evolution for this specific species. If there was already a mechanism that conferred a low level of resistance to DDT, the changes might even have been epigenetic, but I don’t know the details of the study so this is speculative.

    If you call reductionism unscientific, than I wonder if you know what science is. Apart from high-throughput -omics studies in the systems biology field, pretty much all molecular biology is based on and supports reductionist approaches.

    The tree of life is called wrong by scientists because in the early stages of evolution (the single-cellular stage if you will), horizontal gene transfer events and the acquiring of endosymbionts (which basically enhance the speed of evolution) don’t fit the picture of a tree anymore. However, bigger organisms aren’t capable of horizontal gene transfer anymore and no endosymbionts have been acquired at that stage anymore as far as we know. So for all organims that you can see with a naked eye, the tree of life is still undisputed, the metafor of a tree just doesn’t go for micro-organismal evolution. Epigenetics comes on top of that and accelerates evolution even more, allowing adaptations during a lifetime. And again, I can’t acknowledge often enough that the beginning of life is most mysterious, but even for these very early stages, there are mechanisms imaginable. It is just impossible to prove that they occurred, because we can’t go back in time. And again, 99.9% of scientists in relevant fields like biology, chemistry, biochemistry and geology regard evolution theory as the best possible explanation. I’m sure you can find a handful of evolution-denying scientists out of the thousands, that are probably too indoctrinated by religion or otherwise, but I’ve been in academia since my secondary school and I haven’t met ANY scientist that disputes evolution theory or advocates intelligent design. And as you said, it indeed “would be better to argue with those who spent their whole lives wrestling with these problems – the scientists themselves”.

  16. Still the same problem – evolutionary pressure is evoked whenever Nature comes up with a solution. Whenever there is no change, we just say “no evolutionary pressure”. The flaw is that at the level of molecules, there is no pressure at all. There is no reason for mutations to suddenly accrue just because there is a difficulty. The molecules have no awareness of what is needed. They behave in the same way under pressure as not under pressure. They don’t care if the organism dies or not. How can they? It makes no sense to say the emergence of solutions can happen one minute, but not the next.

    The reason we can’t prove the various theories about the origin of life is not because we can’t go back in time – it is because every imagined scenario never pans out in the lab. Never. Even James Watson admits, we have no idea at all how life arose. Suppose that the mechanism of combustion was a mystery, then how could we build imaginative theories of how fire works, how it spreads, how it functions? Layer after layer of ideas, theories, memes, skyhooks, fantastic genetic cranes, and book after book after book. But that’s exactly what we have – a theory of biological progression from simple to complex, without any understanding at all of how it started. None whatever.

    The intelligence in nature idea meets with hostility because it requires mind to be imagined in another form than the brain; a much stronger form, and a much faster intelligence. Here is the problem at its core: biologist have extreme difficulty in explaining mind. This is why there are 500 schools of psychology! Nobody knows where mind comes from, how it emerges from physical energy, whatform it takes, and why it should be stronger in one person than another, or different in an animal and a human. We know it depends on the brain, of course. But mind is something which cannot yet be measured, apart from IQ tests and so on. The essence behind it cannot be measured apart from what it produces. And yet all these theories of mind have arisen, all conflicting and all making different assumptions.

    There’s only one theory of blood because we understand it. But mind is a free for all ni which any theory can be proposed and find followers. So if we cannot yet measure consciousness, apart from what it produces, how are we able to say that nature has no consciousness? It’s embarrassing, the state of our ignorance. It’s really awful, but nobody will admit it. We are free to study mind and have always been, but still, we can’t explain it; we may as well call ourselves plumbers when we have no idea at all about where water comes from, how it can be tainted, or even dry up in cases. We barely even have theories of insanity and genius, let alone hard facts. We just guess and try to cope with whatever happens.

    But in evolution, the pre Cambrian explosion is still a serious problem. Yuo can sense scientists being glad the problem is so far in the past, it’s that embarrassing. The lack of previous fossils was blamed on their forms being too soft. But where the fossil area beneath this time period was so sensitive that it recorded even soft tissue, as in China, they found no precursors to the complex creatures of the Cambrian. The entire record was there and it was still a mystery. They still just assumed the theories were right, and that they would find proof somewhere else. They never did!

    What more can i say? The theories are imaginative, but they are crazy – that perfected machinery just happens by chance. We never see it happen in the human world, but they just push the problem away and say that with enough time, you can get perfect machinery out of flukes. But how? There is no reason. No motive force. The only force suggested is procreation, but that itself depends on perfected machinery! So the one mechanism supporting the whole theory, is itself a product of the theory but which otherwise we can’t explain. It’s a nonsense.

    You can’t really argue with someone who believes in randomness, as I have found before and I should know better than to try. Because their ideas are that whatever has already happened, must have happened their way. Why? Because they believe it. If you dare to doubt them, they just point to many others who believe the same thing, the sheer number of books, etc. That isn’t science at all.

  17. biochemist says:

    I’ll give you this point: you seem to be right about non-random mutations (in bacteria at least), according to an article in the latest issue of Nature: Evidence of non-random mutation rates suggests an evolutionary risk management strategy (3 may 2012, Martincorena et al.)
    Some quotes: “Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases.” [..] “Our observations suggest that purifying selection has driven the evolution of the local point mutation rate in E. coli to reduce the risk of deleterious mutations.” [..] “Instead our observations are in line with an evolutionary risk-management strategy in which sustained stronger purifying selection at specific genes favours individuals with preferential protection or repair at these loci, even at a cost of reduced protection of other genes” [..] “In this way, the rate of deleterious mutations in the genome can be efficiently reduced without excessive investment in protection or repair. In addition, this could increase the rate of non-deleterious mutations, so raising the adaptive potential of the population in case of an environmental change.”

    They also speculate about the molecular mechanisms involved, but the study was mainly phylogenetic. The point is, bacteria evolved in such a way that they could evolve safer and faster than other bacteria, using these mechanisms. So you were right, mutation is not completely random! I admit my wrong-being. But it still doesn’t require a higher form of intelligence to drive this, everything can again be explained by reductionistic molecular mechanisms!

    • It’s impressive to me that dead, disinterested, inert molecules decide they need to find an evolutionary risk management strategy!

      Or is it that we decided they decided to formulate a complex strategy..? Or did they not decide to formulate a complex strategy, or manage all the other problems of organisation and design, but just act blindly until what they achieved was a perfect facsimile of deciding on an ingenious method for evolutionary risk management?

      Either way, it looks pretty smart to me!

  18. biochemist says:

    By the way, if you would have read my earlier posts more carefully, you wouldn’t have needed to say this: “The reason we can’t prove the various theories about the origin of life is not because we can’t go back in time – it is because every imagined scenario never pans out in the lab. Never.”
    The example of evolution of multicellularity is pretty close to the beginning of life and I gave you an example how this was simulated in a lab. The discovery of ribozymes that catalyze their own synthesis is even closer to the beginning of life. We’re not there yet, but some essential parts can definitely be simulated in a lab.

    • In that case, then what I said was correct – the current theories, however promising they may be, do not actually explain the beginning of life.

      I can say I nearly jumped across the Grand canyon; I can explain in great detail how I one day will jump across the Grand Canyon, I can draw a complicated picture of myself jumping across the Grand canyon or I explain all my theories about how it must be possible to jump across the Grand Canyon given exactly the right wind, air density, cloud cover, solar radiation, passing pigeons etc, but the the observant will notice I haven’t actually jumped across the Grand Canyon. Being of a polite disposition they offer encouragement, keen on seeing the feat for themselves, but after decades of failures, fear the worst.

      The theories are clever because they need to be: the gap between a problem and a solution is always intelligence. The gap between random chaos and organised codes is intelligence. The gap between failure and success is intelligence. The gap between a pile of rubbish and precision engineering is intelligence. None of these ordered and purposeful conditions can be achieved with blind energy. Codes never arise from random causes, and time increases disorder. All things tend to decay. In fact one of the best definitions of living things is that they actively resist decay. All this we know from our own experience of codes, of engineering, of problem solving, and of life on Earth.

      We never see life without intelligence. Even plants have intelligence, and perform surprising acts of communciation between each other. They have a measurable IQ. This shows that intelligence ie not limited to the brain. Ants display a group intelligence which never comes from one ant brain: again, a variation in intelligence which we cannot account for. The smallest microbes possess a kind of intelligence, a purposefulness. Even the tiny machines in our cells have a kind of intelligence. The humble bacteria has devices which sense nutrients, and send signals to the motors to change direction towards areas of greater promise. There isn’t a single example of life which does not show intelligence. The field of intelligence is one which shows the greatest promise and the most profound challenges in all of science, greater by far than an investigation of molecules and the patterns behind the atomic elements.

      At the moment we do not even have an accepted definition of intelligence! The field seems almost completely abandoned, from what I can see.Who should know more about the extreme value of intelligence, than the most intelligent species on the planet? Who should show more interest in intelligence in all its forms on this small planet, than the species with the biggest brain? Where would we be, without intelligence? Where would our engineering be, our language, our codes, our art, our complex organisations, our considerations of problems, our triumphs over difficulty? It all comes from intelligence.

      If this is our experience of intelligent life, why do we not apply the same reasoning to the problems of biology, and form our scientific theories in a new and more perceptive way? We do not, because it means we have to consider that intelligence might not be confined to us, and may exist in far greater, more subtle and more capable forms, just as our investigation of the universe has revealed colossal variations in matter from the smallest speck in our hand to stars which beggar the imagination. Apart from this reluctance it’s a perfectly logical hypothesis; it doesn’t limit science, it expands it in an entirely new direction. But nobody dares to say it for fear of rocknig the boat, so they keep on with the farce, that intelligence is a fluke, without any basis in the universe. A fluke! Our own intelligence! How terrible is that, when we base everything on it?

      With absolute certainty, the gap between living and dead matter can only be filled by intelligence. Without it, matter remains what it appears to be when divested of life: disinterested, inert, dead.

  19. biochemist says:

    Another recent report in Cell (journal) shows the importance of gene duplications for evolutionary development of the human brain: (from the nature website)

    DNA-duplication errors that upped the number of copies of a gene may have catalysed the evolution of complex brains in early humans.

    The gene SRGAP2 is expressed during development of the brain’s neocortex — a region involved in cognition. Evan Eichler at the University of Washington in Seattle and his team report that humans have four different versions of SRGAP2, as did Neanderthals, whereas other primates have just one. The group estimates that successive duplications of SRGAP2 occurred between 3.4 million and 1 million years ago, as Homo species evolved.

    Meanwhile, Franck Polleux at the Scripps Research Institute in La Jolla, California, and his team show that one of the newer versions of the gene, SRGAP2C, blocks the activity of the ancestral SRGAP2 when it is artificially expressed in the brains of mice. Mouse neurons expressing SRGAP2C develop features of human neurons, such as a denser array of projections called dendritic spines that forge connections with neighbouring neurons. The cells also migrated across the developing brain faster than normal mouse neurons.

    The authors suggest that these changes, driven by the emergence of SRGAP2C, could have occurred in early humans, who had much larger brains than their ancestors.

    Cell http://dx.doi.org/10.1016/j.cell.2012.03.033; http://dx.doi.org/10.1016/j.cell.2012.03.034 (2012)

    • I would say in a device which manages 100bn neurons there is very little room for “error”. We talk airlily about larger brains, forgetting that the leathery coating around it needs to grow, as also all the protective layers, not least the skull itself, and the blood supply; all the neurons themselves are arranged into precisely functioning areas. The design is absolutely stunning, and the wiring, as has been shown recently, is arranged in criss-cross strips like a three dimensional chess board.

      If brains were subject to random duplication errors which produced spurts of growth, the most likely candidates for this lucky fluke would be the oldest specimes with brains, namely the insects – who by now should have colossal brains! Something different has developed the human brain, something which opens up a mental world not accessible to any other species, something we can all be very grateful for, whatever the cause we believe in. This undeniable good fortune is what spirituality tries to celebrate and encompass; the feeling of gratitude and hope for a more evolved future.

  20. biochemist says:

    The denial of scientific results is typical for a non-scientific theory like intelligent design. You clearly have no idea how hard it is to get a paper past editors and referees for a journal like cell. Apart from less than a handful of fraudulent papers it is extremely exceptional that Cell papers later turn out to be scientifically wrong. As for skull size etc., in the embryonic stage where the brainsize is mostly determined, the skull is not yet closed nor is the meninges fully developed, so a bigger brain is allowed, the skull and meninges will automatically grow with it. Insects (devonian) aren’t the oldest species with brains, cephalopods (octopusses etc., cambrian) are only about a 100 millions of years older. And how surprising, their brain is indeed incredibly well-evolved.

    • Dark Star says:

      There seems to be a false assumption on this site that DNA provides some kind of a (semi) ‘rigid’ template for an organism that must evolve simultaneously with other changes or ones brain would be crush in a fixed skull — the evidence suggests it is based on local communication w/layers of signaling gradients and subtle changes in timing of expression driven by geometry and epigenetic factors (good examples to be found in the highly-conserved Hox complex). This is vastly more flexible.

      Duplication and subsequent modification of signaling gradients and their adaptation to new functions also makes sense. We see evidence for this.

      Bigger brains carry high costs, it is entirely possible that, despite an eventual benefit, individual mutations would fail to cross that barrier and proliferate. Our lineage is one that managed to successfully grow brain size. For all we know some insect on the path to galactic domination was killed when it was swallowed by a bird, or destroyed in a large impact. ‘Better’ (this is a subjective valuation) genes don’t necessarily survive – that has never been the argument. The genes we have today are the ones that were *able to* replicate.

      The use of ‘More evolved’ is also a misnomer based on a false (presumptive) valuation, everything living on Earth today (to the best of our knowledge based on the evidence) is the same ‘amount’ of evolved. This is just not a measurement that makes any sense. If you want to compare things there are better metrics you can use.

      • DNA is probably the most interesting field in the world at the moment. The horizontal transfer of DNA is remarkable: according to research, bacteria transfer it to plants during tumorigenesis or symbiosis and bacterial sequences have been shown to transfer into an insect host genome, pathogens can collect host DNA, and so on. There is no regard to taxonomy; this mechanism seems to be a function of living things.

        All of which means that the strictly vertical inheritance model, which seems to have been frozen in the mass mind through popular Darwinist images, should be jettisoned, unless we value dogma over discovery. Using chromatin binding proteins, and transcription factors as examples, Nature’s 2001 report showed that protein evolution did not occur one amino acid at a time, but by shuffling functional domains already in use. This is a radically different idea than haphazard, random accretion of single nucleotide changes, but accepting it means revising the only mechanism acceptable to Darwinists, that of random, aimless incremental building. Any alternative, to their mind, seems to be the plunging of all science into a crowded, ancient pantheon.

        Common sense – forbidden all too often – and any experience of mechanical engineering should tell us that devices, with highly complex moving parts involving tens of thousands of atoms cannot hope to function effectively when relying on thousands of other randomly altering devices, all in a state of genetic meandering. The genome is clearly a place of law bound events, or else there would be no point whatever in studying it. The ribosome does not slowly edge toward being kinesin, and so on. Everything is specialised, and behind this highly functional facade we expect to find useful laws and principles, not chaos.

        To search for law and order seems a healthy aspect of the mind; a belief in chaos, a kind of nihilism or anarchy on the other hand, should put a halt to any investigation before it begins. Fortunately the solidity of DNA and the uncovering of more and more levels of predictability seem to bear out this hope of law and order, which all of evolution must have adhered to.

  21. Whether it’s hard to get a paper past reviewers or not, means nothing at all. It certainly doesn’t mean the conclusions of the experts are correct. It was very hard to get a painting into the Salon in Paris at the turn of the century, and there was absurd outrage at the work of “Impressionists” as they were insultingly called at the time. The cure for scurvy was laughed off for 70 years and was of no interest to the Admiralty experts, who had invested their careers in promoting commercial cures, none of which worked.

    The computer, not the perfectly functioning one Babbage designed 170 years ago, which was ridiculed by government experts, but a post-war improvement on the Colossus designed during WW2 by Tommy Flowers – was turned down by financial experts on the grounds that it would fail to work, or be useless. Even the government which had seen the thing give valuable information time and again, had it dismantled and refused to fund Flowers’ new attempts. “Not useful, dear boy,” the experts said. As a result, decades of computing advances were lost due only to Expert Ignorance.

    Television in the early 1930′s was considered an absurdity, and even when the possibility was demonstrated, was written off as a useless novelty – by the BBC, the experts at the time in broadcasting. Only time has shown all these unusual ideas to be correct – genius is one thing, but the opinions of the “experts” are, often as not, overturned eventually.

    There were scientific experts who believed eugenics was a sound idea; there were scientific experts who for decades denied there was any link between smoking and cancer – condemning millions to death by suffocation; there are scientific experts today who deny that being knocked into concussion repeatedly is a cause of mental degeneration. There are scientific experts who still recommend prostate surgery when their own statistics prove it to be a painful, debilitating and useless measure in most cases. The expert doctors are on a share of the chemo revenue so they continue on as long as possible, in the hope nobody finds out the truth.

    There were scientific experts who denied Fukushima would be any kind of a problem. Britain’s chief scientist, Sir John Beddington, became infamous for his callous and stupid remarks. And of course, there are scientific experts who spend their time developing monstrous weapons, for roasting their own species alive – children, infants, mothers, whole families. All of these experts are either demented, crooked, or have lost contact with their own senses: how can anyone use the opinion of scientific experts be a measuring stick for what is right and what is wrong?

    Regardless of the morality, it seems to me experts only consider themselves experts when they believe there is nothing more to learn beyond what they already know. This kind of attitude is always overturned in time. The only people worthy of respect are eager to learn more. Apart from that, experts display a kind of geeky, blinkered certainty which is applauded mainly by their own kind, to keep the whole farce going as long as possible. How can anyone be an expert in micro biology when its spee and complexity is entirely beyond the human brain? How did humble bacteria manage to outwit the entire assembled group of technologists and researchers in the human race, and defeat our antibiotics? “Oh, just evolution,” is the throwaway answer. But the answer should be, “oh, just our ignorance,” because if you can’t understand a problem enough to come up with a solution, how can you call yourself an expert?

    It is exceptionally hard to criticise a theory which is not based on anything. How exactly can there be an effect, with no underlying cause? How can you have a fully developed code, with no motive anywhere to build, record and transmit? Random causes cannot be consistent. What they do one year will never be what they do another year. Why should they be? They are random. People search instinctively for laws and principles, in spite of a Dawkinian science that claims there aren’t any. The procreation frequency which is cited as a cause, is actually an effect. An effect of what? Of procreation! It’s just nonsense. Why should atoms jump into hugely complex components and tirelessly adapt to overcome every conceivable difficulty? Just “because they did” is no theory. It’s actually shameful. If I say computers are random technology, without cause and effect, things which unpredictably do one thing one minute, and something completely unforseen the next, can I possibly say I am an expert in them, if suddenly I am lost for an answer to their difficult problem? Who could call such an engineer for advice?

    Random evolution is based on chance, that is, nothing. No principle, no motive power, nothing at all. How is anyone expected to disprove something so intangible? The problem with this theory is purely in the minds of those supporting it, because it doesn’t stand up to common sense – or scientific principles, as Darwin himself was quick to point out. A wiser man, he realised chance was unscientific, and the questions still open. Since then the problems have got exponentially greater. So the whole edifice is based on the guesswork of a 19th century naturalist, who readily admitted to problems with it even then.

    But if you already know all the answers, if chance and randomness are the only causes, what really is the point of investigating further? There isn’t anything more to discover. Since you already know about all the energies in the universe, then let’s stop the big pretence of an investigation! And leave that to people who still have an open mind.. the ones who are shouted down because they are not experts. But only they may come up with something, because you never stumble over something when sitting back, nice and comfy.

  22. Biochemist says:

    “Random evolution is based on chance, that is, nothing.” Again, so are thermodynamics (read on Boltzmann and statistical mechanics) and quantum mechanics (Heisenberger). Chance/probability can be the motive power itself, ask any chemist or physicist. I don’t recall calling anybody an expert so I don’t understand where this tirade comes from. Sure, some scientists have been wrong and amoral, but that’s something else than 99% of the whole scientific community agreeing with a theory (like with relativity or with evolution theory). Furthermore, science is designed as a continuously self-improving knowledge base, so if enough evidence is present against certain dogmas (like Newtonian mechanics, vs. quantum mechanics and relativity), the better theory will be adopted. Matter of fact, this is much like natural evolution itself and unlike any religion, which are based on old books and refuse to revise their theories because of new perspectives. A good example is the non-random evolution in bacteria that I posted before; whereas if evolution was like a religion this would be blasphemy or at least wrong. Science however adopts this and tries different hypotheses about how this works and how this came to be.

    • But science isn’t following the evidence – random forces like heat and wind do not produce codes. The DNA is a code, and all codes that we know about come from minds. There is the evidence – how does logic manage to wriggle out of that? I feel I’m about to find out…

      And the tirade isn’t aimed at you, and I apologise if it seemed so – the tirade is from having to live on a planet being turned into Hell on Earth because of a disregard for fellow – feeling and humanity; and nowhere is this disregard more strongly distilled than in the impartial, emotionally stunted language of science, which would be fine for a` testtube but now politics has adopted it, because of its ability to murder unpleasant emotions and hide the bodies so well that it really does look like a new patio..

      “it was felt it appropriate, by a certified, authorative body, to apportion the naturally occurring resources of a given area, formerly under private stewardship, to one better suited to leverage stronger commercial progress; therefore an appropriately equipped contingent was dispatched to said area with the primary objective of securing the immediate future of said resources, whilst prepared for possible sentiment of the local populace to the contary.”

      In real language? We invaded, slaughtered and stole the oil!

  23. biochemist says:

    I have always from the beginning strongly opposed any foreign military intervention in Iraq or Afghanistan and I couldn’t agree more that politics often use difficult language to hide their real motives. It was however a severely conservative government with a high regard of (Christian) religion and a high disregard of science (global warming) that started both invasions. Science is using un-emotional language to remain unbiased and objective, just like law and politics. But I feel like we’re getting a bit off-topic with this. As for your argument that randomness cannot build a code, I agree that it is counterintuitive. However, many things seem counterintuitive at first but are undisputed after severe investigation (relativity theory to name just one example). “A code is a rule for converting a piece of information (for example, a letter, word, phrase, or gesture) into another form or representation (one sign into another sign), not necessarily of the same type” is a good starting point for a definition. Indeed, DNA forms a code according to this definition. However, the definition nowhere mentions that it has to be created by an intelligent being. I cannot think of any example where a code of the complexity of DNA is formed by randomness, but that doesn’t prove the evolution theory wrong. Spontaneously formed codes do exist, like for example year-rings in trees. Your argument is indeed a valid argument against evolution, but it doesn’t disprove evolution, it is just based upon experience and intuition. Not everything is intuitive (like the exponential growth example you mentioned before). Intuition is not something scientific theories are built upon, facts are.

    • It is strange to see a man of logic abandon logic when it comes to looking at the world. George Bush is no more a Christian than Josef Mengeles was a research scientist, or Idi Amin a sous chef. Bush simply makes use of religion the way he abuses alcohol: Christianity is a shool of thought which recommends extreme respect for all other humans. It virtually forbids conflict of any sort. A person can call themselves an optician, if they want, but if their technique is to use a Black & Decker and sulphuric acid, how can men of science such as yourself look at the dreadful results and say, “well, look what opticians are capable of”! Down with opticians!

      It is this slipshod thinking which I take issue with. As you say, it is hard to think of any random process causing a code, because there cannot be one: to do so would be to defy a basic law of the universe, that information systems require information, and the retention of information requires intelligence. A person of average IQ, according to your shool of thought, is infinitely – and that’s a lot – more equipped with intelligence than the zero-intelligence biological systems which actually create and maintain his brain, which keep his body in a constant state of readiness, and which deal with millions of problems every second so seamlessly that he is completely unaware of their existence

      As for the rings around the trees, these are created by speeds of growth. They do not store information, they simply show a result of external conditions. If you occasionally hold your finger over a flame, you will record red marks. This is not a code. A mountain range shows patterns of internal pressure and external weathering, but this is not a code. A code is a system of symbols which is used to represent the potential expression of something else, of a different nature than the symbols themselves.

      Intuition is part of human life: if science was only ever based on facts, there would not be very much of it. Intuition has played a role in all the great discoveries; without intuition you don’t really have anything, which is why science grinds to a halt without great minds. From where are discoveries made? From consciousness. Otherwise, they could be made by sheep and by grass. It is acknowledged that great discoveries are made only by great minds; and these rely on mental attributes which do not exist in the objects they are studying, but within themselves. Einstein is revered not for his hair or his pipe, but for the deeply intuitive, perceptive nature of his mind. Why else show respect for thinkers? To say you only respect facts is like a writer saying he is a purist in that he only respects letters. Words are misleading, and are liable to error. Another writer goes further and says, “I am interested not in letters, I am even purer – I am interested in straight and curved lines, which construct the letters – for even letters can be distorted, and there is no room in my world for distortions.”

      Another writer declares himself superior to all of them, by saying he is only interested in the fibre of the paper, because without that, there is no place to put any letters or words. His books, therefore, will be superior, and less liable to error, because the pages are all blank – a more pure form of writing can never be imagined.

      And then a scientists comes along and says, “I am a purer writer than all of you – I am interested in the molecules which make up the ink. There can be no purer writer than myself. In fact, I dimsiss you, Shakespeare, and you, Socrates, and you, Tolstoy – for you do not base your work on absolute facts like I do. You talk of intuition and what have you produced? Tons of paper. Paper has very little worth once it has been printed – for it cannot now be used to record anything new. It is useless – therefore, your work is equally useless! Begone, worthless peddlers of ideas and intuition! Bow down, before my absolute facts of protons!”

      Before science, man’s knowledge came from intuition, verified perhaps by experiment, but it was not random. Primitive tribes, as do animals, retain a psychic link between each other which is fully explained by intuition. It is not the worthless chaff which you describe it as. Traces of this natural intelligence remain even in modern man, and of course, is written off as non-factual. Nevertheless, science grew out of tens of thousands of years of intuition. Intuition is still at the heart of science. Without it, science is mereley accountancy. How would a person become a scientist at all, unless that urge came from within? If he based his decisionon facts, he would weigh up salaries and distance from home and pension plans. Can such a man be worthy of respect, that he used dry facts to arrange his life, in place of his own feelings? What kind of a human would do that?

      If a scientist is drawn to science by his intuition, drawn to his partner by intuition, drawn to his great insights by intuition, how can he suddenly abandon it and say, my life might be based on intuition, but my science is not based on intuition? He declares his science to be impotent and irrelevant to life, because for life, he uses his mind, his intuition, as superior to facts. In that case, what good is it for other humans? It’s like saying a car is not based on petrol, it is based on motion. It is a half truth, which is sometimes worse than an outright lie, because of the possibility of it being accepted and justidied under completely false pretences. “We removed Saddam because he used weapons of mass destruction,” said Cheney. A half truth. Cheny’s country sold him those weapons, supported him in their use, and looking further back, even helped Saddam come to power, and protected him in exchange for oil. Of course, Cheney can say, “I am telling the truth!” But intelligence – intuition, the kind you declare science to have abandoned in exhcnage for dry facts – shows us it is based on the deception of a psychopath.

      Logic can be abused in so many ways, to border on falsheood, that intuition is always needed to form an intelligent view. Otherwise, a spreadsheet could make discoveries, because it can store many more facts than a human. Why do spreadsheets not make new discoveries? Because they are inactive. They simply record facts as put there by a mind. But without the mind, they do nothing. If you discovered a spreadsheet with the designs for all of biology, along with the plans for upgrading it, it would be a massive database indeed. But that exists in the DNA. Is it a code? No, no, you say, it is nothing.

      As an example, I write software, which is indeed a code – and a client asked me once for some free extra licences, saying, “what does it cost you to install them? It only takes you ten minutes.” His logic was sound! But a more intelligent person would not just look at that micro-context, and realised that 25 years of my time spent honing this marvellous piece of software is worth something. Of course I explained that if they didn’t think the licence was worth paying for, I would entirely respect their decision and agree, it would be better not to trouble them with it at all! In the end they paid, of course, and the manager I spoke to even apologised “Sorry, mate – it’s these f***ing accountants, they’re always complaining – you can’t reason with them.”

  24. biochemist says:

    I wonder in what physics book you found the universal law that “information systems require information”. It certainly didn’t pass in any of my physics classes and I think I had plenty. It can also easily be disproved by the notion that there is information present now (be it biological (DNA) or created by man), so it has to come from information, which has to come from information, which has to come from information etc. to infinity. At some point information must have emerged without an information template if you will, assuming that we’re not living in some sort of cyclic universe.

    To get back to my year rings example; unlike you claim they do store information (how many years old a tree is, what the levels of certain nutrients are in different years etc.). This falls under your definition of “A code is a system of symbols [rings] which is used to represent the potential expression of something else [information about the environment in the past], of a different nature than the symbols themselves”. But I agree, they are indeed a result of external growing conditions. Just like DNA is a result of a cascade of biochemical reactions that make up nucleotides and that perform template-based DNA replication.

    I don’t say intuition is worthless, I just want to stress it isn’t flawless (e.g. quantum mechanics or relativity are far from intuitive). Therefore, any theory (made up by minds of whatever size) that is based on more than pure logic needs experimental verification. True, this is sometimes hard, as is the case for evolution theory as well. However, many principles of evolution are indeed already experimentally verified: hereditary transmission of genes, mechanisms that induce changes in the genome and therefore in the phenotype (mutation), the fact that random mutations can result in advantageous phenotypes and the fact that advantageous traits can become dominant among a population (for the last two principles, I would like to refer back to my example of antibiotic resistance). Because it happened over extremely long timescales and it is not always possible to speed up processes, it is probably impossible to perform an experiment in which for example a chimp turns into a human, but for single cellular organisms, many experiments have demonstrated that the principles of evolution are all sound. And with strong evolutionary pressures (like with dog-breeding), you can indeed get mammalian organisms to differentiate so much that in all technical definitions they become different organisms. The question remains whether it is possible that it happened within the timescales of the earth, as you rightly question in this blog. However, because of the complexity of ecosystems, the lack of knowledge about the environmental changes during the oldest geological epochs, the random nature of evolution and the different mechanisms of mutation, these timescales can not be simply approximated in the hand-waving type of approach that you’re employing.

    I don’t deny DNA is a code, I explicitly agreed with you on that in a previous post. I just disagree with your statement that codes cannot be generated by randomness, this is not a law of nature.

    Finally I don’t get the point of your last example. I don’t agree this is the type of logic that is employed by science and I don’t think it is sound either.

  25. biochemist says:

    An example to disprove your universal law that codes cannot be generated by randomness: randomly generated code, generated by artificial evolution, can fix software bugs as well as create new combinations of existing software functionality:

    http://cacm.acm.org/blogs/blog-cacm/100384-can-randomly-generated-code-fix-software-bugs/fulltext

  26. Well, if information systems do not require information, they can’t be information systems. A water system is not a water system without water. And a comunication system is not a communication system unless there is communication. Perhaps many other examples will spring to mind as well, which I’m sure will require a bare minimum of intelligence to agree on!

    In fact I refer you to the first class I ever took on computers, when I was about 14 – the teacher said “The most important rule in computer software is this: GIGO: GARBAGE IN – GARBAGE OUT.” No, everyone in computing – a real world experiential science – agrees on this, but everyone in evolution seems to think: ANY OLD CRAP IN – PERFECTION OUT. A subtle difference…

    The tree rings do contain information, yes, but those patterns only become information when they connect with intelligence, just like sound only becomes sound when it is processed by many systems – chemical, physical, and electrical – and interpreted as such by consciousness. They mean nothing to a block of stone, and tree rings mean nothing even to a sheep – an intelligent creature – happening across the tree stump, because in those two situations, even the one with living intelligence, there is not sufficient intelligence to decode the signs. The input into the rings is heat and cold; the storage is a product of biological forces, but their significance can only be interpreted by intelligence.

    The inability of the sheep to decode the rings points to another very important poitn: that individual consciousness sees the world to a limit of the depth within itself. A sheep looking at the night sky does not see vast distances and histories and uncounted billions of potential systems, because its consciousness is strictly limited to its sensory input. It still cannot decode the rings on a tree stump because this requires abstract concepts not contained within its consciousness. It is clear that what we all see in the world, in the sense of abstractions, is a result of our own capacity. This is the reason why a materialist mind and a spiritualist mind can never agree: they see different things, each based on the components of their own consciousness.

    This “world as our mirror” is well known to psychologists. So the greediest people are the ones with the biggest locks on their houses – certain that all are out to get their stuff, the altruistic sees the good in others, the violent sees a threat in every sideways glance from a stranger, the depressed see a world with no hope, the egotistical sees all men as an audience, and so on. But the materialist is at a disadvantage when discussing life because while admitting that the real world exists, he is forced to explain away all abstract concepts – such as the essential reality of consciousness itself, the first component needed to build any knowledge on – as a trivial byproduct resulting only from a series of lucky flukes of the interactions of dead materials. Because life and consciouenss are not presently measurable by his own instruments, he is forced to deny their reality – an absurd position for an intelligent mind to take, especially one asking us to accept his conclusions in place of our own! Nevertheless, this is why professors say life elsewhere in the universe is not likely – they see it as a freakish exception, and themselves the grandest product of 14 billion years of otherwise wasted time, a fantastic conclusion of the ego!

    of course, it’s an obvious conclusion that the biological world bears all the hallmarks of intelligence, but the materialist only sees particles. Stuck at this limited level, in a world he knows full well is nearly all out of sight of human senses, he nevertheless builds his worldview on the physical particles and sees them as indivisible; he certainly does not see consciousness the way he sees these real objects – even though he should know that their quality of mass is lent to them only by their interaction with consciousness – something pointed to by quantum mechanics, in which reality as we know it can only be assessed by adding the dimension of time, another product of consciousness – and there he remains stranded unless he builds a new consciousness of his own – an impossibility without mental evolution, and spiritual discipline. This is why his theories must become ever more elaborate and far fetched to explain the fantastic precision and speed of these (according to him) dead machines; as man evolves, the technology to reach into these now hidden layers will emerge, and the materialst mind will gradually fade away, as also the fundamentalist religious type. At the momemtn, men of science are largely materialists, which is holding back the progress of the field as a whole, but funeral by funeral, it will advance, I’m certain of it.

    But back to the rings: their interpretation requires a concept of past and present, it requires a fixed and agreed measurement of time, a concept of hot and cold as it can be reflected by the habits of a tree, it requires the concept of a tree as having a past of its own which may be different from ours, and perhaps substantially longer. Therefore it also requires a concept of the world as existing apart from our own individual self. It requires time to have been regulated into the concept of years and seasons, and all of this is impossible without an abstract intelligence matching each required point. It is far more complicated than just saying the word “rings”. To us, this word is a concatenation of many concepts, and it cannot be described in its entirey without reference to them. Interesting, one day it may become apparent that the brains of people contain a system of recordings which like the rings of these trees, show seasonal difficulties or advances in its genetic past, even into the past of its parents and grandparents. This can’t be ruled out: epigenetics is already pointing in this direction. These are very advanced concepts, and would not have been possible before the invisible mechanisms of life came in for examination. So they have relied also on technology, which has tended to mirror the interests of people.

    In the DNA you have a living code. The code has, somehow, built itself. We do not know how this happens, but the creative force clearly requires intelligence, because the system itself shows all the signs of intelligence, and a complexity we are having a hard time unravelling even with the combined intelligence of millions of researchers. The tree stump is actually a bad example, because the mechanisms of the tree themselves depend on DNA. In fact just the mechanisms of photosynthesis are so complicated that it takes a large amount of intelligence to understand them. From our end, unless we can duplicate the photosynthesis without using intelligence, we are forced to admit that it would take intelligence to create it! Why the deep-seated resistance to the idea that Nature is intelligent? It seems almost a deep rooted phobia, causing the same reaction as one who fears spiders in a nest of tarantulas.

    As for fixing bugs in software you’ll notice that the article mentions “evolvable software”. Now, the evolvable software itself was created by intelligence. It is not random. It has a repertoire of things to watch out for, and a repertoire of fixes. It is as far from randoma as it is possible to go! A random fix would be to throw random letters andn umbers and punctuation in at random places at random times and see what happens. Any ideas how that would turn out?

    Not only this, it works on machines which were created by intelligence. The consistency of the language was agreed on by intelligence: it is not a random affair, no matter what they may say, and nor could it be as it serves a specific purpose and is designed around specific limitations. The very idea of software, and its division from hardware, required intelligence. These systems are used by energetic life forms which also possess intelligence. They use the software for intelligent purposes – that is, purposes which could not be arrived at by a block of cement.

    The idea that a condition of the software is unwanted – ie, a bug – can only come from intelligence. The concept of improving or degrading the software’s function can also only come from intelligence. The labelling of the condition as desirable or not – labelling it by any name whatsoever – requires intelligence. Without agreement between many individuals, as to the desirability of improvement and the disadvantage of errors, the term bug could not even find favour. So we find a concept which exists in many minds at the same time, all of which agree about its valuable description as an exception from order.

    The key quality searched for by intelligence is order, and progress. All these minds are engaged on the same search for order,and the bug is described as an exception from it. This shows that genuinely intelligent concepts have a standard measure enlisting support not just from one but from many minds; in other words, the concept itself is beyond manipulation by an individual. Should an individual declare himself devoted to the creation of hidden bugs, he would be an outcast in a software house. Why? Because of the general agreement as to the nature of progress and the disadvantage of disorder.

    The concept of “bug” and “order” and “disorder” do not just emerge willy nilly from human idiosyncracy or whim, but rest on something deeper. This leads to a concept of truth as being a standard to which intelligent minds are forced to submit themselves, and agree on its non-random quality. So we find intelligence has yet another surface, required to connect with concepts not of its own making, but which it is free to discover as true by its own experimentation if it wishes. If by one’s research he comes up with the conclusion that bugs are desirable, and software should be desigend to crash unexpectedly, a normal mind would have no difficulty labelling him a disruption and eliminating him from the production chain. But why? Because the information systems require order and predictability, or they become impossible to maintain.

    I once was given the task of upgrading some Unix software written by a paranoid alcoholic who had become unfit to work any longer. The software was a nightmare. It was chaotic, deceptive, designed to stop anyone from decoding it. I had to virtually rewrite it. You see, the software takes on the shape of the mind creating it. Order does not come automatically from energy – it requires a measure of intelligence and a measure of precision. The ultimate code is the DNA: if I could write such a great system, I would be happy – but it’s impossible. We don’t even understand it in full: the thing seems more of a mystery than anything else. The difficulty in accepting a mind being behind DNA is that the mind would need to be so vastly superior to our own. So the phobia results from ego: Dawkins has said, there is a strong case to be made for an intelligent designer, but he made the qualification that that designer would himself have had to evolve through random mutations! The same old phobia ends up on top.

    And what are we using to evaluate all these arguments, conditions, environments, modifications, and potentials? Of course, we are using intelligence. Therefore although it is obvious that information systems require information, they must require intelligence as well, defining them as systems by evaluating their cohesion through consciousness, and to distinguish them from random chaos – say a stinking pile of rotting fish, or a deteriorating corpse, conditions in which life (by which I mean the cohesive force formerly uniting all cells of the original entity, and rendering it liable to purposeful order; not the ensuing parasites and maggots) is now absent. The absence of life creates a disorder in these two examples which lends support to the idea that order is part of life, as we see from living systems and our own consciousness.

    Either way, without intelligence, there can be no arbiter, no agreed measure, and no observing consciousness to decide one way or the other. We cannot even imagine what the universe woudl look like, divested of all consciousness, since the concepts of distance, size, colour, sound, mass and form, are all mental constucts, and they vary from species to species. The one thing on which all this tottering edifice of proposal, conclusion, experiment and deduction rests – is intelligence. Life displays these qualities and of course, yes, DNA is a living, intelligent, information system.

    GIGO!

  27. biochemist says:

    I haven’t heard a single professor doubting that there’s life outside earth in the universe, so I’m curious what professors you listen to. In fact, current opinion in science is that it is almost certain that there is intelligent life outside earth. They only rightly say that it is very unlikely that the nearest planet with intelligent life is close enough for us to ever meet (even if we could travel at the speed of light).

    I still don’t agree that “information requires information” is a universal law of nature, the same way for example electromagnetism is defined by universal laws. If you could give me a scientific reference, you would strengthen your case, but I’m rather sure there isn’t any because of the circular nature of the argument.

    Although the second law of thermodynamics predicts the total entropy (chaos) in a system always has to increase, it doesn’t mean that within the system local/temporal entropy cannot decrease. Since the earth is not a closed system (sun radiation), high energy with low entropy is constantly available in the form of sunlight, which can result in local and temporary decreases of entropy (photosynthesis is a good example). Even for dead systems, entropy can increase whilst “order” increases; for example the hydrophobic effect on which biological membranes, detergents and micelles base their order are actually stabilized by a higher entropy as compared to a situation with more random dispersion.

    It isn’t clear to me what part of evolution theory you think still needs further evidence, in my previous post I summed up 4 important principles. I agree that the beginning of life is hard to conceive and investigate, but we’re working on that. If you agree that these 4 principles are all sound, but the timescale is not fitting, we can discuss that. If you don’t agree on hereditary transmission of genes or mutation, I can suggest literature on that. For the other two principles I already posted examples that prove the validity of these, but I can try to find more examples if you’re still sceptical and think these are artifacts. If you agree on the soundness of all these four principles, the timescales and the possibility that an organism can acquire enough mutations to become a new species, then I’m happy. I’m not going to try to prove the beginning of life, that would still be too speculative, but basically you would already have excepted evolution theory by that point.

    • I see we mix in different circles. or perhaps I just go around looking for trouble! How evolution can have basic principles, when the whole of it is supposed to be based on random chaos is something I will never understand. Anyway, here is a professor who particularly irritated me by his conclusions (I wrote what I thought in Seeding Planets of Life):

      http://www.sciencedaily.com/releases/2008/04/080416110124.htm

      All I can say is, I remain convinced by the marvellous intelligence present in all forms, and all levels, of life – even exhibited by bacteria, that intelligence must be a property of living systems. The idea of open systems is of course well known but fails to consider that life on Earth is protected from the harshest elements of sunlight by its own internal elements that could not have been present at its formation, such as the ozone layer, which is odd if we assume that order is being invested from external sources, which are apparently dangerous to life in its raw state. Feynman used to say that his father played a game with him as a child: he had to think of something not coming from the sun. He would suggest, milk, for example, and his father would say, ah, but milk comes from cows, which eat grass, which grow from the sun! So you can see how his analytical and inventive mind was encouraged right from the start.

      Apparently every second in sunlight causes most of our skin cells to develop and then fix several hundred errors! Every second! If I could write software like this – wow. There are dozens of machines specifically designed for this immensely challenging problem, and they’re ingenious beyond belief! Slicing the DNA, untwisting it, repairing it, working from templates, zipping it open, zipping it shut, using the spiral shape for rotary power. And how do they know an error has taken place? It’s stunning, just wonderful stuff. So if the mechanics are designed to protect from errors, then how such an error detection system can arise from an error is a circular argument without equal, and surely deserves its own monument the size of the London Eye! The quantiy of time is rendered irrelevant once you claim that life is without intelligence; a hundred trillion trillion trillion times zero is, sadly, still zero.

      If you think sunlight can improve the order of a system, you clearly never left a chocolate cake out in the garden in August; if you think random errors can improve the functionality of a system, you have never programmed computers (I’ve made my living from this for the last quarter century and never once found a random error useful. Even a full stop in the wrong place is a catastrophe. To me, the DNA is the ultimate database and software system. I only wish I could design systems on this level!), and if you think random words injected into a conversation improve its comprehensible state, you probably are not running around loose at the moment! I joke of course; I think intelligence should be a field of study in itself, but at the moment there is not even an agreed definition of it, so how anyone can become an expert in it is hard to understand. I tried to formulate an all-purpose description in Intelligence and Stupidity, which I still think is a worthwhile essay.

      At the moment I am a little distrated by the project to build a working hemoglobin molecule (yes, I will be using intelligence – actually, buying it in, as mine is insufficient, only increasing my respect for those with the required amount!) as I may have found a technical place willing to attempt it. I would certainly like to return to this discussion in about ten years, during which time I am certain that technology will have reached the stage at which presently undetectable elements such as consciousness can at least be registered, perhaps with some kind of quantum device, I don’t know. Until then I see we must agree to differ; I think the issue is, like a sheep staring unimpressed at a tree trunk revealing the meteorology of the last 2000 years, not so much one of what is seen, but what is perceived. I am absolutely certain in what I perceive with my own mind, as I am sure you are too.

      All the best

      Iain

  28. Biochemist says:

    One last thing I can’t really agree with (albeit not evolution-related): “Christianity is a shool of thought which recommends extreme respect for all other humans.” Have you ever read 1 Samuel chapter 15, verse 3? In every translation I could find, God commands what would be under any definition genocide. Later He even gets mad at Raul because he didn’t kill everybody.

    New International Version (©1984)
    Now go, attack the Amalekites and totally destroy everything that belongs to them. Do not spare them; put to death men and women, children and infants, cattle and sheep, camels and donkeys.’”

    New Living Translation (©2007)
    Now go and completely destroy the entire Amalekite nation–men, women, children, babies, cattle, sheep, goats, camels, and donkeys.”

    English Standard Version (©2001)
    Now go and strike Amalek and devote to destruction all that they have. Do not spare them, but kill both man and woman, child and infant, ox and sheep, camel and donkey.’”

    New American Standard Bible (©1995)
    ‘Now go and strike Amalek and utterly destroy all that he has, and do not spare him; but put to death both man and woman, child and infant, ox and sheep, camel and donkey.’”

    http://bible.cc/1_samuel/15-3.htm

    • I might be mistaken but I believe the book of Samuel was written around 2,600 years ago, and even then, was a compilation of previous writings. There is a reason why the Bible has an old and new testament – it has evolved as a record of man’s understanding. But Christianity is necessarily based on the life of Christ, and Christ was born around 600 years after this. If so, Christianity is based on The life of Christ – his sayings, his morality, his example – and the Sermon on the Mount, and the Lord’s Prayer, documents which virtually forbid conflict. Can you find a fault with that? Even conflict of a mild nature between a person and his neighbour is avoided: forgive they neighbour unto seventy times seven.

      Even a humanist like Christ never spoke out against slavery – or appalling hygiene, or open sewers,for that matter – because he, as a person, was a product of his time. It is often said that if Christ was in a state of higher consciousness, he should have immediately proposed vaccines, electricty, television and powered flight, then reformed society into a democracy and installed flushing toilets, perhaps opening a series of universities and launching rockets into outer space to study the stars. This criticism utterly fails to take into account the nature of human progress, which is laboriously slow at the best of times, relying as it does on the co-operation of the mass of mankind over long periods of time. When the first man reached self consciousness, a step away – however you decide to measure it – from the instinctive animal consciousness, he did not at a stroke devise medicine, astronomy, education, vaccines, television and nuclear physics, embelllish language with another twenty thousand words, and sit down to draw out plans for the world’s first science museum, even though all these studies toook place in the field of self-conscious intellect.

      Progress in all these fields was slow, sometimes painfully so, and continued in fits and starts; even today they are subject to experimentation and debate, and conclusions are only slowly arrived at, and often overturned only a few years after the fanfare attending their announcement. Tonsils, appendix, Junk DNA, the backwards retina, anyone? In the field of spirituality, how could it be any different, bearing in mind that it too relies on the slow development of the human brain: not just of the genius but of the huge slow-moving mass mind, often unable to move even an inch out of its accustomed rut? To expect the first geniuses in the field of spirituality, or even those ordinary men and women who simply felt the urge to record life from the point of view of their newly forming sense of the soul, to instantly solve all the problems of mankind in a day betrays a strangely immature wish for magical solutions, and the inevitable disappointment from such a childish view of life is what, presumably, finds vent in hostility, criticism and mockery.

      The Bible, one of our first books, is partly a historical document, written by humans, and partly a record, written by humans, of man’s spiritual nature, a quality worthy of report as it does not exist in the animal world, which is untroubled by a yearning for deeper understanding. If you can find me a book of medicine from 2,600 BC, I am sure we can, between us, uncover some practices there to find fault with – but rather than tearing them to shreds with our wit, and making a parody of them to shine a light on our own excellence, should we not take the sensible approach of praising the fact that humans from so long ago and in such difficult times, thought biology and medicine worthy of an attempt to formulate ideas and record them for others? The same logic would aply to the earliest beliefs of atoms, of disease, even of the weather. Why, in the field of religion, do people expect miraculous leaps in understanding which defy everything we know about the growth in human knowledge and the behaviour of the mass mind?

      You can criticise the pyramids on their health and safety record – and I expect you can mock a modern person’s childhood mementoes as being unsuited to the adult mind; would tearing up his precious childhood photos on the basis of their immaturity be a worthy task for the modern intellectual? The vital fact about the pyramids is that they will outlast everything built today; the Bible has a similar quality, in that it has found a home within the human mind, even the modern mind, forming the philosophical cradle from which modern society – including science – emerged.

      It is this weird, and I have to say, almost inhuman attitude that in the comfort of our modern warm homes and secure lifestyles we hurl daggers at those who stood to gain nothign from recording their thoughts at a time when survival was not a matter of walking to the corner shop but of life and death, which seems to be the root of religious mockery, and the single element of militant atheosm which the great mass of people find utterly repugnant: perhaps you can go back further, and find the world’s earliest attempts at art, on a cave wall – and ridicule their anatomy and perspective? This would show you to be superior in every way to those who roamed the Earth at a time when fear was probably the most dominant emotion.

      Cezanne’s work with colour is no doubt superior, but for our own ancestors to have formed the very concept of art – an astonishing achievement outclassing, by virtue of its radical nature, many inventions of our own time – and then find the materials, manufactured the pigments, no doubt by trial and error, and then make the time to create pictures lasting 10,000 years or more – under such oppressive conditions rightly generates awe in a normal mind, as it signifies the triumph of the human spirit and the immense value which man rightly placed on his own ideas, and also the exuberance with which he recorded them. To threaten to wipe the walls clean on the basis of their poor execution, and replace them with posters of Michelangelo would be an act of vandalism that could never be repaired.

      It is these creative emotions in the ancient mind, and the bond that people feel between themselves and their defiant, struggling ancestor (a figure whose problems we should understand all too well) which draw people to the caves of Lascaux, and which causes spiritual documents from earliest times to be regarded as remarkable, worthwhile achievements. In fact if anything sums up ancient man’s right to respect from us, it would be exactly this bold behaviour and self-belief: traits humanity is sorely in need of today; I would go so far as to say the mockery which is often aimed at those who wrote the Bible is a sign not of intelligence, but of the weird separation of the modern braggart from his own race, and from the debt of gratitude he owes to the forceful minds of the past, which virtually invented literature, science and art, crude though they may have been. In this regard the smug Dawkinite seems little different than the yob urinating gleefully on the war memorials, desecrating 17th century graves with fancy grafitti, or, drunk with his own importance, ridiculing scriptures that his ancient ancestors gave their lives to create.

  29. Biochemist says:

    I certainly agree that ancient people did amazing things. My point was that the notion that Christianity is inherently peaceful is just not consistent with the one document that the whole religion is based upon. Health and safety is something of a whole other level than commanding genocide, I don’t even think Osama bin Laden ever did that. From the crusades to 19th century imperialism, Western countries always found themselves morally superior to the non-Christian countries they invaded, because of a religion that apparently advertises genocide of peoples that stand in the way of the religion. I also know that Jesus is going on a more pacifistic tour, but according to theology, every word in the bible is holy and therefore true. Jewish people even call Palestines “Amalekites” to justify their war crimes and oppression against them. Of course, the Koran also has a lot of extremely violent verses, so I’m not saying they’re any better. But if you really claim to be a pacifist, you should protest against these religions. As far as I know, only Buddhism is generally pacifistic, although I’ve never thoroughly read any Buddhist literature.

    • What can I say? This criticism of religion shows an illogical bias. How did the first massacres take place? By advancing technology. Stones, spears, arrows, bullets, tanks, nuclear bombs. And what is behind technology? Science! How were the prisoners taken to concentration camps? Trains – a product of technology. Who came up wioth Zyklon B? Scientists. Mustard gas? Scientists. Landmines? Scientists. Depleted Uranium bullets? Scientists. Cruise missiles, drones? Scientists.

      And how did the millions who died in WWI and WW2 meet their end? Technology. Where does technology come from? Science. Why do we not criticise technology in the same way? Where does Christ say, you should burn your enemies alive, roasting the flesh, even from the women and children, with nuclear ovens?

      Today the largest industries in all of mankind – are devoted to designing new weapons. Trillions spent every year. And who pays for these? You do.. we all do. Who is at the helm of these teams of dedicated engineers? Vicars, monks, lay clergy, pastors, Buddhist meditators, thelogians, Bible study groups, priests, nuns? No, scientists. Who came up with eugenics? Scientists. Cluster bombs, flamethrowers? Scientists. The human being today is much closer to the animal than we would like to believe. We are still bent on dividing up the planet into ours and theirs, divisions which do not exist in nature.

      It is human nature which is to blame. It’s as simple as that, and religion is one of the only forces powerful enough to encourage a love of something else besides conquest; to encourage self control, to foster an inner world. A love of miolecules won’t do this – as we can see from the actions of some scientists. Some are engaged in humanitarian work – and if you can find any, I would be very pleased to write about them. Meantime, some are busy designing massacres, some have become cultural vandals attacking the scriptures. In the riots in the UK last year, a man’s son was killed and an angry mob formed: this man spoke from the Quran, and urged everyone to forgive. The mob melted away. The police credited him with averting a riot. His inspiration? Survival of the fittest? Actually, it was religion. To mock religion on the basis of its origins is a strange way of thinking, when science is busy raping the planet, arming the invaders, filling the oceans with plastic, filling the atmosphere with junk metal, enabling the razing of the Amazon and so on. Even the causes of th eoil spills, if you trace them back, are technological in nature.

      Of course, as a powerful force, religion is abused by the power mad. So is science – should this be any surprise? The experiments on orphans at the ICC, the Tuskagee experiments, the Eugenics of Peru, all show that scientists can vary not at all from mass murderers when there’s some money to be made. “For the love of money is the root of all evil.” And Mengeles was grandpapa to them all. Biology is even used now to devise plagues to launch from missiles. So even biologists have become mass killers. Where is the protest? Tsk, we’d rather make fun of 1 Samuel: 15. In the midst of gigantic armies, pumped up on steroids, armed to the teeth with monstrous weapons, a time when slavery is rife all over the world, and where a billion people starve for want of a little compassion, what reason can there be behind ridiculing scriptures which contain urges towards compassion?

      Israel is, without doubt, the world’s worst brand. I lost count of the letters and emails I’ve written to the Israeli embassy. They are a sickening bunch. But I’ve met ordinary Israelis and they are as aghast at their leadership as ordinary Americans are at Obama’s remote controlled Spanish Inquisitions: burning people alive on suspicion of being a militant – and, incidentally, all those around them at the time – even children, wives, lovers, shopkeepers, grandparents. Anyone 16 and over is “militant”. That would also mean you and me, not that anyone is able to identify the charred corpses afterwards. How many times can a person complain to the White House? How many posts can a person write about people getting away with mass murder? I’m on twitter now and I’ve written to Barack Obama’s campaign group. What they’re doing is insane – I don’t think this is a time to be making polite noises.

      But, tell you what: when the atheists are picketing the weapons companies, when the atheists are demanding that technology not be used for violence, when the atheists are going on hunger strike to support the oppressed, you will find me joining their ranks and probably writing with excitement about nothing else. But when they focus their energy on mocking religion, it is like watching Nero fiddle while Rome burns – what sane person will not only sit entranced by such a display of talent, while the place falls down around their ears?

  30. Biochemist says:

    First of all, I don’t want to condone the scientists that are or have been employed for morally questionable objectives. However, it was rarely a scientist that ordered the development of the weapons you mentioned, but usually a politician. Apart from that, all the weaponry is technology and designed by engineers, whereas science and scientist are more in the truth-finding business than in the design, although there is overlap. Furthermore, I don’t claim that all science is pacifistic, where some religions seem to do so. Although I agree that far too much money and effort goes into developing weaponry, most scientists are still working on more peaceful projects like curing cancer, HIV, malaria, Alzheimers and bacterial infections or designing better sources of durable energy like solar panels, biofuels, hydrogen storage and fuel cells.

    In North-West Europe, many governments have become atheist or highly secular during the past century. Scandinavian countries, Belgium, the Netherlands and Germany haven’t started any war, although their NATO ties oblige them to sometimes join or support an American project in the Middle-East. Parties like die Grune in Germany and Groenlinks in the Netherlands are completely pacifistic and atheistic at the same time. These parties seem to be the most popular amongst atheist scientists, whereas Christian Democrats have always fully supported American-lead invasions. I’m not saying all Christians/Jews are non-pacifistic, but some passages in the Bible/Tora clearly indicate that these religions can be easily misused as excuses for violence, which has happened too often in the past to my opinion.

    • Yes, those are valid points about science – I and many other people owe my life to science, no question about it. My father was a Lancet-quoted medical scientist who made important discoveries early on in his career, and over my whole lifetime he gave me invaluable insight into the dual nature of the profession: some members were out for cash – and lots of it – and some worked for the betterment of the field.

      There are elements of religion that need to be eliminated, but the underlying school of thought is sound, and science is bearing this out. The idea is stated, in many different ways, that adherence to a certain set of principles leads to higher states of consciousness. The graphic imagery of each religion is due to their origin before technology and the media. It had to be memorable to be effective. The problem now is the inability of an intellectual to separate out what is valuable from what is not, and this is inexplicable unless you assume they don’t want anything of religion to be true. We can’t throw away all of science just because of the nuclear bomb. It would make more sense to get rid of the nuclear bomb and keep science. We can’t throw away medicine because of eugenics: better to lose eugenics, and keep the rest of medicine. We can’t throw away the genome project just because the “junk DNA” theory (touted recently by Richard Dawkins, and given endless publicity) itself turned out to be “junk science” .

      But what science is finding now is that the emotions stressed in all original scriptures (including the i-Ching, Vedas, Quran, Buddhism, Bhagavad Gita and the Bible) activate priceless neurotransmitters that maintain hygiene in the brain. This is an incredible discovery! Meditation also strengthens the cortex, trains the amygdala to very high efficiency, and increases levels of telomerase. Meantime gratitude, generosity, confession and the contemplation of items considered beautiful, produce oxytocin and vasopressin. The lack of these neurotransmitters is implicated in severe mental disorders, and strange genetic deterioration, as quoted research elsewhere on this site shows. The social mechanisms also seem to affect mirror neutron activity; I point this out elsewhere in the blog.

      Fasting, another religious custom, something the disciples practiced before important decisions, strengthens the chemical pathways between neurons: nobody is quite sure why. But a sudden drop in calorie intake causes this boost and makes the neurons work harder. It only needs to be for a short time, but what an amazing discovery! Owed to science, and to the ages-old intuitive nature of many religious ideas.

      The other aspect about religion is that it is well known that the mind gravitates to a mental model put before it. Put 100 new recruits in the IDF under a sergeant with a psychopathic hatred of the Arabs, and despite their better selves, these soldiers are within days, stamping on toddlers and shooting civilians. So to have an image in the mind of a human being with the qualities of divinity – a Jesus or Buddha for example – is a benign influence. Which is better: to ask “what would Buddha have done about this parking warden?” or “how would Vlad the Impaler have handled it?” All these aspects of religion are soothing and beneficial to the brain.

      Even an atheist like de Botton finds endless aspects of religion to be admirable, very healthy, cohesive to society and superior to their secular equivalent: and he is as die-hard an atheist as you will find. I had an offer two weeks ago to give away his books and only one atheist wrote in, despite the page receiving nearly 3,000 hits.

      I think to uproot the entire tree of religion and pulp it into toilet paper is a vandalism which is even more inexcusable when science has shown spiritual disciplines are healthy for the brain and genetics, and when even hardline atheists evaluate religion as being healthy and cohesive to society. Even Dawkins and Faircloth are announcing atheism must now embody compassion – the very thing scriptures have encouraged all along. Far better to use science to prune the branches, and keep what is of value to humanity – that is all what this blog is all about.

  31. Biochemist says:

    I wouldn’t want to deny anybody their right to believe whatever they want, in China the opposite is happening and it is not for the better. However, (smart) people should advocate not to read the bible/koran/thora literally (especially not the old testament in case of the bible), because it is insanely ridiculous what is said about the age of the earth, what happens to gay people and people that masturbate and to Amalekites. In part you seem to do this, which I respect, but in part you still stick to claims that are completely at odds with what science is seeing. You do seem like a smart person, but denying evolution is something I associate with the same people that deny climate change against all evidence. I think I have given you enough arguments, although there are still mountains of evidence that I haven’t covered, but I’m afraid I can’t make you change your mind. So I’ll quit here, all the best, and I hope something or somebody else can change your mind.

  32. My claims are not at odds with science – my claims are all BASED on science. Check out the references and see.

    As biologist Shapiro says more eloquently than me, this unbearably crude view of evolution which says “it all happens randomly” is finally being carried away in a stretcher out the back. He has a book out called “Evolution: a view from the 21st Century” with more than one thousand references to scientific papers in the appendix. Nobody can say science doesn’t support his view. Like many people, he knows that the age of quill pens and chimney sweeps was unlikely to produce a theory about evolution that was going to last forever.

    James A. Shapiro proposes an important new paradigm for understanding biological evolution, the core organizing principle of biology. Shapiro introduces crucial new molecular evidence that tests the conventional scientific view of evolution based on the neo-Darwinian synthesis, and shows why this view is inadequate to today’s evidence. He then presents a compelling alternative view of the evolutionary process that reflects the shift in life sciences towards a more information- and systems-based approach.

    Shapiro integrates advances in symbiogenesis, epigenetics, and saltationism into a unified approach that views evolutionary change as an active cell process, regulated epigenetically and capable of making rapid large changes by horizontal DNA transfer, inter-specific hybridization, whole genome doubling, symbiogenesis, or massive genome restructuring.

    You’d think this well-supported view would be excitedly embraced by biologists. But random lucky-dip flukery, a novel idea in Darwin’s day, has become Zombie Science: a theory now dead and rotting, and causing a revolting smell, but which refuses to lie down and be buried. The blame for this lies with people such as yourself, and public figures like Richard Dawkins who won’t admit the absurdity of highly focused machinery changing shape in a completely random way, making every possibility, no matter how improbable, equally likely. Children will laugh about this in 20 years time and these silly ideas will make our society a laughing stock. It’s inexcusable for scientists to abandon common sense.

    With Dawkins we can partly understand it because he needs to protect his career and his book-signing lecture tours fast as he can, while the gettin’ is good, but for an independent thinker, there isn’t any such excuse. Until science deals with the spiritual tendency as a bona fide phenomenon, gaining the attention and respect of society, and until it treats biology as a law-driven engine of creativity, the fanatics will wallow around in gloomy mid-19th century muck, making all the book sales they can but growing more isolated every year until humanity eventually bypasses them altogether and leaves them in the 19th century gloom, along with chimney sweeps and quill pens.

  33. Biochemist says:

    Please correct me if I’m wrong, but I don’t believe Dr. Shapiro is suggesting anything related to intelligent design. Sure, new mechanisms of mutation (gene/genome duplication) and inheritance (epigenetics, horizontal gene transfer) were not present in Darwins theory, but they only disprove creationism in providing evidence that evolution can happen at an even faster pace (I mentioned these before in my comments as well). The principles of Darwins theory are still valid, albeit the mechanisms appear to be way more elaborate than he could have discovered. Still no need for an intelligent designer. It is sad to see that indeed the public gets more and more stupid watching only television and that spiritual explanations are gaining favor.

    • Well, I haven’t read the book but it’s on the way to me; when I do read it perhaps I can comment.

      People sign up to complicated theories of physics without protest, and I doubt many people understand magnetism or even gravity, but the formulas are waved through without demur. so, assuming Darwin’s ideas of random mutations and natural selection are completely perfect – as Dawkins insists – if people dislike it, maybe the problem is really the people presenting it, accusing the audience of being “ignorant, stupid or insane (or wicked, but I don’t want to contemplate that!)” if they disagree. Wow, way to win ‘em over!

      A little like the ex who cursed and threatened if we didn’t love them back in the same needy, possessive, all-or-nothing way. A charming partner – for someone else. But who knows? Maybe calling people stupid will win their hearts in the end. Let’s hope so!

      Because, let’s face it: if there was any single thing guaranteed to make society more generous, more tolerant of our differences, more compassionate, and more keen to abandon greed and intellectual snobbery, to see us all as equals and dedicate oneself to helping the downtrodden – it’s believing in random mutations and natural selection.

  34. the human body is the most amazing piece of machinery in the universe!!! A living super robot WOW!!!! I am proof of that Im 6-1-200lbs 4% bodyfat and super athletic and 34 years old . Yet I spent my whole twenties partying and doing tons of drugs. Yet Im in perfect health!!!!

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